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commit/galaxy-central: jgoecks: Partially addressing packing bugs that cause features to be drawn overlapping. Pack scripts.
by Bitbucket 07 Feb '11
by Bitbucket 07 Feb '11
07 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/6f2d6842f282/
changeset: r5015:6f2d6842f282
user: jgoecks
date: 2011-02-07 21:22:23
summary: Partially addressing packing bugs that cause features to be drawn overlapping. Pack scripts.
affected #: 4 files (619 bytes)
--- a/static/scripts/packed/galaxy.base.js Mon Feb 07 11:38:34 2011 -0500
+++ b/static/scripts/packed/galaxy.base.js Mon Feb 07 15:22:23 2011 -0500
@@ -1,1 +1,1 @@
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\ No newline at end of file
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--- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Mon Feb 07 11:38:34 2011 -0500
+++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Mon Feb 07 15:22:23 2011 -0500
@@ -1,1 +1,1 @@
-function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropinit",function(g,h){return $(h.drag).hasClass("output-terminal")&&f.can_accept(h.drag.terminal)}).bind("dropstart",function(g,h){h.proxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g,h){h.proxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g,h){(new Connector(h.drag.terminal,f)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});$("body").remove(b);i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tipsy({delayIn:500,fallback:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)==-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}m.bind("hover",function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small-yellow.png")});m.bind("mouseleave",function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small.png");if($.inArray(b.name,d.workflow_outputs)==-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});$("body").remove(m);a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions);h.find("div[name="+j.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var a=false;$.each(this.nodes,function(b,c){if(c.workflow_outputs&&c.workflow_outputs.length>0){a=true}});if(a==false){return true}wf=this;$.each(this.nodes,function(b,f){if(f.type=="tool"){var d=false;if(f.post_job_actions==null){f.post_job_actions={}}var c=[];$.each(f.post_job_actions,function(h,g){if(g.action_type=="HideDatasetAction"){c.push(h)}});if(c.length>0&&f==workflow.active_node){$.each(c,function(g,h){d=true;delete f.post_job_actions[h]})}$.each(f.output_terminals,function(h,i){var g=true;$.each(f.workflow_outputs,function(k,l){if(i.name==l){g=false}});if(g==true){d=true;var j={action_type:"HideDatasetAction",output_name:i.name,action_arguments:{}};f.post_job_actions["HideDatasetAction"+i.name]=null;f.post_job_actions["HideDatasetAction"+i.name]=j}});if(wf.active_node==f&&d==true){wf.reload_active_node()}}})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}});
\ No newline at end of file
+function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;this.handle1.connect(this);this.handle2=a;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(d,a,b){var c=this;$(d).each(function(){var f=this.terminal=new InputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dropinit",function(g,h){return $(h.drag).hasClass("output-terminal")&&f.can_accept(h.drag.terminal)}).bind("dropstart",function(g,h){h.proxy.terminal.connectors[0].inner_color="#BBFFBB"}).bind("dropend",function(g,h){h.proxy.terminal.connectors[0].inner_color="#FFFFFF"}).bind("drop",function(g,h){(new Connector(h.drag.terminal,f)).redraw()}).bind("hover",function(){if(f.connectors.length>0){var g=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(){$.each(f.connectors,function(i,h){h.destroy()});g.remove()}))).bind("mouseleave",function(){$(this).remove()});g.css({top:$(this).offset().top-2,left:$(this).offset().left-g.width(),"padding-right":$(this).width()}).show()}});c.input_terminals[a]=f})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",image_path+"/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tipsy({delayIn:500,fallback:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)==-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}m.bind("hover",function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small-yellow.png")});m.bind("mouseleave",function(){l.find("img").attr("src",image_path+"/fugue/asterisk-small.png");if($.inArray(b.name,d.workflow_outputs)==-1){l.find("img").attr("src",image_path+"/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",image_path+"/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.remove();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions);h.find("div[name="+j.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var a=false;$.each(this.nodes,function(b,c){if(c.workflow_outputs&&c.workflow_outputs.length>0){a=true}});if(a==false){return true}wf=this;$.each(this.nodes,function(b,f){if(f.type=="tool"){var d=false;if(f.post_job_actions==null){f.post_job_actions={}}var c=[];$.each(f.post_job_actions,function(h,g){if(g.action_type=="HideDatasetAction"){c.push(h)}});if(c.length>0&&f==workflow.active_node){$.each(c,function(g,h){d=true;delete f.post_job_actions[h]})}$.each(f.output_terminals,function(h,i){var g=true;$.each(f.workflow_outputs,function(k,l){if(i.name==l){g=false}});if(g==true){d=true;var j={action_type:"HideDatasetAction",output_name:i.name,action_arguments:{}};f.post_job_actions["HideDatasetAction"+i.name]=null;f.post_job_actions["HideDatasetAction"+i.name]=j}});if(wf.active_node==f&&d==true){wf.reload_active_node()}}})},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(h,i){g[i.name]=null;$.each(i.connectors,function(j,k){g[i.name]={id:k.handle1.node.id,output_name:k.handle1.name}})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(a){wf=this;var b=0;wf.name=a.name;$.each(a.steps,function(f,d){var c=prebuild_node("tool",d.name,d.tool_id);c.init_field_data(d);if(d.position){c.element.css({top:d.position.top,left:d.position.left})}c.id=d.id;wf.nodes[c.id]=c;b=Math.max(b,parseInt(f))});wf.id_counter=b+1;$.each(a.steps,function(f,d){var c=wf.nodes[f];$.each(d.input_connections,function(h,g){if(g){var i=wf.nodes[g.id];var j=new Connector();j.connect(i.output_terminals[g.output_name],c.input_terminals[h]);j.redraw()}})})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+image_path+"/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<img/>").attr("src",image_path+"/delete_icon.png").click(function(b){g.destroy()}).hover(function(){$(this).attr("src",image_path+"/delete_icon_dark.png")},function(){$(this).attr("src",image_path+"/delete_icon.png")}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}});
\ No newline at end of file
--- a/static/scripts/packed/trackster.js Mon Feb 07 11:38:34 2011 -0500
+++ b/static/scripts/packed/trackster.js Mon Feb 07 15:22:23 2011 -0500
@@ -1,1 +1,1 @@
-CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSE_HEIGHT=1,SQUISH_HEIGHT=3,PACK_HEIGHT=9,DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(d,h){if(!h.hidden){var i="param_"+d;var g=$("<div class='form-row' />").appendTo(a);g.append($("<label />").attr("for",i).text(h.label+":"));if(h.type=="bool"){g.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",b.values[h.key]))}else{if(h.type=="color"){var f=b.values[h.key];var c=$("<input />").attr("id",i).attr("name",i).val(f);var e=$("<div class='tipsy tipsy-north' style='position: absolute;' />").append($("<div class='tipsy-inner' />").farbtastic({width:100,height:100,callback:c,color:f})).hide();$("<div />").append(c).append(e).appendTo(g).bind("click",function(j){e.css({left:$(this).position().left+($(c).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){e.hide();$(document).unbind("click.color-picker")});j.stopPropagation()})}else{g.append($("<input />").attr("id",i).attr("name",i).val(b.values[h.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k);if(l){var m=$("<div class='track-tile'>").prepend(l);if(l.hasClass(FILTERABLE_CLASS)){m.addClass(FILTERABLE_CLASS)}l=m}}if(l){d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=5;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?SQUISH_HEIGHT:DENSE_HEIGHT))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ag,n,r,aw){var M=n*DENSITY*ag,al=(n+1)*DENSITY*ag,L=al-M;var H=this.data_cache.get_data(M,al,this.mode);if(H===undefined||H==="pending"||(this.mode!=="Auto"&&H.dataset_type==="summary_tree")){this.data_queue[[M,al]]=true;this.get_data(M,al);return}var a=Math.ceil(L*aw),ai=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ae=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(H.extra_info==="no_detail")),X=this.left_offset,av,C,ax;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(H.dataset_type==="summary_tree"){C=this.summary_draw_height}else{if(q==="Dense"){C=v;ax=10}else{ax=(ae?this.vertical_nodetail_px:this.vertical_detail_px);var w=(aw<0.0001?1/this.view.zoom_res:aw);C=this.incremental_slots(w,H.data,ae,q)*ax+v;av=this.inc_slots[w]}}p.get(0).width=a+X;p.get(0).height=C;r.parent().css("height",Math.max(this.height_px,C)+"px");var I=p.get(0).getContext("2d");I.fillStyle=h;I.font=this.default_font;I.textAlign="right";this.container_div.find(".yaxislabel").remove();if(H.dataset_type=="summary_tree"){var Z=H.data,K=H.max,b=Math.ceil(H.delta*aw);var o=$("<div />").addClass("yaxislabel");o.text(K);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var ap=0,G=Z.length;ap<G;ap++){var ab=Math.floor((Z[ap][0]-M)*aw);var aa=Z[ap][1];if(!aa){continue}var am=aa/K*this.summary_draw_height;I.fillStyle="black";I.fillRect(ab+X,this.summary_draw_height-am,b,am);if(this.prefs.show_counts&&I.measureText(aa).width<b){I.fillStyle="#bbb";I.textAlign="center";I.fillText(aa,ab+X+(b/2),this.summary_draw_height-5)}}return p}if(H.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});I.fillStyle="red";I.textAlign="left";I.fillText(H.message,100+X,ax);return p}for(var at=0;at<this.filters.length;at++){if(H.data.length&&this.filters[at].applies_to(H.data[0])){p.addClass(FILTERABLE_CLASS);break}}var au=H.data;var ao=0;for(var ap=0,G=au.length;ap<G;ap++){var T=au[ap],Q=T[0],ar=T[1],ad=T[2],N=T[3];if(this.mode!="Dense"&&av[Q]===undefined){continue}var ac=false;var V;for(var at=0;at<this.filters.length;at++){V=this.filters[at];V.update_attrs(T);if(!V.keep(T)){ac=true;break}}if(ac){continue}if(ar<=al&&ad>=M){if(H.dataset_type=="interval_index"){ad-=1}var af=Math.floor(Math.max(0,(ar-M)*aw)),J=Math.ceil(Math.min(a,Math.max(0,(ad-M)*aw))),Y=(q==="Dense"?1:(1+av[Q]))*ax;var F,aj,O=null,ay=null;if(H.dataset_type==="bai"){I.fillStyle=h;if(T[5] instanceof Array){var D=Math.floor(Math.max(0,(T[4][0]-M)*aw)),P=Math.ceil(Math.min(a,Math.max(0,(T[4][1]-M)*aw))),B=Math.floor(Math.max(0,(T[5][0]-M)*aw)),u=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-M)*aw)));if(T[4][1]>=M&&T[4][0]<=al&&T[4][2]){this.rect_or_text(I,aw,M,al,T[4][0],T[4][2],T[4][3],Y)}if(T[5][1]>=M&&T[5][0]<=al&&T[5][2]){this.rect_or_text(I,aw,M,al,T[5][0],T[5][2],T[5][3],Y)}if(B>P){I.fillStyle=CONNECTOR_COLOR;I.dashedLine(P+X,Y+5,X+B,Y+5)}}else{I.fillStyle=h;this.rect_or_text(I,aw,M,al,ar,T[4],T[5],Y)}if(q!=="Dense"&&!ae&&ar>M){I.fillStyle=this.prefs.label_color;if(n===0&&af-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+X,Y+8)}else{I.textAlign="right";I.fillText(N,af-2+X,Y+8)}I.fillStyle=h}}else{if(H.dataset_type==="interval_index"){if(q=="Auto"){if(T.length<=4){q="Squish"}else{q="Pack"}}if(q=="Dense"){I.fillStyle=h;I.fillRect(af+X,Y+5,J-af,DENSE_HEIGHT)}else{if(T.length<=4){I.fillStyle=h;I.fillRect(af+X,Y+5,J-af,1)}else{var E=T[5],W=T[6],ah=T[7],g=T[8];if(W&&ah){O=Math.floor(Math.max(0,(W-M)*aw));ay=Math.ceil(Math.min(a,Math.max(0,(ah-M)*aw)))}var aq,R;if(q=="Squish"){aq=1;R=SQUISH_HEIGHT}else{aq=5;R=PACK_HEIGHT}if(!g){if(T.strand){if(T.strand=="+"){I.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){I.fillStyle=LEFT_STRAND_INV}}}else{I.fillStyle=CONNECTOR_COLOR}I.fillRect(af+X,Y+(R-aq)/2+1,J-af,R)}else{var A,S;if(q=="Squish"){I.fillStyle=CONNECTOR_COLOR;A=Y+Math.floor(SQUISH_HEIGHT/2)+1;S=1}else{if(E){var A=Y;var S=R;if(E=="+"){I.fillStyle=RIGHT_STRAND}else{if(E=="-"){I.fillStyle=LEFT_STRAND}}}else{I.fillStyle=CONNECTOR_COLOR;A+=(SQUISH_HEIGHT/2)+1;S=1}}I.fillRect(af+X,A,J-af,S);for(var an=0,e=g.length;an<e;an++){var t=g[an],d=Math.floor(Math.max(0,(t[0]-M)*aw)),U=Math.ceil(Math.min(a,Math.max((t[1]-M)*aw)));if(d>U){continue}I.fillStyle=h;I.fillRect(d+X,Y+(R-aq)/2+1,U-d,aq);if(O!==undefined&&!(d>ay||U<O)){var ak=Math.max(d,O),z=Math.min(U,ay-1);I.fillRect(ak+X,Y+1,z-ak,R)}}}if(q=="Pack"&&ar>M){I.fillStyle=ai;if(n===0&&af-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+X,Y+8)}else{I.textAlign="right";I.fillText(N,af-2+X,Y+8)}I.fillStyle=h}}}}else{if(H.dataset_type==="vcf"){if(ae){I.fillStyle=h;I.fillRect(af+X,Y+5,J-af,1)}else{var s=T[4],m=T[5],c=T[6];F=9;aj=1;I.fillRect(af+X,Y,J-af,F);if(q!=="Dense"&&N!==undefined&&ar>M){I.fillStyle=ai;if(n===0&&af-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+X,Y+8)}else{I.textAlign="right";I.fillText(N,af-2+X,Y+8)}I.fillStyle=h}var l=s+" / "+m;if(ar>M&&I.measureText(l).width<(J-af)){I.fillStyle="white";I.textAlign="center";I.fillText(l,X+af+(J-af)/2,Y+8);I.fillStyle=h}}}}}ao++}}return p}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
+CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSE_HEIGHT=1,SQUISH_HEIGHT=3,PACK_HEIGHT=9,DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(d,h){if(!h.hidden){var i="param_"+d;var g=$("<div class='form-row' />").appendTo(a);g.append($("<label />").attr("for",i).text(h.label+":"));if(h.type=="bool"){g.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",b.values[h.key]))}else{if(h.type=="color"){var f=b.values[h.key];var c=$("<input />").attr("id",i).attr("name",i).val(f);var e=$("<div class='tipsy tipsy-north' style='position: absolute;' />").append($("<div class='tipsy-inner' />").farbtastic({width:100,height:100,callback:c,color:f})).hide();$("<div />").append(c).append(e).appendTo(g).bind("click",function(j){e.css({left:$(this).position().left+($(c).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){e.hide();$(document).unbind("click.color-picker")});j.stopPropagation()})}else{g.append($("<input />").attr("id",i).attr("name",i).val(b.values[h.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k);if(l){var m=$("<div class='track-tile'>").prepend(l);if(l.hasClass(FILTERABLE_CLASS)){m.addClass(FILTERABLE_CLASS)}l=m}}if(l){d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=5;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){u+=(2+4);if(d-u>0){d-=u;e="left"}else{f+=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?SQUISH_HEIGHT:DENSE_HEIGHT))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ag,n,r,aw){var M=n*DENSITY*ag,al=(n+1)*DENSITY*ag,L=al-M;var H=this.data_cache.get_data(M,al,this.mode);if(H===undefined||H==="pending"||(this.mode!=="Auto"&&H.dataset_type==="summary_tree")){this.data_queue[[M,al]]=true;this.get_data(M,al);return}var a=Math.ceil(L*aw),ai=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ae=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(H.extra_info==="no_detail")),X=this.left_offset,av,C,ax;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(H.dataset_type==="summary_tree"){C=this.summary_draw_height}else{if(q==="Dense"){C=v;ax=10}else{ax=(ae?this.vertical_nodetail_px:this.vertical_detail_px);var w=(aw<0.0001?1/this.view.zoom_res:aw);C=this.incremental_slots(w,H.data,ae,q)*ax+v;av=this.inc_slots[w]}}p.get(0).width=a+X;p.get(0).height=C;r.parent().css("height",Math.max(this.height_px,C)+"px");var I=p.get(0).getContext("2d");I.fillStyle=h;I.font=this.default_font;I.textAlign="right";this.container_div.find(".yaxislabel").remove();if(H.dataset_type=="summary_tree"){var Z=H.data,K=H.max,b=Math.ceil(H.delta*aw);var o=$("<div />").addClass("yaxislabel");o.text(K);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var ap=0,G=Z.length;ap<G;ap++){var ab=Math.floor((Z[ap][0]-M)*aw);var aa=Z[ap][1];if(!aa){continue}var am=aa/K*this.summary_draw_height;I.fillStyle="black";I.fillRect(ab+X,this.summary_draw_height-am,b,am);if(this.prefs.show_counts&&I.measureText(aa).width<b){I.fillStyle="#bbb";I.textAlign="center";I.fillText(aa,ab+X+(b/2),this.summary_draw_height-5)}}return p}if(H.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});I.fillStyle="red";I.textAlign="left";I.fillText(H.message,100+X,ax);return p}for(var at=0;at<this.filters.length;at++){if(H.data.length&&this.filters[at].applies_to(H.data[0])){p.addClass(FILTERABLE_CLASS);break}}var au=H.data;var ao=0;for(var ap=0,G=au.length;ap<G;ap++){var T=au[ap],Q=T[0],ar=T[1],ad=T[2],N=T[3];if(this.mode!="Dense"&&av[Q]===undefined){continue}var ac=false;var V;for(var at=0;at<this.filters.length;at++){V=this.filters[at];V.update_attrs(T);if(!V.keep(T)){ac=true;break}}if(ac){continue}if(ar<=al&&ad>=M){if(H.dataset_type=="interval_index"){ad-=1}var af=Math.floor(Math.max(0,(ar-M)*aw)),J=Math.ceil(Math.min(a,Math.max(0,(ad-M)*aw))),Y=(q==="Dense"?1:(1+av[Q]))*ax;var F,aj,O=null,ay=null;if(H.dataset_type==="bai"){I.fillStyle=h;if(T[5] instanceof Array){var D=Math.floor(Math.max(0,(T[4][0]-M)*aw)),P=Math.ceil(Math.min(a,Math.max(0,(T[4][1]-M)*aw))),B=Math.floor(Math.max(0,(T[5][0]-M)*aw)),u=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-M)*aw)));if(T[4][1]>=M&&T[4][0]<=al&&T[4][2]){this.rect_or_text(I,aw,M,al,T[4][0],T[4][2],T[4][3],Y)}if(T[5][1]>=M&&T[5][0]<=al&&T[5][2]){this.rect_or_text(I,aw,M,al,T[5][0],T[5][2],T[5][3],Y)}if(B>P){I.fillStyle=CONNECTOR_COLOR;I.dashedLine(P+X,Y+5,X+B,Y+5)}}else{I.fillStyle=h;this.rect_or_text(I,aw,M,al,ar,T[4],T[5],Y)}if(q!=="Dense"&&!ae&&ar>M){I.fillStyle=this.prefs.label_color;if(n===0&&af-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+X,Y+8)}else{I.textAlign="right";I.fillText(N,af-2+X,Y+8)}I.fillStyle=h}}else{if(H.dataset_type==="interval_index"){if(q=="Auto"){if(T.length<=4){q="Squish"}else{q="Pack"}}if(q=="Dense"){I.fillStyle=h;I.fillRect(af+X,Y+5,J-af,DENSE_HEIGHT)}else{if(T.length<=4){I.fillStyle=h;I.fillRect(af+X,Y+5,J-af,1)}else{var E=T[5],W=T[6],ah=T[7],g=T[8];if(W&&ah){O=Math.floor(Math.max(0,(W-M)*aw));ay=Math.ceil(Math.min(a,Math.max(0,(ah-M)*aw)))}var aq,R;if(q=="Squish"){aq=1;R=SQUISH_HEIGHT}else{aq=5;R=PACK_HEIGHT}if(!g){if(T.strand){if(T.strand=="+"){I.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){I.fillStyle=LEFT_STRAND_INV}}}else{I.fillStyle=CONNECTOR_COLOR}I.fillRect(af+X,Y+(R-aq)/2+1,J-af,R)}else{var A,S;if(q=="Squish"){I.fillStyle=CONNECTOR_COLOR;A=Y+Math.floor(SQUISH_HEIGHT/2)+1;S=1}else{if(E){var A=Y;var S=R;if(E=="+"){I.fillStyle=RIGHT_STRAND}else{if(E=="-"){I.fillStyle=LEFT_STRAND}}}else{I.fillStyle=CONNECTOR_COLOR;A+=(SQUISH_HEIGHT/2)+1;S=1}}I.fillRect(af+X,A,J-af,S);for(var an=0,e=g.length;an<e;an++){var t=g[an],d=Math.floor(Math.max(0,(t[0]-M)*aw)),U=Math.ceil(Math.min(a,Math.max((t[1]-M)*aw)));if(d>U){continue}I.fillStyle=h;I.fillRect(d+X,Y+(R-aq)/2+1,U-d,aq);if(O!==undefined&&!(d>ay||U<O)){var ak=Math.max(d,O),z=Math.min(U,ay-1);I.fillRect(ak+X,Y+1,z-ak,R)}}}if(q=="Pack"&&ar>M){I.fillStyle=ai;if(n===0&&af-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+X,Y+8)}else{I.textAlign="right";I.fillText(N,af-2+X,Y+8)}I.fillStyle=h}}}}else{if(H.dataset_type==="vcf"){if(ae){I.fillStyle=h;I.fillRect(af+X,Y+5,J-af,1)}else{var s=T[4],m=T[5],c=T[6];F=9;aj=1;I.fillRect(af+X,Y,J-af,F);if(q!=="Dense"&&N!==undefined&&ar>M){I.fillStyle=ai;if(n===0&&af-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+X,Y+8)}else{I.textAlign="right";I.fillText(N,af-2+X,Y+8)}I.fillStyle=h}var l=s+" / "+m;if(ar>M&&I.measureText(l).width<(J-af)){I.fillStyle="white";I.textAlign="center";I.fillText(l,X+af+(J-af)/2,Y+8);I.fillStyle=h}}}}}ao++}}return p}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
--- a/static/scripts/trackster.js Mon Feb 07 11:38:34 2011 -0500
+++ b/static/scripts/trackster.js Mon Feb 07 15:22:23 2011 -0500
@@ -61,6 +61,7 @@
DENSE_HEIGHT = 1,
SQUISH_HEIGHT = 3,
PACK_HEIGHT = 9,
+ LABEL_SPACING = 2,
// Other constants.
DENSITY = 200,
@@ -2123,11 +2124,16 @@
// Update start, end drawing locations to include feature name.
// Try to put the name on the left, if not, put on right.
if (feature_name !== undefined && !no_detail) {
- if (f_start - text_len < 0) {
- f_end += text_len;
+ // +2 for gap b/t text and feature, +3 for packing issue. (TODO: it's not clear what
+ // the packing issue is, other than that packing is global but features are drawn locally;
+ // it seems this mismatch is causing features to slightly overlap, perhaps due to features
+ // being compressed onto tiles.)
+ text_len += (LABEL_SPACING + 4);
+ if (f_start - text_len >= 0) {
+ f_start -= text_len;
text_align = "left";
} else {
- f_start -= text_len;
+ f_end += text_len;
text_align = "right";
}
}
@@ -2457,10 +2463,10 @@
ctx.fillStyle = this.prefs.label_color;
if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) {
ctx.textAlign = "left";
- ctx.fillText(feature_name, f_end + 2 + left_offset, y_center + 8);
+ ctx.fillText(feature_name, f_end + left_offset + LABEL_SPACING, y_center + 8);
} else {
ctx.textAlign = "right";
- ctx.fillText(feature_name, f_start - 2 + left_offset, y_center + 8);
+ ctx.fillText(feature_name, f_start + left_offset + LABEL_SPACING, y_center + 8);
}
ctx.fillStyle = block_color;
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
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1
0
4 new changesets in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/dfff9d99b410/
changeset: r5011:dfff9d99b410
user: james_taylor
date: 2011-02-06 17:29:04
summary: trackster: tiny tweaks
affected #: 1 file (131 bytes)
--- a/static/scripts/trackster.js Sun Feb 06 10:27:53 2011 -0500
+++ b/static/scripts/trackster.js Sun Feb 06 11:29:04 2011 -0500
@@ -389,7 +389,8 @@
// to zoom in
this.top_labeltrack.bind( "dragstart", function( e, d ) {
return $("<div />").css( {
- "height": view.content_div.height() + view.top_labeltrack.height() + view.nav_labeltrack.height(),
+ "height": view.content_div.height() + view.top_labeltrack.height()
+ + view.nav_labeltrack.height() + 1,
"top": "0px",
"position": "absolute",
"background-color": "#ccf",
@@ -1485,7 +1486,7 @@
show_tile: function( tile_element, parent_element, tile_low ) {
// Readability.
var track = this;
-
+
// Position tile element, recalculate left position at display time
var range = this.view.high - this.view.low,
w_scale = this.content_div.width() / range,
@@ -1761,6 +1762,7 @@
this.prefs = this.track_config.values;
this.height_px = this.track_config.values.height;
+ this.vertical_range = this.track_config.values.max_value - this.track_config.values.min_value;
// Add control for resizing
// Trickery here to deal with the hovering drag handle, can probably be
http://bitbucket.org/galaxy/galaxy-central/changeset/a0a66548cb69/
changeset: r5012:a0a66548cb69
user: james_taylor
date: 2011-02-06 20:42:11
summary: jquery updated to 1.5, fixed minor bugs in use of jStore and some dom manipulation in workflows (both problems in our code, not backward incompatibility). Please help test.
affected #: 5 files (61.3 KB)
--- a/static/scripts/galaxy.base.js Sun Feb 06 11:29:04 2011 -0500
+++ b/static/scripts/galaxy.base.js Sun Feb 06 14:42:11 2011 -0500
@@ -496,7 +496,7 @@
} else {
// Load jStore for local storage
$.jStore.init("galaxy"); // Auto-select best storage
- $.jStore.engineReady(function() {
+ $.jStore.ready(function() {
action();
});
}
--- a/static/scripts/galaxy.workflow_editor.canvas.js Sun Feb 06 11:29:04 2011 -0500
+++ b/static/scripts/galaxy.workflow_editor.canvas.js Sun Feb 06 14:42:11 2011 -0500
@@ -316,7 +316,7 @@
left:'',
top:'',
display:'' });
- $('body').remove(ib);
+ ib.remove();
ibox.append( ib.prepend( t ) );
});
if ( ( data.data_inputs.length > 0 ) && ( data.data_outputs.length > 0 ) ) {
@@ -381,7 +381,7 @@
left:'',
top:'',
display:'' });
- $('body').remove(r);
+ r.remove();
b.append( r.append( t ) );
});
f.css( "width", Math.min(250, Math.max(f.width(), output_width )));
--- a/static/scripts/jquery.js Sun Feb 06 11:29:04 2011 -0500
+++ b/static/scripts/jquery.js Sun Feb 06 14:42:11 2011 -0500
@@ -1,24 +1,28 @@
/*
- * jQuery JavaScript Library v1.4.2
+ * jQuery JavaScript Library v1.5
* http://jquery.com/
*
- * Copyright 2010, John Resig
+ * Copyright 2011, John Resig
* Dual licensed under the MIT or GPL Version 2 licenses.
* http://jquery.org/license
*
* Includes Sizzle.js
* http://sizzlejs.com/
- * Copyright 2010, The Dojo Foundation
+ * Copyright 2011, The Dojo Foundation
* Released under the MIT, BSD, and GPL Licenses.
*
- * Date: Sat Feb 13 22:33:48 2010 -0500
+ * Date: Mon Jan 31 08:31:29 2011 -0500
*/
(function( window, undefined ) {
+// Use the correct document accordingly with window argument (sandbox)
+var document = window.document;
+var jQuery = (function() {
+
// Define a local copy of jQuery
var jQuery = function( selector, context ) {
// The jQuery object is actually just the init constructor 'enhanced'
- return new jQuery.fn.init( selector, context );
+ return new jQuery.fn.init( selector, context, rootjQuery );
},
// Map over jQuery in case of overwrite
@@ -27,52 +31,70 @@
// Map over the $ in case of overwrite
_$ = window.$,
- // Use the correct document accordingly with window argument (sandbox)
- document = window.document,
-
// A central reference to the root jQuery(document)
rootjQuery,
// A simple way to check for HTML strings or ID strings
// (both of which we optimize for)
- quickExpr = /^[^<]*(<[\w\W]+>)[^>]*$|^#([\w-]+)$/,
-
- // Is it a simple selector
- isSimple = /^.[^:#\[\.,]*$/,
+ quickExpr = /^(?:[^<]*(<[\w\W]+>)[^>]*$|#([\w\-]+)$)/,
// Check if a string has a non-whitespace character in it
rnotwhite = /\S/,
// Used for trimming whitespace
- rtrim = /^(\s|\u00A0)+|(\s|\u00A0)+$/g,
+ trimLeft = /^\s+/,
+ trimRight = /\s+$/,
+
+ // Check for digits
+ rdigit = /\d/,
// Match a standalone tag
rsingleTag = /^<(\w+)\s*\/?>(?:<\/\1>)?$/,
+ // JSON RegExp
+ rvalidchars = /^[\],:{}\s]*$/,
+ rvalidescape = /\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g,
+ rvalidtokens = /"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,
+ rvalidbraces = /(?:^|:|,)(?:\s*\[)+/g,
+
+ // Useragent RegExp
+ rwebkit = /(webkit)[ \/]([\w.]+)/,
+ ropera = /(opera)(?:.*version)?[ \/]([\w.]+)/,
+ rmsie = /(msie) ([\w.]+)/,
+ rmozilla = /(mozilla)(?:.*? rv:([\w.]+))?/,
+
// Keep a UserAgent string for use with jQuery.browser
userAgent = navigator.userAgent,
// For matching the engine and version of the browser
browserMatch,
-
+
// Has the ready events already been bound?
readyBound = false,
-
- // The functions to execute on DOM ready
- readyList = [],
+
+ // The deferred used on DOM ready
+ readyList,
+
+ // Promise methods
+ promiseMethods = "then done fail isResolved isRejected promise".split( " " ),
// The ready event handler
DOMContentLoaded,
// Save a reference to some core methods
toString = Object.prototype.toString,
- hasOwnProperty = Object.prototype.hasOwnProperty,
+ hasOwn = Object.prototype.hasOwnProperty,
push = Array.prototype.push,
slice = Array.prototype.slice,
- indexOf = Array.prototype.indexOf;
+ trim = String.prototype.trim,
+ indexOf = Array.prototype.indexOf,
+
+ // [[Class]] -> type pairs
+ class2type = {};
jQuery.fn = jQuery.prototype = {
- init: function( selector, context ) {
+ constructor: jQuery,
+ init: function( selector, context, rootjQuery ) {
var match, elem, ret, doc;
// Handle $(""), $(null), or $(undefined)
@@ -86,9 +108,9 @@
this.length = 1;
return this;
}
-
+
// The body element only exists once, optimize finding it
- if ( selector === "body" && !context ) {
+ if ( selector === "body" && !context && document.body ) {
this.context = document;
this[0] = document.body;
this.selector = "body";
@@ -106,6 +128,7 @@
// HANDLE: $(html) -> $(array)
if ( match[1] ) {
+ context = context instanceof jQuery ? context[0] : context;
doc = (context ? context.ownerDocument || context : document);
// If a single string is passed in and it's a single tag
@@ -122,17 +145,19 @@
}
} else {
- ret = buildFragment( [ match[1] ], [ doc ] );
- selector = (ret.cacheable ? ret.fragment.cloneNode(true) : ret.fragment).childNodes;
+ ret = jQuery.buildFragment( [ match[1] ], [ doc ] );
+ selector = (ret.cacheable ? jQuery.clone(ret.fragment) : ret.fragment).childNodes;
}
-
+
return jQuery.merge( this, selector );
-
+
// HANDLE: $("#id")
} else {
elem = document.getElementById( match[2] );
- if ( elem ) {
+ // Check parentNode to catch when Blackberry 4.6 returns
+ // nodes that are no longer in the document #6963
+ if ( elem && elem.parentNode ) {
// Handle the case where IE and Opera return items
// by name instead of ID
if ( elem.id !== match[2] ) {
@@ -149,13 +174,6 @@
return this;
}
- // HANDLE: $("TAG")
- } else if ( !context && /^\w+$/.test( selector ) ) {
- this.selector = selector;
- this.context = document;
- selector = document.getElementsByTagName( selector );
- return jQuery.merge( this, selector );
-
// HANDLE: $(expr, $(...))
} else if ( !context || context.jquery ) {
return (context || rootjQuery).find( selector );
@@ -163,7 +181,7 @@
// HANDLE: $(expr, context)
// (which is just equivalent to: $(context).find(expr)
} else {
- return jQuery( context ).find( selector );
+ return this.constructor( context ).find( selector );
}
// HANDLE: $(function)
@@ -184,7 +202,7 @@
selector: "",
// The current version of jQuery being used
- jquery: "1.4.2",
+ jquery: "1.5",
// The default length of a jQuery object is 0
length: 0,
@@ -207,18 +225,18 @@
this.toArray() :
// Return just the object
- ( num < 0 ? this.slice(num)[ 0 ] : this[ num ] );
+ ( num < 0 ? this[ this.length + num ] : this[ num ] );
},
// Take an array of elements and push it onto the stack
// (returning the new matched element set)
pushStack: function( elems, name, selector ) {
// Build a new jQuery matched element set
- var ret = jQuery();
+ var ret = this.constructor();
if ( jQuery.isArray( elems ) ) {
push.apply( ret, elems );
-
+
} else {
jQuery.merge( ret, elems );
}
@@ -244,25 +262,17 @@
each: function( callback, args ) {
return jQuery.each( this, callback, args );
},
-
+
ready: function( fn ) {
// Attach the listeners
jQuery.bindReady();
- // If the DOM is already ready
- if ( jQuery.isReady ) {
- // Execute the function immediately
- fn.call( document, jQuery );
-
- // Otherwise, remember the function for later
- } else if ( readyList ) {
- // Add the function to the wait list
- readyList.push( fn );
- }
+ // Add the callback
+ readyList.done( fn );
return this;
},
-
+
eq: function( i ) {
return i === -1 ?
this.slice( i ) :
@@ -287,9 +297,9 @@
return callback.call( elem, i, elem );
}));
},
-
+
end: function() {
- return this.prevObject || jQuery(null);
+ return this.prevObject || this.constructor(null);
},
// For internal use only.
@@ -303,8 +313,11 @@
jQuery.fn.init.prototype = jQuery.fn;
jQuery.extend = jQuery.fn.extend = function() {
- // copy reference to target object
- var target = arguments[0] || {}, i = 1, length = arguments.length, deep = false, options, name, src, copy;
+ var options, name, src, copy, copyIsArray, clone,
+ target = arguments[0] || {},
+ i = 1,
+ length = arguments.length,
+ deep = false;
// Handle a deep copy situation
if ( typeof target === "boolean" ) {
@@ -338,10 +351,15 @@
continue;
}
- // Recurse if we're merging object literal values or arrays
- if ( deep && copy && ( jQuery.isPlainObject(copy) || jQuery.isArray(copy) ) ) {
- var clone = src && ( jQuery.isPlainObject(src) || jQuery.isArray(src) ) ? src
- : jQuery.isArray(copy) ? [] : {};
+ // Recurse if we're merging plain objects or arrays
+ if ( deep && copy && ( jQuery.isPlainObject(copy) || (copyIsArray = jQuery.isArray(copy)) ) ) {
+ if ( copyIsArray ) {
+ copyIsArray = false;
+ clone = src && jQuery.isArray(src) ? src : [];
+
+ } else {
+ clone = src && jQuery.isPlainObject(src) ? src : {};
+ }
// Never move original objects, clone them
target[ name ] = jQuery.extend( deep, clone, copy );
@@ -368,41 +386,46 @@
return jQuery;
},
-
+
// Is the DOM ready to be used? Set to true once it occurs.
isReady: false,
-
+
+ // A counter to track how many items to wait for before
+ // the ready event fires. See #6781
+ readyWait: 1,
+
// Handle when the DOM is ready
- ready: function() {
+ ready: function( wait ) {
+ // A third-party is pushing the ready event forwards
+ if ( wait === true ) {
+ jQuery.readyWait--;
+ }
+
// Make sure that the DOM is not already loaded
- if ( !jQuery.isReady ) {
+ if ( !jQuery.readyWait || (wait !== true && !jQuery.isReady) ) {
// Make sure body exists, at least, in case IE gets a little overzealous (ticket #5443).
if ( !document.body ) {
- return setTimeout( jQuery.ready, 13 );
+ return setTimeout( jQuery.ready, 1 );
}
// Remember that the DOM is ready
jQuery.isReady = true;
+ // If a normal DOM Ready event fired, decrement, and wait if need be
+ if ( wait !== true && --jQuery.readyWait > 0 ) {
+ return;
+ }
+
// If there are functions bound, to execute
- if ( readyList ) {
- // Execute all of them
- var fn, i = 0;
- while ( (fn = readyList[ i++ ]) ) {
- fn.call( document, jQuery );
- }
-
- // Reset the list of functions
- readyList = null;
- }
+ readyList.resolveWith( document, [ jQuery ] );
// Trigger any bound ready events
- if ( jQuery.fn.triggerHandler ) {
- jQuery( document ).triggerHandler( "ready" );
- }
- }
- },
-
+ if ( jQuery.fn.trigger ) {
+ jQuery( document ).trigger( "ready" ).unbind( "ready" );
+ }
+ }
+ },
+
bindReady: function() {
if ( readyBound ) {
return;
@@ -413,14 +436,15 @@
// Catch cases where $(document).ready() is called after the
// browser event has already occurred.
if ( document.readyState === "complete" ) {
- return jQuery.ready();
+ // Handle it asynchronously to allow scripts the opportunity to delay ready
+ return setTimeout( jQuery.ready, 1 );
}
// Mozilla, Opera and webkit nightlies currently support this event
if ( document.addEventListener ) {
// Use the handy event callback
document.addEventListener( "DOMContentLoaded", DOMContentLoaded, false );
-
+
// A fallback to window.onload, that will always work
window.addEventListener( "load", jQuery.ready, false );
@@ -429,7 +453,7 @@
// ensure firing before onload,
// maybe late but safe also for iframes
document.attachEvent("onreadystatechange", DOMContentLoaded);
-
+
// A fallback to window.onload, that will always work
window.attachEvent( "onload", jQuery.ready );
@@ -451,35 +475,50 @@
// Since version 1.3, DOM methods and functions like alert
// aren't supported. They return false on IE (#2968).
isFunction: function( obj ) {
- return toString.call(obj) === "[object Function]";
- },
-
- isArray: function( obj ) {
- return toString.call(obj) === "[object Array]";
+ return jQuery.type(obj) === "function";
+ },
+
+ isArray: Array.isArray || function( obj ) {
+ return jQuery.type(obj) === "array";
+ },
+
+ // A crude way of determining if an object is a window
+ isWindow: function( obj ) {
+ return obj && typeof obj === "object" && "setInterval" in obj;
+ },
+
+ isNaN: function( obj ) {
+ return obj == null || !rdigit.test( obj ) || isNaN( obj );
+ },
+
+ type: function( obj ) {
+ return obj == null ?
+ String( obj ) :
+ class2type[ toString.call(obj) ] || "object";
},
isPlainObject: function( obj ) {
// Must be an Object.
// Because of IE, we also have to check the presence of the constructor property.
// Make sure that DOM nodes and window objects don't pass through, as well
- if ( !obj || toString.call(obj) !== "[object Object]" || obj.nodeType || obj.setInterval ) {
+ if ( !obj || jQuery.type(obj) !== "object" || obj.nodeType || jQuery.isWindow( obj ) ) {
return false;
}
-
+
// Not own constructor property must be Object
- if ( obj.constructor
- && !hasOwnProperty.call(obj, "constructor")
- && !hasOwnProperty.call(obj.constructor.prototype, "isPrototypeOf") ) {
+ if ( obj.constructor &&
+ !hasOwn.call(obj, "constructor") &&
+ !hasOwn.call(obj.constructor.prototype, "isPrototypeOf") ) {
return false;
}
-
+
// Own properties are enumerated firstly, so to speed up,
// if last one is own, then all properties are own.
-
+
var key;
for ( key in obj ) {}
-
- return key === undefined || hasOwnProperty.call( obj, key );
+
+ return key === undefined || hasOwn.call( obj, key );
},
isEmptyObject: function( obj ) {
@@ -488,11 +527,11 @@
}
return true;
},
-
+
error: function( msg ) {
throw msg;
},
-
+
parseJSON: function( data ) {
if ( typeof data !== "string" || !data ) {
return null;
@@ -500,12 +539,12 @@
// Make sure leading/trailing whitespace is removed (IE can't handle it)
data = jQuery.trim( data );
-
+
// Make sure the incoming data is actual JSON
// Logic borrowed from http://json.org/json2.js
- if ( /^[\],:{}\s]*$/.test(data.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g, "@")
- .replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g, "]")
- .replace(/(?:^|:|,)(?:\s*\[)+/g, "")) ) {
+ if ( rvalidchars.test(data.replace(rvalidescape, "@")
+ .replace(rvalidtokens, "]")
+ .replace(rvalidbraces, "")) ) {
// Try to use the native JSON parser first
return window.JSON && window.JSON.parse ?
@@ -517,6 +556,28 @@
}
},
+ // Cross-browser xml parsing
+ // (xml & tmp used internally)
+ parseXML: function( data , xml , tmp ) {
+
+ if ( window.DOMParser ) { // Standard
+ tmp = new DOMParser();
+ xml = tmp.parseFromString( data , "text/xml" );
+ } else { // IE
+ xml = new ActiveXObject( "Microsoft.XMLDOM" );
+ xml.async = "false";
+ xml.loadXML( data );
+ }
+
+ tmp = xml.documentElement;
+
+ if ( ! tmp || ! tmp.nodeName || tmp.nodeName === "parsererror" ) {
+ jQuery.error( "Invalid XML: " + data );
+ }
+
+ return xml;
+ },
+
noop: function() {},
// Evalulates a script in a global context
@@ -529,7 +590,7 @@
script.type = "text/javascript";
- if ( jQuery.support.scriptEval ) {
+ if ( jQuery.support.scriptEval() ) {
script.appendChild( document.createTextNode( data ) );
} else {
script.text = data;
@@ -584,9 +645,20 @@
return object;
},
- trim: function( text ) {
- return (text || "").replace( rtrim, "" );
- },
+ // Use native String.trim function wherever possible
+ trim: trim ?
+ function( text ) {
+ return text == null ?
+ "" :
+ trim.call( text );
+ } :
+
+ // Otherwise use our own trimming functionality
+ function( text ) {
+ return text == null ?
+ "" :
+ text.toString().replace( trimLeft, "" ).replace( trimRight, "" );
+ },
// results is for internal usage only
makeArray: function( array, results ) {
@@ -596,7 +668,10 @@
// The window, strings (and functions) also have 'length'
// The extra typeof function check is to prevent crashes
// in Safari 2 (See: #3039)
- if ( array.length == null || typeof array === "string" || jQuery.isFunction(array) || (typeof array !== "function" && array.setInterval) ) {
+ // Tweaked logic slightly to handle Blackberry 4.7 RegExp issues #6930
+ var type = jQuery.type(array);
+
+ if ( array.length == null || type === "string" || type === "function" || type === "regexp" || jQuery.isWindow( array ) ) {
push.call( ret, array );
} else {
jQuery.merge( ret, array );
@@ -621,13 +696,14 @@
},
merge: function( first, second ) {
- var i = first.length, j = 0;
+ var i = first.length,
+ j = 0;
if ( typeof second.length === "number" ) {
for ( var l = second.length; j < l; j++ ) {
first[ i++ ] = second[ j ];
}
-
+
} else {
while ( second[j] !== undefined ) {
first[ i++ ] = second[ j++ ];
@@ -640,12 +716,14 @@
},
grep: function( elems, callback, inv ) {
- var ret = [];
+ var ret = [], retVal;
+ inv = !!inv;
// Go through the array, only saving the items
// that pass the validator function
for ( var i = 0, length = elems.length; i < length; i++ ) {
- if ( !inv !== !callback( elems[ i ], i ) ) {
+ retVal = !!callback( elems[ i ], i );
+ if ( inv !== retVal ) {
ret.push( elems[ i ] );
}
}
@@ -667,6 +745,7 @@
}
}
+ // Flatten any nested arrays
return ret.concat.apply( [], ret );
},
@@ -701,23 +780,234 @@
return proxy;
},
+ // Mutifunctional method to get and set values to a collection
+ // The value/s can be optionally by executed if its a function
+ access: function( elems, key, value, exec, fn, pass ) {
+ var length = elems.length;
+
+ // Setting many attributes
+ if ( typeof key === "object" ) {
+ for ( var k in key ) {
+ jQuery.access( elems, k, key[k], exec, fn, value );
+ }
+ return elems;
+ }
+
+ // Setting one attribute
+ if ( value !== undefined ) {
+ // Optionally, function values get executed if exec is true
+ exec = !pass && exec && jQuery.isFunction(value);
+
+ for ( var i = 0; i < length; i++ ) {
+ fn( elems[i], key, exec ? value.call( elems[i], i, fn( elems[i], key ) ) : value, pass );
+ }
+
+ return elems;
+ }
+
+ // Getting an attribute
+ return length ? fn( elems[0], key ) : undefined;
+ },
+
+ now: function() {
+ return (new Date()).getTime();
+ },
+
+ // Create a simple deferred (one callbacks list)
+ _Deferred: function() {
+ var // callbacks list
+ callbacks = [],
+ // stored [ context , args ]
+ fired,
+ // to avoid firing when already doing so
+ firing,
+ // flag to know if the deferred has been cancelled
+ cancelled,
+ // the deferred itself
+ deferred = {
+
+ // done( f1, f2, ...)
+ done: function() {
+ if ( !cancelled ) {
+ var args = arguments,
+ i,
+ length,
+ elem,
+ type,
+ _fired;
+ if ( fired ) {
+ _fired = fired;
+ fired = 0;
+ }
+ for ( i = 0, length = args.length; i < length; i++ ) {
+ elem = args[ i ];
+ type = jQuery.type( elem );
+ if ( type === "array" ) {
+ deferred.done.apply( deferred, elem );
+ } else if ( type === "function" ) {
+ callbacks.push( elem );
+ }
+ }
+ if ( _fired ) {
+ deferred.resolveWith( _fired[ 0 ], _fired[ 1 ] );
+ }
+ }
+ return this;
+ },
+
+ // resolve with given context and args
+ resolveWith: function( context, args ) {
+ if ( !cancelled && !fired && !firing ) {
+ firing = 1;
+ try {
+ while( callbacks[ 0 ] ) {
+ callbacks.shift().apply( context, args );
+ }
+ }
+ finally {
+ fired = [ context, args ];
+ firing = 0;
+ }
+ }
+ return this;
+ },
+
+ // resolve with this as context and given arguments
+ resolve: function() {
+ deferred.resolveWith( jQuery.isFunction( this.promise ) ? this.promise() : this, arguments );
+ return this;
+ },
+
+ // Has this deferred been resolved?
+ isResolved: function() {
+ return !!( firing || fired );
+ },
+
+ // Cancel
+ cancel: function() {
+ cancelled = 1;
+ callbacks = [];
+ return this;
+ }
+ };
+
+ return deferred;
+ },
+
+ // Full fledged deferred (two callbacks list)
+ Deferred: function( func ) {
+ var deferred = jQuery._Deferred(),
+ failDeferred = jQuery._Deferred(),
+ promise;
+ // Add errorDeferred methods, then and promise
+ jQuery.extend( deferred, {
+ then: function( doneCallbacks, failCallbacks ) {
+ deferred.done( doneCallbacks ).fail( failCallbacks );
+ return this;
+ },
+ fail: failDeferred.done,
+ rejectWith: failDeferred.resolveWith,
+ reject: failDeferred.resolve,
+ isRejected: failDeferred.isResolved,
+ // Get a promise for this deferred
+ // If obj is provided, the promise aspect is added to the object
+ promise: function( obj , i /* internal */ ) {
+ if ( obj == null ) {
+ if ( promise ) {
+ return promise;
+ }
+ promise = obj = {};
+ }
+ i = promiseMethods.length;
+ while( i-- ) {
+ obj[ promiseMethods[ i ] ] = deferred[ promiseMethods[ i ] ];
+ }
+ return obj;
+ }
+ } );
+ // Make sure only one callback list will be used
+ deferred.then( failDeferred.cancel, deferred.cancel );
+ // Unexpose cancel
+ delete deferred.cancel;
+ // Call given func if any
+ if ( func ) {
+ func.call( deferred, deferred );
+ }
+ return deferred;
+ },
+
+ // Deferred helper
+ when: function( object ) {
+ var args = arguments,
+ length = args.length,
+ deferred = length <= 1 && object && jQuery.isFunction( object.promise ) ?
+ object :
+ jQuery.Deferred(),
+ promise = deferred.promise(),
+ resolveArray;
+
+ if ( length > 1 ) {
+ resolveArray = new Array( length );
+ jQuery.each( args, function( index, element ) {
+ jQuery.when( element ).then( function( value ) {
+ resolveArray[ index ] = arguments.length > 1 ? slice.call( arguments, 0 ) : value;
+ if( ! --length ) {
+ deferred.resolveWith( promise, resolveArray );
+ }
+ }, deferred.reject );
+ } );
+ } else if ( deferred !== object ) {
+ deferred.resolve( object );
+ }
+ return promise;
+ },
+
// Use of jQuery.browser is frowned upon.
// More details: http://docs.jquery.com/Utilities/jQuery.browser
uaMatch: function( ua ) {
ua = ua.toLowerCase();
- var match = /(webkit)[ \/]([\w.]+)/.exec( ua ) ||
- /(opera)(?:.*version)?[ \/]([\w.]+)/.exec( ua ) ||
- /(msie) ([\w.]+)/.exec( ua ) ||
- !/compatible/.test( ua ) && /(mozilla)(?:.*? rv:([\w.]+))?/.exec( ua ) ||
- [];
+ var match = rwebkit.exec( ua ) ||
+ ropera.exec( ua ) ||
+ rmsie.exec( ua ) ||
+ ua.indexOf("compatible") < 0 && rmozilla.exec( ua ) ||
+ [];
return { browser: match[1] || "", version: match[2] || "0" };
},
+ sub: function() {
+ function jQuerySubclass( selector, context ) {
+ return new jQuerySubclass.fn.init( selector, context );
+ }
+ jQuery.extend( true, jQuerySubclass, this );
+ jQuerySubclass.superclass = this;
+ jQuerySubclass.fn = jQuerySubclass.prototype = this();
+ jQuerySubclass.fn.constructor = jQuerySubclass;
+ jQuerySubclass.subclass = this.subclass;
+ jQuerySubclass.fn.init = function init( selector, context ) {
+ if ( context && context instanceof jQuery && !(context instanceof jQuerySubclass) ) {
+ context = jQuerySubclass(context);
+ }
+
+ return jQuery.fn.init.call( this, selector, context, rootjQuerySubclass );
+ };
+ jQuerySubclass.fn.init.prototype = jQuerySubclass.fn;
+ var rootjQuerySubclass = jQuerySubclass(document);
+ return jQuerySubclass;
+ },
+
browser: {}
});
+// Create readyList deferred
+readyList = jQuery._Deferred();
+
+// Populate the class2type map
+jQuery.each("Boolean Number String Function Array Date RegExp Object".split(" "), function(i, name) {
+ class2type[ "[object " + name + "]" ] = name.toLowerCase();
+});
+
browserMatch = jQuery.uaMatch( userAgent );
if ( browserMatch.browser ) {
jQuery.browser[ browserMatch.browser ] = true;
@@ -735,6 +1025,12 @@
};
}
+// IE doesn't match non-breaking spaces with \s
+if ( rnotwhite.test( "\xA0" ) ) {
+ trimLeft = /^[\s\xA0]+/;
+ trimRight = /[\s\xA0]+$/;
+}
+
// All jQuery objects should point back to these
rootjQuery = jQuery(document);
@@ -765,7 +1061,7 @@
// If IE is used, use the trick by Diego Perini
// http://javascript.nwbox.com/IEContentLoaded/
document.documentElement.doScroll("left");
- } catch( error ) {
+ } catch(e) {
setTimeout( doScrollCheck, 1 );
return;
}
@@ -774,68 +1070,25 @@
jQuery.ready();
}
-function evalScript( i, elem ) {
- if ( elem.src ) {
- jQuery.ajax({
- url: elem.src,
- async: false,
- dataType: "script"
- });
- } else {
- jQuery.globalEval( elem.text || elem.textContent || elem.innerHTML || "" );
- }
-
- if ( elem.parentNode ) {
- elem.parentNode.removeChild( elem );
- }
-}
-
-// Mutifunctional method to get and set values to a collection
-// The value/s can be optionally by executed if its a function
-function access( elems, key, value, exec, fn, pass ) {
- var length = elems.length;
-
- // Setting many attributes
- if ( typeof key === "object" ) {
- for ( var k in key ) {
- access( elems, k, key[k], exec, fn, value );
- }
- return elems;
- }
-
- // Setting one attribute
- if ( value !== undefined ) {
- // Optionally, function values get executed if exec is true
- exec = !pass && exec && jQuery.isFunction(value);
-
- for ( var i = 0; i < length; i++ ) {
- fn( elems[i], key, exec ? value.call( elems[i], i, fn( elems[i], key ) ) : value, pass );
- }
-
- return elems;
- }
-
- // Getting an attribute
- return length ? fn( elems[0], key ) : undefined;
-}
-
-function now() {
- return (new Date).getTime();
-}
+// Expose jQuery to the global object
+return (window.jQuery = window.$ = jQuery);
+
+})();
+
+
(function() {
jQuery.support = {};
- var root = document.documentElement,
- script = document.createElement("script"),
- div = document.createElement("div"),
- id = "script" + now();
+ var div = document.createElement("div");
div.style.display = "none";
div.innerHTML = " <link/><table></table><a href='/a' style='color:red;float:left;opacity:.55;'>a</a><input type='checkbox'/>";
var all = div.getElementsByTagName("*"),
- a = div.getElementsByTagName("a")[0];
+ a = div.getElementsByTagName("a")[0],
+ select = document.createElement("select"),
+ opt = select.appendChild( document.createElement("option") );
// Can't get basic test support
if ( !all || !all.length || !a ) {
@@ -878,44 +1131,65 @@
// Make sure that a selected-by-default option has a working selected property.
// (WebKit defaults to false instead of true, IE too, if it's in an optgroup)
- optSelected: document.createElement("select").appendChild( document.createElement("option") ).selected,
-
- parentNode: div.removeChild( div.appendChild( document.createElement("div") ) ).parentNode === null,
+ optSelected: opt.selected,
// Will be defined later
deleteExpando: true,
+ optDisabled: false,
checkClone: false,
- scriptEval: false,
+ _scriptEval: null,
noCloneEvent: true,
- boxModel: null
+ boxModel: null,
+ inlineBlockNeedsLayout: false,
+ shrinkWrapBlocks: false,
+ reliableHiddenOffsets: true
};
- script.type = "text/javascript";
- try {
- script.appendChild( document.createTextNode( "window." + id + "=1;" ) );
- } catch(e) {}
-
- root.insertBefore( script, root.firstChild );
-
- // Make sure that the execution of code works by injecting a script
- // tag with appendChild/createTextNode
- // (IE doesn't support this, fails, and uses .text instead)
- if ( window[ id ] ) {
- jQuery.support.scriptEval = true;
- delete window[ id ];
- }
+ // Make sure that the options inside disabled selects aren't marked as disabled
+ // (WebKit marks them as diabled)
+ select.disabled = true;
+ jQuery.support.optDisabled = !opt.disabled;
+
+ jQuery.support.scriptEval = function() {
+ if ( jQuery.support._scriptEval === null ) {
+ var root = document.documentElement,
+ script = document.createElement("script"),
+ id = "script" + jQuery.now();
+
+ script.type = "text/javascript";
+ try {
+ script.appendChild( document.createTextNode( "window." + id + "=1;" ) );
+ } catch(e) {}
+
+ root.insertBefore( script, root.firstChild );
+
+ // Make sure that the execution of code works by injecting a script
+ // tag with appendChild/createTextNode
+ // (IE doesn't support this, fails, and uses .text instead)
+ if ( window[ id ] ) {
+ jQuery.support._scriptEval = true;
+ delete window[ id ];
+ } else {
+ jQuery.support._scriptEval = false;
+ }
+
+ root.removeChild( script );
+ // release memory in IE
+ root = script = id = null;
+ }
+
+ return jQuery.support._scriptEval;
+ };
// Test to see if it's possible to delete an expando from an element
// Fails in Internet Explorer
try {
- delete script.test;
-
+ delete div.test;
+
} catch(e) {
jQuery.support.deleteExpando = false;
}
- root.removeChild( script );
-
if ( div.attachEvent && div.fireEvent ) {
div.attachEvent("onclick", function click() {
// Cloning a node shouldn't copy over any
@@ -938,39 +1212,493 @@
// Figure out if the W3C box model works as expected
// document.body must exist before we can do this
jQuery(function() {
- var div = document.createElement("div");
+ var div = document.createElement("div"),
+ body = document.getElementsByTagName("body")[0];
+
+ // Frameset documents with no body should not run this code
+ if ( !body ) {
+ return;
+ }
+
div.style.width = div.style.paddingLeft = "1px";
-
- document.body.appendChild( div );
+ body.appendChild( div );
jQuery.boxModel = jQuery.support.boxModel = div.offsetWidth === 2;
- document.body.removeChild( div ).style.display = 'none';
-
- div = null;
+
+ if ( "zoom" in div.style ) {
+ // Check if natively block-level elements act like inline-block
+ // elements when setting their display to 'inline' and giving
+ // them layout
+ // (IE < 8 does this)
+ div.style.display = "inline";
+ div.style.zoom = 1;
+ jQuery.support.inlineBlockNeedsLayout = div.offsetWidth === 2;
+
+ // Check if elements with layout shrink-wrap their children
+ // (IE 6 does this)
+ div.style.display = "";
+ div.innerHTML = "<div style='width:4px;'></div>";
+ jQuery.support.shrinkWrapBlocks = div.offsetWidth !== 2;
+ }
+
+ div.innerHTML = "<table><tr><td style='padding:0;border:0;display:none'></td><td>t</td></tr></table>";
+ var tds = div.getElementsByTagName("td");
+
+ // Check if table cells still have offsetWidth/Height when they are set
+ // to display:none and there are still other visible table cells in a
+ // table row; if so, offsetWidth/Height are not reliable for use when
+ // determining if an element has been hidden directly using
+ // display:none (it is still safe to use offsets if a parent element is
+ // hidden; don safety goggles and see bug #4512 for more information).
+ // (only IE 8 fails this test)
+ jQuery.support.reliableHiddenOffsets = tds[0].offsetHeight === 0;
+
+ tds[0].style.display = "";
+ tds[1].style.display = "none";
+
+ // Check if empty table cells still have offsetWidth/Height
+ // (IE < 8 fail this test)
+ jQuery.support.reliableHiddenOffsets = jQuery.support.reliableHiddenOffsets && tds[0].offsetHeight === 0;
+ div.innerHTML = "";
+
+ body.removeChild( div ).style.display = "none";
+ div = tds = null;
});
// Technique from Juriy Zaytsev
// http://thinkweb2.com/projects/prototype/detecting-event-support-without-bro…
- var eventSupported = function( eventName ) {
- var el = document.createElement("div");
- eventName = "on" + eventName;
-
- var isSupported = (eventName in el);
- if ( !isSupported ) {
- el.setAttribute(eventName, "return;");
- isSupported = typeof el[eventName] === "function";
- }
- el = null;
-
- return isSupported;
+ var eventSupported = function( eventName ) {
+ var el = document.createElement("div");
+ eventName = "on" + eventName;
+
+ // We only care about the case where non-standard event systems
+ // are used, namely in IE. Short-circuiting here helps us to
+ // avoid an eval call (in setAttribute) which can cause CSP
+ // to go haywire. See: https://developer.mozilla.org/en/Security/CSP
+ if ( !el.attachEvent ) {
+ return true;
+ }
+
+ var isSupported = (eventName in el);
+ if ( !isSupported ) {
+ el.setAttribute(eventName, "return;");
+ isSupported = typeof el[eventName] === "function";
+ }
+ el = null;
+
+ return isSupported;
};
-
+
jQuery.support.submitBubbles = eventSupported("submit");
jQuery.support.changeBubbles = eventSupported("change");
// release memory in IE
- root = script = div = all = a = null;
+ div = all = a = null;
})();
+
+
+var rbrace = /^(?:\{.*\}|\[.*\])$/;
+
+jQuery.extend({
+ cache: {},
+
+ // Please use with caution
+ uuid: 0,
+
+ // Unique for each copy of jQuery on the page
+ // Non-digits removed to match rinlinejQuery
+ expando: "jQuery" + ( jQuery.fn.jquery + Math.random() ).replace( /\D/g, "" ),
+
+ // The following elements throw uncatchable exceptions if you
+ // attempt to add expando properties to them.
+ noData: {
+ "embed": true,
+ // Ban all objects except for Flash (which handle expandos)
+ "object": "clsid:D27CDB6E-AE6D-11cf-96B8-444553540000",
+ "applet": true
+ },
+
+ hasData: function( elem ) {
+ elem = elem.nodeType ? jQuery.cache[ elem[jQuery.expando] ] : elem[ jQuery.expando ];
+
+ return !!elem && !jQuery.isEmptyObject(elem);
+ },
+
+ data: function( elem, name, data, pvt /* Internal Use Only */ ) {
+ if ( !jQuery.acceptData( elem ) ) {
+ return;
+ }
+
+ var internalKey = jQuery.expando, getByName = typeof name === "string", thisCache,
+
+ // We have to handle DOM nodes and JS objects differently because IE6-7
+ // can't GC object references properly across the DOM-JS boundary
+ isNode = elem.nodeType,
+
+ // Only DOM nodes need the global jQuery cache; JS object data is
+ // attached directly to the object so GC can occur automatically
+ cache = isNode ? jQuery.cache : elem,
+
+ // Only defining an ID for JS objects if its cache already exists allows
+ // the code to shortcut on the same path as a DOM node with no cache
+ id = isNode ? elem[ jQuery.expando ] : elem[ jQuery.expando ] && jQuery.expando;
+
+ // Avoid doing any more work than we need to when trying to get data on an
+ // object that has no data at all
+ if ( (!id || (pvt && id && !cache[ id ][ internalKey ])) && getByName && data === undefined ) {
+ return;
+ }
+
+ if ( !id ) {
+ // Only DOM nodes need a new unique ID for each element since their data
+ // ends up in the global cache
+ if ( isNode ) {
+ elem[ jQuery.expando ] = id = ++jQuery.uuid;
+ } else {
+ id = jQuery.expando;
+ }
+ }
+
+ if ( !cache[ id ] ) {
+ cache[ id ] = {};
+ }
+
+ // An object can be passed to jQuery.data instead of a key/value pair; this gets
+ // shallow copied over onto the existing cache
+ if ( typeof name === "object" ) {
+ if ( pvt ) {
+ cache[ id ][ internalKey ] = jQuery.extend(cache[ id ][ internalKey ], name);
+ } else {
+ cache[ id ] = jQuery.extend(cache[ id ], name);
+ }
+ }
+
+ thisCache = cache[ id ];
+
+ // Internal jQuery data is stored in a separate object inside the object's data
+ // cache in order to avoid key collisions between internal data and user-defined
+ // data
+ if ( pvt ) {
+ if ( !thisCache[ internalKey ] ) {
+ thisCache[ internalKey ] = {};
+ }
+
+ thisCache = thisCache[ internalKey ];
+ }
+
+ if ( data !== undefined ) {
+ thisCache[ name ] = data;
+ }
+
+ // TODO: This is a hack for 1.5 ONLY. It will be removed in 1.6. Users should
+ // not attempt to inspect the internal events object using jQuery.data, as this
+ // internal data object is undocumented and subject to change.
+ if ( name === "events" && !thisCache[name] ) {
+ return thisCache[ internalKey ] && thisCache[ internalKey ].events;
+ }
+
+ return getByName ? thisCache[ name ] : thisCache;
+ },
+
+ removeData: function( elem, name, pvt /* Internal Use Only */ ) {
+ if ( !jQuery.acceptData( elem ) ) {
+ return;
+ }
+
+ var internalKey = jQuery.expando, isNode = elem.nodeType,
+
+ // See jQuery.data for more information
+ cache = isNode ? jQuery.cache : elem,
+
+ // See jQuery.data for more information
+ id = isNode ? elem[ jQuery.expando ] : jQuery.expando;
+
+ // If there is already no cache entry for this object, there is no
+ // purpose in continuing
+ if ( !cache[ id ] ) {
+ return;
+ }
+
+ if ( name ) {
+ var thisCache = pvt ? cache[ id ][ internalKey ] : cache[ id ];
+
+ if ( thisCache ) {
+ delete thisCache[ name ];
+
+ // If there is no data left in the cache, we want to continue
+ // and let the cache object itself get destroyed
+ if ( !jQuery.isEmptyObject(thisCache) ) {
+ return;
+ }
+ }
+ }
+
+ // See jQuery.data for more information
+ if ( pvt ) {
+ delete cache[ id ][ internalKey ];
+
+ // Don't destroy the parent cache unless the internal data object
+ // had been the only thing left in it
+ if ( !jQuery.isEmptyObject(cache[ id ]) ) {
+ return;
+ }
+ }
+
+ var internalCache = cache[ id ][ internalKey ];
+
+ // Browsers that fail expando deletion also refuse to delete expandos on
+ // the window, but it will allow it on all other JS objects; other browsers
+ // don't care
+ if ( jQuery.support.deleteExpando || cache != window ) {
+ delete cache[ id ];
+ } else {
+ cache[ id ] = null;
+ }
+
+ // We destroyed the entire user cache at once because it's faster than
+ // iterating through each key, but we need to continue to persist internal
+ // data if it existed
+ if ( internalCache ) {
+ cache[ id ] = {};
+ cache[ id ][ internalKey ] = internalCache;
+
+ // Otherwise, we need to eliminate the expando on the node to avoid
+ // false lookups in the cache for entries that no longer exist
+ } else if ( isNode ) {
+ // IE does not allow us to delete expando properties from nodes,
+ // nor does it have a removeAttribute function on Document nodes;
+ // we must handle all of these cases
+ if ( jQuery.support.deleteExpando ) {
+ delete elem[ jQuery.expando ];
+ } else if ( elem.removeAttribute ) {
+ elem.removeAttribute( jQuery.expando );
+ } else {
+ elem[ jQuery.expando ] = null;
+ }
+ }
+ },
+
+ // For internal use only.
+ _data: function( elem, name, data ) {
+ return jQuery.data( elem, name, data, true );
+ },
+
+ // A method for determining if a DOM node can handle the data expando
+ acceptData: function( elem ) {
+ if ( elem.nodeName ) {
+ var match = jQuery.noData[ elem.nodeName.toLowerCase() ];
+
+ if ( match ) {
+ return !(match === true || elem.getAttribute("classid") !== match);
+ }
+ }
+
+ return true;
+ }
+});
+
+jQuery.fn.extend({
+ data: function( key, value ) {
+ var data = null;
+
+ if ( typeof key === "undefined" ) {
+ if ( this.length ) {
+ data = jQuery.data( this[0] );
+
+ if ( this[0].nodeType === 1 ) {
+ var attr = this[0].attributes, name;
+ for ( var i = 0, l = attr.length; i < l; i++ ) {
+ name = attr[i].name;
+
+ if ( name.indexOf( "data-" ) === 0 ) {
+ name = name.substr( 5 );
+ dataAttr( this[0], name, data[ name ] );
+ }
+ }
+ }
+ }
+
+ return data;
+
+ } else if ( typeof key === "object" ) {
+ return this.each(function() {
+ jQuery.data( this, key );
+ });
+ }
+
+ var parts = key.split(".");
+ parts[1] = parts[1] ? "." + parts[1] : "";
+
+ if ( value === undefined ) {
+ data = this.triggerHandler("getData" + parts[1] + "!", [parts[0]]);
+
+ // Try to fetch any internally stored data first
+ if ( data === undefined && this.length ) {
+ data = jQuery.data( this[0], key );
+ data = dataAttr( this[0], key, data );
+ }
+
+ return data === undefined && parts[1] ?
+ this.data( parts[0] ) :
+ data;
+
+ } else {
+ return this.each(function() {
+ var $this = jQuery( this ),
+ args = [ parts[0], value ];
+
+ $this.triggerHandler( "setData" + parts[1] + "!", args );
+ jQuery.data( this, key, value );
+ $this.triggerHandler( "changeData" + parts[1] + "!", args );
+ });
+ }
+ },
+
+ removeData: function( key ) {
+ return this.each(function() {
+ jQuery.removeData( this, key );
+ });
+ }
+});
+
+function dataAttr( elem, key, data ) {
+ // If nothing was found internally, try to fetch any
+ // data from the HTML5 data-* attribute
+ if ( data === undefined && elem.nodeType === 1 ) {
+ data = elem.getAttribute( "data-" + key );
+
+ if ( typeof data === "string" ) {
+ try {
+ data = data === "true" ? true :
+ data === "false" ? false :
+ data === "null" ? null :
+ !jQuery.isNaN( data ) ? parseFloat( data ) :
+ rbrace.test( data ) ? jQuery.parseJSON( data ) :
+ data;
+ } catch( e ) {}
+
+ // Make sure we set the data so it isn't changed later
+ jQuery.data( elem, key, data );
+
+ } else {
+ data = undefined;
+ }
+ }
+
+ return data;
+}
+
+
+
+
+jQuery.extend({
+ queue: function( elem, type, data ) {
+ if ( !elem ) {
+ return;
+ }
+
+ type = (type || "fx") + "queue";
+ var q = jQuery._data( elem, type );
+
+ // Speed up dequeue by getting out quickly if this is just a lookup
+ if ( !data ) {
+ return q || [];
+ }
+
+ if ( !q || jQuery.isArray(data) ) {
+ q = jQuery._data( elem, type, jQuery.makeArray(data) );
+
+ } else {
+ q.push( data );
+ }
+
+ return q;
+ },
+
+ dequeue: function( elem, type ) {
+ type = type || "fx";
+
+ var queue = jQuery.queue( elem, type ),
+ fn = queue.shift();
+
+ // If the fx queue is dequeued, always remove the progress sentinel
+ if ( fn === "inprogress" ) {
+ fn = queue.shift();
+ }
+
+ if ( fn ) {
+ // Add a progress sentinel to prevent the fx queue from being
+ // automatically dequeued
+ if ( type === "fx" ) {
+ queue.unshift("inprogress");
+ }
+
+ fn.call(elem, function() {
+ jQuery.dequeue(elem, type);
+ });
+ }
+
+ if ( !queue.length ) {
+ jQuery.removeData( elem, type + "queue", true );
+ }
+ }
+});
+
+jQuery.fn.extend({
+ queue: function( type, data ) {
+ if ( typeof type !== "string" ) {
+ data = type;
+ type = "fx";
+ }
+
+ if ( data === undefined ) {
+ return jQuery.queue( this[0], type );
+ }
+ return this.each(function( i ) {
+ var queue = jQuery.queue( this, type, data );
+
+ if ( type === "fx" && queue[0] !== "inprogress" ) {
+ jQuery.dequeue( this, type );
+ }
+ });
+ },
+ dequeue: function( type ) {
+ return this.each(function() {
+ jQuery.dequeue( this, type );
+ });
+ },
+
+ // Based off of the plugin by Clint Helfers, with permission.
+ // http://blindsignals.com/index.php/2009/07/jquery-delay/
+ delay: function( time, type ) {
+ time = jQuery.fx ? jQuery.fx.speeds[time] || time : time;
+ type = type || "fx";
+
+ return this.queue( type, function() {
+ var elem = this;
+ setTimeout(function() {
+ jQuery.dequeue( elem, type );
+ }, time );
+ });
+ },
+
+ clearQueue: function( type ) {
+ return this.queue( type || "fx", [] );
+ }
+});
+
+
+
+
+var rclass = /[\n\t\r]/g,
+ rspaces = /\s+/,
+ rreturn = /\r/g,
+ rspecialurl = /^(?:href|src|style)$/,
+ rtype = /^(?:button|input)$/i,
+ rfocusable = /^(?:button|input|object|select|textarea)$/i,
+ rclickable = /^a(?:rea)?$/i,
+ rradiocheck = /^(?:radio|checkbox)$/i;
+
jQuery.props = {
"for": "htmlFor",
"class": "className",
@@ -983,238 +1711,10 @@
usemap: "useMap",
frameborder: "frameBorder"
};
-var expando = "jQuery" + now(), uuid = 0, windowData = {};
-
-jQuery.extend({
- cache: {},
-
- expando:expando,
-
- // The following elements throw uncatchable exceptions if you
- // attempt to add expando properties to them.
- noData: {
- "embed": true,
- "object": true,
- "applet": true
- },
-
- data: function( elem, name, data ) {
- if ( elem.nodeName && jQuery.noData[elem.nodeName.toLowerCase()] ) {
- return;
- }
-
- elem = elem == window ?
- windowData :
- elem;
-
- var id = elem[ expando ], cache = jQuery.cache, thisCache;
-
- if ( !id && typeof name === "string" && data === undefined ) {
- return null;
- }
-
- // Compute a unique ID for the element
- if ( !id ) {
- id = ++uuid;
- }
-
- // Avoid generating a new cache unless none exists and we
- // want to manipulate it.
- if ( typeof name === "object" ) {
- elem[ expando ] = id;
- thisCache = cache[ id ] = jQuery.extend(true, {}, name);
-
- } else if ( !cache[ id ] ) {
- elem[ expando ] = id;
- cache[ id ] = {};
- }
-
- thisCache = cache[ id ];
-
- // Prevent overriding the named cache with undefined values
- if ( data !== undefined ) {
- thisCache[ name ] = data;
- }
-
- return typeof name === "string" ? thisCache[ name ] : thisCache;
- },
-
- removeData: function( elem, name ) {
- if ( elem.nodeName && jQuery.noData[elem.nodeName.toLowerCase()] ) {
- return;
- }
-
- elem = elem == window ?
- windowData :
- elem;
-
- var id = elem[ expando ], cache = jQuery.cache, thisCache = cache[ id ];
-
- // If we want to remove a specific section of the element's data
- if ( name ) {
- if ( thisCache ) {
- // Remove the section of cache data
- delete thisCache[ name ];
-
- // If we've removed all the data, remove the element's cache
- if ( jQuery.isEmptyObject(thisCache) ) {
- jQuery.removeData( elem );
- }
- }
-
- // Otherwise, we want to remove all of the element's data
- } else {
- if ( jQuery.support.deleteExpando ) {
- delete elem[ jQuery.expando ];
-
- } else if ( elem.removeAttribute ) {
- elem.removeAttribute( jQuery.expando );
- }
-
- // Completely remove the data cache
- delete cache[ id ];
- }
- }
-});
-
-jQuery.fn.extend({
- data: function( key, value ) {
- if ( typeof key === "undefined" && this.length ) {
- return jQuery.data( this[0] );
-
- } else if ( typeof key === "object" ) {
- return this.each(function() {
- jQuery.data( this, key );
- });
- }
-
- var parts = key.split(".");
- parts[1] = parts[1] ? "." + parts[1] : "";
-
- if ( value === undefined ) {
- var data = this.triggerHandler("getData" + parts[1] + "!", [parts[0]]);
-
- if ( data === undefined && this.length ) {
- data = jQuery.data( this[0], key );
- }
- return data === undefined && parts[1] ?
- this.data( parts[0] ) :
- data;
- } else {
- return this.trigger("setData" + parts[1] + "!", [parts[0], value]).each(function() {
- jQuery.data( this, key, value );
- });
- }
- },
-
- removeData: function( key ) {
- return this.each(function() {
- jQuery.removeData( this, key );
- });
- }
-});
-jQuery.extend({
- queue: function( elem, type, data ) {
- if ( !elem ) {
- return;
- }
-
- type = (type || "fx") + "queue";
- var q = jQuery.data( elem, type );
-
- // Speed up dequeue by getting out quickly if this is just a lookup
- if ( !data ) {
- return q || [];
- }
-
- if ( !q || jQuery.isArray(data) ) {
- q = jQuery.data( elem, type, jQuery.makeArray(data) );
-
- } else {
- q.push( data );
- }
-
- return q;
- },
-
- dequeue: function( elem, type ) {
- type = type || "fx";
-
- var queue = jQuery.queue( elem, type ), fn = queue.shift();
-
- // If the fx queue is dequeued, always remove the progress sentinel
- if ( fn === "inprogress" ) {
- fn = queue.shift();
- }
-
- if ( fn ) {
- // Add a progress sentinel to prevent the fx queue from being
- // automatically dequeued
- if ( type === "fx" ) {
- queue.unshift("inprogress");
- }
-
- fn.call(elem, function() {
- jQuery.dequeue(elem, type);
- });
- }
- }
-});
-
-jQuery.fn.extend({
- queue: function( type, data ) {
- if ( typeof type !== "string" ) {
- data = type;
- type = "fx";
- }
-
- if ( data === undefined ) {
- return jQuery.queue( this[0], type );
- }
- return this.each(function( i, elem ) {
- var queue = jQuery.queue( this, type, data );
-
- if ( type === "fx" && queue[0] !== "inprogress" ) {
- jQuery.dequeue( this, type );
- }
- });
- },
- dequeue: function( type ) {
- return this.each(function() {
- jQuery.dequeue( this, type );
- });
- },
-
- // Based off of the plugin by Clint Helfers, with permission.
- // http://blindsignals.com/index.php/2009/07/jquery-delay/
- delay: function( time, type ) {
- time = jQuery.fx ? jQuery.fx.speeds[time] || time : time;
- type = type || "fx";
-
- return this.queue( type, function() {
- var elem = this;
- setTimeout(function() {
- jQuery.dequeue( elem, type );
- }, time );
- });
- },
-
- clearQueue: function( type ) {
- return this.queue( type || "fx", [] );
- }
-});
-var rclass = /[\n\t]/g,
- rspace = /\s+/,
- rreturn = /\r/g,
- rspecialurl = /href|src|style/,
- rtype = /(button|input)/i,
- rfocusable = /(button|input|object|select|textarea)/i,
- rclickable = /^(a|area)$/i,
- rradiocheck = /radio|checkbox/;
jQuery.fn.extend({
attr: function( name, value ) {
- return access( this, name, value, true, jQuery.attr );
+ return jQuery.access( this, name, value, true, jQuery.attr );
},
removeAttr: function( name, fn ) {
@@ -1235,7 +1735,7 @@
}
if ( value && typeof value === "string" ) {
- var classNames = (value || "").split( rspace );
+ var classNames = (value || "").split( rspaces );
for ( var i = 0, l = this.length; i < l; i++ ) {
var elem = this[i];
@@ -1245,7 +1745,9 @@
elem.className = value;
} else {
- var className = " " + elem.className + " ", setClass = elem.className;
+ var className = " " + elem.className + " ",
+ setClass = elem.className;
+
for ( var c = 0, cl = classNames.length; c < cl; c++ ) {
if ( className.indexOf( " " + classNames[c] + " " ) < 0 ) {
setClass += " " + classNames[c];
@@ -1269,7 +1771,7 @@
}
if ( (value && typeof value === "string") || value === undefined ) {
- var classNames = (value || "").split(rspace);
+ var classNames = (value || "").split( rspaces );
for ( var i = 0, l = this.length; i < l; i++ ) {
var elem = this[i];
@@ -1293,7 +1795,8 @@
},
toggleClass: function( value, stateVal ) {
- var type = typeof value, isBool = typeof stateVal === "boolean";
+ var type = typeof value,
+ isBool = typeof stateVal === "boolean";
if ( jQuery.isFunction( value ) ) {
return this.each(function(i) {
@@ -1305,9 +1808,11 @@
return this.each(function() {
if ( type === "string" ) {
// toggle individual class names
- var className, i = 0, self = jQuery(this),
+ var className,
+ i = 0,
+ self = jQuery( this ),
state = stateVal,
- classNames = value.split( rspace );
+ classNames = value.split( rspaces );
while ( (className = classNames[ i++ ]) ) {
// check each className given, space seperated list
@@ -1318,11 +1823,11 @@
} else if ( type === "undefined" || type === "boolean" ) {
if ( this.className ) {
// store className if set
- jQuery.data( this, "__className__", this.className );
+ jQuery._data( this, "__className__", this.className );
}
// toggle whole className
- this.className = this.className || value === false ? "" : jQuery.data( this, "__className__" ) || "";
+ this.className = this.className || value === false ? "" : jQuery._data( this, "__className__" ) || "";
}
});
},
@@ -1339,12 +1844,15 @@
},
val: function( value ) {
- if ( value === undefined ) {
+ if ( !arguments.length ) {
var elem = this[0];
if ( elem ) {
if ( jQuery.nodeName( elem, "option" ) ) {
- return (elem.attributes.value || {}).specified ? elem.value : elem.text;
+ // attributes.value is undefined in Blackberry 4.7 but
+ // uses .value. See #6932
+ var val = elem.attributes.value;
+ return !val || val.specified ? elem.value : elem.text;
}
// We need to handle select boxes special
@@ -1363,8 +1871,11 @@
for ( var i = one ? index : 0, max = one ? index + 1 : options.length; i < max; i++ ) {
var option = options[ i ];
- if ( option.selected ) {
- // Get the specifc value for the option
+ // Don't return options that are disabled or in a disabled optgroup
+ if ( option.selected && (jQuery.support.optDisabled ? !option.disabled : option.getAttribute("disabled") === null) &&
+ (!option.parentNode.disabled || !jQuery.nodeName( option.parentNode, "optgroup" )) ) {
+
+ // Get the specific value for the option
value = jQuery(option).val();
// We don't need an array for one selects
@@ -1384,7 +1895,6 @@
if ( rradiocheck.test( elem.type ) && !jQuery.support.checkOn ) {
return elem.getAttribute("value") === null ? "on" : elem.value;
}
-
// Everything else, we just grab the value
return (elem.value || "").replace(rreturn, "");
@@ -1407,10 +1917,15 @@
val = value.call(this, i, self.val());
}
- // Typecast each time if the value is a Function and the appended
- // value is therefore different each time.
- if ( typeof val === "number" ) {
+ // Treat null/undefined as ""; convert numbers to string
+ if ( val == null ) {
+ val = "";
+ } else if ( typeof val === "number" ) {
val += "";
+ } else if ( jQuery.isArray(val) ) {
+ val = jQuery.map(val, function (value) {
+ return value == null ? "" : value + "";
+ });
}
if ( jQuery.isArray(val) && rradiocheck.test( this.type ) ) {
@@ -1445,10 +1960,10 @@
height: true,
offset: true
},
-
+
attr: function( elem, name, value, pass ) {
- // don't set attributes on text and comment nodes
- if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 ) {
+ // don't get/set attributes on text, comment and attribute nodes
+ if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || elem.nodeType === 2 ) {
return undefined;
}
@@ -1474,7 +1989,7 @@
var parent = elem.parentNode;
if ( parent ) {
parent.selectedIndex;
-
+
// Make sure that it also works with optgroups, see #5701
if ( parent.parentNode ) {
parent.parentNode.selectedIndex;
@@ -1483,14 +1998,22 @@
}
// If applicable, access the attribute via the DOM 0 way
- if ( name in elem && notxml && !special ) {
+ // 'in' checks fail in Blackberry 4.7 #6931
+ if ( (name in elem || elem[ name ] !== undefined) && notxml && !special ) {
if ( set ) {
// We can't allow the type property to be changed (since it causes problems in IE)
if ( name === "type" && rtype.test( elem.nodeName ) && elem.parentNode ) {
jQuery.error( "type property can't be changed" );
}
- elem[ name ] = value;
+ if ( value === null ) {
+ if ( elem.nodeType === 1 ) {
+ elem.removeAttribute( name );
+ }
+
+ } else {
+ elem[ name ] = value;
+ }
}
// browsers index elements by id/name on forms, give priority to attributes.
@@ -1526,6 +2049,12 @@
elem.setAttribute( name, "" + value );
}
+ // Ensure that missing attributes return undefined
+ // Blackberry 4.7 returns "" from getAttribute #6938
+ if ( !elem.attributes[ name ] && (elem.hasAttribute && !elem.hasAttribute( name )) ) {
+ return undefined;
+ }
+
var attr = !jQuery.support.hrefNormalized && notxml && special ?
// Some attributes require a special call on IE
elem.getAttribute( name, 2 ) :
@@ -1534,18 +2063,26 @@
// Non-existent attributes return null, we normalize to undefined
return attr === null ? undefined : attr;
}
-
- // elem is actually elem.style ... set the style
- // Using attr for specific style information is now deprecated. Use style instead.
- return jQuery.style( elem, name, value );
+ // Handle everything which isn't a DOM element node
+ if ( set ) {
+ elem[ name ] = value;
+ }
+ return elem[ name ];
}
});
+
+
+
+
var rnamespaces = /\.(.*)$/,
+ rformElems = /^(?:textarea|input|select)$/i,
+ rperiod = /\./g,
+ rspace = / /g,
+ rescape = /[^\w\s.|`]/g,
fcleanup = function( nm ) {
- return nm.replace(/[^\w\s\.\|`]/g, function( ch ) {
- return "\\" + ch;
- });
- };
+ return nm.replace(rescape, "\\$&");
+ },
+ eventKey = "events";
/*
* A number of helper functions used for managing events.
@@ -1563,10 +2100,17 @@
// For whatever reason, IE has trouble passing the window object
// around, causing it to be cloned in the process
- if ( elem.setInterval && ( elem !== window && !elem.frameElement ) ) {
+ if ( jQuery.isWindow( elem ) && ( elem !== window && !elem.frameElement ) ) {
elem = window;
}
+ if ( handler === false ) {
+ handler = returnFalse;
+ } else if ( !handler ) {
+ // Fixes bug #7229. Fix recommended by jdalton
+ return;
+ }
+
var handleObjIn, handleObj;
if ( handler.handler ) {
@@ -1580,7 +2124,7 @@
}
// Init the element's event structure
- var elemData = jQuery.data( elem );
+ var elemData = jQuery._data( elem );
// If no elemData is found then we must be trying to bind to one of the
// banned noData elements
@@ -1588,8 +2132,25 @@
return;
}
- var events = elemData.events = elemData.events || {},
- eventHandle = elemData.handle, eventHandle;
+ var events = elemData[ eventKey ],
+ eventHandle = elemData.handle;
+
+ if ( typeof events === "function" ) {
+ // On plain objects events is a fn that holds the the data
+ // which prevents this data from being JSON serialized
+ // the function does not need to be called, it just contains the data
+ eventHandle = events.handle;
+ events = events.events;
+
+ } else if ( !events ) {
+ if ( !elem.nodeType ) {
+ // On plain objects, create a fn that acts as the holder
+ // of the values to avoid JSON serialization of event data
+ elemData[ eventKey ] = elemData = function(){};
+ }
+
+ elemData.events = events = {};
+ }
if ( !eventHandle ) {
elemData.handle = eventHandle = function() {
@@ -1628,7 +2189,9 @@
}
handleObj.type = type;
- handleObj.guid = handler.guid;
+ if ( !handleObj.guid ) {
+ handleObj.guid = handler.guid;
+ }
// Get the current list of functions bound to this event
var handlers = events[ type ],
@@ -1651,9 +2214,9 @@
}
}
}
-
- if ( special.add ) {
- special.add.call( elem, handleObj );
+
+ if ( special.add ) {
+ special.add.call( elem, handleObj );
if ( !handleObj.handler.guid ) {
handleObj.handler.guid = handler.guid;
@@ -1680,14 +2243,23 @@
return;
}
- var ret, type, fn, i = 0, all, namespaces, namespace, special, eventType, handleObj, origType,
- elemData = jQuery.data( elem ),
- events = elemData && elemData.events;
+ if ( handler === false ) {
+ handler = returnFalse;
+ }
+
+ var ret, type, fn, j, i = 0, all, namespaces, namespace, special, eventType, handleObj, origType,
+ elemData = jQuery.hasData( elem ) && jQuery._data( elem ),
+ events = elemData && elemData[ eventKey ];
if ( !elemData || !events ) {
return;
}
+ if ( typeof events === "function" ) {
+ elemData = events;
+ events = events.events;
+ }
+
// types is actually an event object here
if ( types && types.type ) {
handler = types.handler;
@@ -1720,8 +2292,8 @@
namespaces = type.split(".");
type = namespaces.shift();
- namespace = new RegExp("(^|\\.)" +
- jQuery.map( namespaces.slice(0).sort(), fcleanup ).join("\\.(?:.*\\.)?") + "(\\.|$)")
+ namespace = new RegExp("(^|\\.)" +
+ jQuery.map( namespaces.slice(0).sort(), fcleanup ).join("\\.(?:.*\\.)?") + "(\\.|$)");
}
eventType = events[ type ];
@@ -1731,7 +2303,7 @@
}
if ( !handler ) {
- for ( var j = 0; j < eventType.length; j++ ) {
+ for ( j = 0; j < eventType.length; j++ ) {
handleObj = eventType[ j ];
if ( all || namespace.test( handleObj.namespace ) ) {
@@ -1745,7 +2317,7 @@
special = jQuery.event.special[ type ] || {};
- for ( var j = pos || 0; j < eventType.length; j++ ) {
+ for ( j = pos || 0; j < eventType.length; j++ ) {
handleObj = eventType[ j ];
if ( handler.guid === handleObj.guid ) {
@@ -1769,7 +2341,7 @@
// remove generic event handler if no more handlers exist
if ( eventType.length === 0 || pos != null && eventType.length === 1 ) {
if ( !special.teardown || special.teardown.call( elem, namespaces ) === false ) {
- removeEvent( elem, type, elemData.handle );
+ jQuery.removeEvent( elem, type, elemData.handle );
}
ret = null;
@@ -1787,8 +2359,11 @@
delete elemData.events;
delete elemData.handle;
- if ( jQuery.isEmptyObject( elemData ) ) {
- jQuery.removeData( elem );
+ if ( typeof elemData === "function" ) {
+ jQuery.removeData( elem, eventKey, true );
+
+ } else if ( jQuery.isEmptyObject( elemData ) ) {
+ jQuery.removeData( elem, undefined, true );
}
}
},
@@ -1802,7 +2377,7 @@
if ( !bubbling ) {
event = typeof event === "object" ?
// jQuery.Event object
- event[expando] ? event :
+ event[ jQuery.expando ] ? event :
// Object literal
jQuery.extend( jQuery.Event(type), event ) :
// Just the event type (string)
@@ -1820,9 +2395,16 @@
// Only trigger if we've ever bound an event for it
if ( jQuery.event.global[ type ] ) {
+ // XXX This code smells terrible. event.js should not be directly
+ // inspecting the data cache
jQuery.each( jQuery.cache, function() {
- if ( this.events && this.events[type] ) {
- jQuery.event.trigger( event, data, this.handle.elem );
+ // internalKey variable is just used to make it easier to find
+ // and potentially change this stuff later; currently it just
+ // points to jQuery.expando
+ var internalKey = jQuery.expando,
+ internalCache = this[ internalKey ];
+ if ( internalCache && internalCache.events && internalCache.events[type] ) {
+ jQuery.event.trigger( event, data, internalCache.handle.elem );
}
});
}
@@ -1847,7 +2429,10 @@
event.currentTarget = elem;
// Trigger the event, it is assumed that "handle" is a function
- var handle = jQuery.data( elem, "handle" );
+ var handle = elem.nodeType ?
+ jQuery._data( elem, "handle" ) :
+ (jQuery._data( elem, eventKey ) || {}).handle;
+
if ( handle ) {
handle.apply( elem, data );
}
@@ -1859,41 +2444,44 @@
if ( !(elem && elem.nodeName && jQuery.noData[elem.nodeName.toLowerCase()]) ) {
if ( elem[ "on" + type ] && elem[ "on" + type ].apply( elem, data ) === false ) {
event.result = false;
+ event.preventDefault();
}
}
// prevent IE from throwing an error for some elements with some event types, see #3533
- } catch (e) {}
+ } catch (inlineError) {}
if ( !event.isPropagationStopped() && parent ) {
jQuery.event.trigger( event, data, parent, true );
} else if ( !event.isDefaultPrevented() ) {
- var target = event.target, old,
- isClick = jQuery.nodeName(target, "a") && type === "click",
- special = jQuery.event.special[ type ] || {};
-
- if ( (!special._default || special._default.call( elem, event ) === false) &&
+ var old,
+ target = event.target,
+ targetType = type.replace( rnamespaces, "" ),
+ isClick = jQuery.nodeName( target, "a" ) && targetType === "click",
+ special = jQuery.event.special[ targetType ] || {};
+
+ if ( (!special._default || special._default.call( elem, event ) === false) &&
!isClick && !(target && target.nodeName && jQuery.noData[target.nodeName.toLowerCase()]) ) {
try {
- if ( target[ type ] ) {
+ if ( target[ targetType ] ) {
// Make sure that we don't accidentally re-trigger the onFOO events
- old = target[ "on" + type ];
+ old = target[ "on" + targetType ];
if ( old ) {
- target[ "on" + type ] = null;
+ target[ "on" + targetType ] = null;
}
jQuery.event.triggered = true;
- target[ type ]();
+ target[ targetType ]();
}
// prevent IE from throwing an error for some elements with some event types, see #3533
- } catch (e) {}
+ } catch (triggerError) {}
if ( old ) {
- target[ "on" + type ] = old;
+ target[ "on" + targetType ] = old;
}
jQuery.event.triggered = false;
@@ -1902,9 +2490,11 @@
},
handle: function( event ) {
- var all, handlers, namespaces, namespace, events;
-
- event = arguments[0] = jQuery.event.fix( event || window.event );
+ var all, handlers, namespaces, namespace_re, events,
+ namespace_sort = [],
+ args = jQuery.makeArray( arguments );
+
+ event = args[0] = jQuery.event.fix( event || window.event );
event.currentTarget = this;
// Namespaced event handlers
@@ -1913,10 +2503,19 @@
if ( !all ) {
namespaces = event.type.split(".");
event.type = namespaces.shift();
- namespace = new RegExp("(^|\\.)" + namespaces.slice(0).sort().join("\\.(?:.*\\.)?") + "(\\.|$)");
- }
-
- var events = jQuery.data(this, "events"), handlers = events[ event.type ];
+ namespace_sort = namespaces.slice(0).sort();
+ namespace_re = new RegExp("(^|\\.)" + namespace_sort.join("\\.(?:.*\\.)?") + "(\\.|$)");
+ }
+
+ event.namespace = event.namespace || namespace_sort.join(".");
+
+ events = jQuery._data(this, eventKey);
+
+ if ( typeof events === "function" ) {
+ events = events.events;
+ }
+
+ handlers = (events || {})[ event.type ];
if ( events && handlers ) {
// Clone the handlers to prevent manipulation
@@ -1926,14 +2525,14 @@
var handleObj = handlers[ j ];
// Filter the functions by class
- if ( all || namespace.test( handleObj.namespace ) ) {
+ if ( all || namespace_re.test( handleObj.namespace ) ) {
// Pass in a reference to the handler function itself
// So that we can later remove it
event.handler = handleObj.handler;
event.data = handleObj.data;
event.handleObj = handleObj;
-
- var ret = handleObj.handler.apply( this, arguments );
+
+ var ret = handleObj.handler.apply( this, args );
if ( ret !== undefined ) {
event.result = ret;
@@ -1953,10 +2552,10 @@
return event.result;
},
- props: "altKey attrChange attrName bubbles button cancelable charCode clientX clientY ctrlKey currentTarget data detail eventPhase fromElement handler keyCode layerX layerY metaKey newValue offsetX offsetY originalTarget pageX pageY prevValue relatedNode relatedTarget screenX screenY shiftKey srcElement target toElement view wheelDelta which".split(" "),
+ props: "altKey attrChange attrName bubbles button cancelable charCode clientX clientY ctrlKey currentTarget data detail eventPhase fromElement handler keyCode layerX layerY metaKey newValue offsetX offsetY pageX pageY prevValue relatedNode relatedTarget screenX screenY shiftKey srcElement target toElement view wheelDelta which".split(" "),
fix: function( event ) {
- if ( event[ expando ] ) {
+ if ( event[ jQuery.expando ] ) {
return event;
}
@@ -1972,7 +2571,8 @@
// Fix target property, if necessary
if ( !event.target ) {
- event.target = event.srcElement || document; // Fixes #1925 where srcElement might not be defined either
+ // Fixes #1925 where srcElement might not be defined either
+ event.target = event.srcElement || document;
}
// check if target is a textnode (safari)
@@ -1987,14 +2587,16 @@
// Calculate pageX/Y if missing and clientX/Y available
if ( event.pageX == null && event.clientX != null ) {
- var doc = document.documentElement, body = document.body;
+ var doc = document.documentElement,
+ body = document.body;
+
event.pageX = event.clientX + (doc && doc.scrollLeft || body && body.scrollLeft || 0) - (doc && doc.clientLeft || body && body.clientLeft || 0);
event.pageY = event.clientY + (doc && doc.scrollTop || body && body.scrollTop || 0) - (doc && doc.clientTop || body && body.clientTop || 0);
}
// Add which for key events
- if ( !event.which && ((event.charCode || event.charCode === 0) ? event.charCode : event.keyCode) ) {
- event.which = event.charCode || event.keyCode;
+ if ( event.which == null && (event.charCode != null || event.keyCode != null) ) {
+ event.which = event.charCode != null ? event.charCode : event.keyCode;
}
// Add metaKey to non-Mac browsers (use ctrl for PC's and Meta for Macs)
@@ -2026,36 +2628,24 @@
live: {
add: function( handleObj ) {
- jQuery.event.add( this, handleObj.origType, jQuery.extend({}, handleObj, {handler: liveHandler}) );
+ jQuery.event.add( this,
+ liveConvert( handleObj.origType, handleObj.selector ),
+ jQuery.extend({}, handleObj, {handler: liveHandler, guid: handleObj.handler.guid}) );
},
remove: function( handleObj ) {
- var remove = true,
- type = handleObj.origType.replace(rnamespaces, "");
-
- jQuery.each( jQuery.data(this, "events").live || [], function() {
- if ( type === this.origType.replace(rnamespaces, "") ) {
- remove = false;
- return false;
- }
- });
-
- if ( remove ) {
- jQuery.event.remove( this, handleObj.origType, liveHandler );
- }
- }
-
+ jQuery.event.remove( this, liveConvert( handleObj.origType, handleObj.selector ), handleObj );
+ }
},
beforeunload: {
setup: function( data, namespaces, eventHandle ) {
// We only want to do this special case on windows
- if ( this.setInterval ) {
+ if ( jQuery.isWindow( this ) ) {
this.onbeforeunload = eventHandle;
}
-
- return false;
},
+
teardown: function( namespaces, eventHandle ) {
if ( this.onbeforeunload === eventHandle ) {
this.onbeforeunload = null;
@@ -2065,12 +2655,16 @@
}
};
-var removeEvent = document.removeEventListener ?
+jQuery.removeEvent = document.removeEventListener ?
function( elem, type, handle ) {
- elem.removeEventListener( type, handle, false );
- } :
+ if ( elem.removeEventListener ) {
+ elem.removeEventListener( type, handle, false );
+ }
+ } :
function( elem, type, handle ) {
- elem.detachEvent( "on" + type, handle );
+ if ( elem.detachEvent ) {
+ elem.detachEvent( "on" + type, handle );
+ }
};
jQuery.Event = function( src ) {
@@ -2083,6 +2677,12 @@
if ( src && src.type ) {
this.originalEvent = src;
this.type = src.type;
+
+ // Events bubbling up the document may have been marked as prevented
+ // by a handler lower down the tree; reflect the correct value.
+ this.isDefaultPrevented = (src.defaultPrevented || src.returnValue === false ||
+ src.getPreventDefault && src.getPreventDefault()) ? returnTrue : returnFalse;
+
// Event type
} else {
this.type = src;
@@ -2090,10 +2690,10 @@
// timeStamp is buggy for some events on Firefox(#3843)
// So we won't rely on the native value
- this.timeStamp = now();
+ this.timeStamp = jQuery.now();
// Mark it as fixed
- this[ expando ] = true;
+ this[ jQuery.expando ] = true;
};
function returnFalse() {
@@ -2113,13 +2713,15 @@
if ( !e ) {
return;
}
-
+
// if preventDefault exists run it on the original event
if ( e.preventDefault ) {
e.preventDefault();
- }
+
// otherwise set the returnValue property of the original event to false (IE)
- e.returnValue = false;
+ } else {
+ e.returnValue = false;
+ }
},
stopPropagation: function() {
this.isPropagationStopped = returnTrue;
@@ -2197,19 +2799,23 @@
jQuery.event.special.submit = {
setup: function( data, namespaces ) {
- if ( this.nodeName.toLowerCase() !== "form" ) {
+ if ( this.nodeName && this.nodeName.toLowerCase() !== "form" ) {
jQuery.event.add(this, "click.specialSubmit", function( e ) {
- var elem = e.target, type = elem.type;
+ var elem = e.target,
+ type = elem.type;
if ( (type === "submit" || type === "image") && jQuery( elem ).closest("form").length ) {
+ e.liveFired = undefined;
return trigger( "submit", this, arguments );
}
});
-
+
jQuery.event.add(this, "keypress.specialSubmit", function( e ) {
- var elem = e.target, type = elem.type;
+ var elem = e.target,
+ type = elem.type;
if ( (type === "text" || type === "password") && jQuery( elem ).closest("form").length && e.keyCode === 13 ) {
+ e.liveFired = undefined;
return trigger( "submit", this, arguments );
}
});
@@ -2229,9 +2835,7 @@
// change delegation, happens here so we have bind.
if ( !jQuery.support.changeBubbles ) {
- var formElems = /textarea|input|select/i,
-
- changeFilters,
+ var changeFilters,
getVal = function( elem ) {
var type = elem.type, val = elem.value;
@@ -2256,31 +2860,34 @@
testChange = function testChange( e ) {
var elem = e.target, data, val;
- if ( !formElems.test( elem.nodeName ) || elem.readOnly ) {
+ if ( !rformElems.test( elem.nodeName ) || elem.readOnly ) {
return;
}
- data = jQuery.data( elem, "_change_data" );
+ data = jQuery._data( elem, "_change_data" );
val = getVal(elem);
// the current data will be also retrieved by beforeactivate
if ( e.type !== "focusout" || elem.type !== "radio" ) {
- jQuery.data( elem, "_change_data", val );
- }
-
+ jQuery._data( elem, "_change_data", val );
+ }
+
if ( data === undefined || val === data ) {
return;
}
if ( data != null || val ) {
e.type = "change";
+ e.liveFired = undefined;
return jQuery.event.trigger( e, arguments[1], elem );
}
};
jQuery.event.special.change = {
filters: {
- focusout: testChange,
+ focusout: testChange,
+
+ beforedeactivate: testChange,
click: function( e ) {
var elem = e.target, type = elem.type;
@@ -2304,10 +2911,10 @@
// Beforeactivate happens also before the previous element is blurred
// with this event you can't trigger a change event, but you can store
- // information/focus[in] is not needed anymore
+ // information
beforeactivate: function( e ) {
var elem = e.target;
- jQuery.data( elem, "_change_data", getVal(elem) );
+ jQuery._data( elem, "_change_data", getVal(elem) );
}
},
@@ -2320,17 +2927,20 @@
jQuery.event.add( this, type + ".specialChange", changeFilters[type] );
}
- return formElems.test( this.nodeName );
+ return rformElems.test( this.nodeName );
},
teardown: function( namespaces ) {
jQuery.event.remove( this, ".specialChange" );
- return formElems.test( this.nodeName );
+ return rformElems.test( this.nodeName );
}
};
changeFilters = jQuery.event.special.change.filters;
+
+ // Handle when the input is .focus()'d
+ changeFilters.focus = changeFilters.beforeactivate;
}
function trigger( type, elem, args ) {
@@ -2350,7 +2960,7 @@
}
};
- function handler( e ) {
+ function handler( e ) {
e = jQuery.event.fix( e );
e.type = fix;
return jQuery.event.handle.call( this, e );
@@ -2367,8 +2977,8 @@
}
return this;
}
-
- if ( jQuery.isFunction( data ) ) {
+
+ if ( jQuery.isFunction( data ) || data === false ) {
fn = data;
data = undefined;
}
@@ -2407,20 +3017,20 @@
return this;
},
-
+
delegate: function( selector, types, data, fn ) {
return this.live( types, data, fn, selector );
},
-
+
undelegate: function( selector, types, fn ) {
if ( arguments.length === 0 ) {
return this.unbind( "live" );
-
+
} else {
return this.die( types, null, fn, selector );
}
},
-
+
trigger: function( type, data ) {
return this.each(function() {
jQuery.event.trigger( type, data, this );
@@ -2439,7 +3049,8 @@
toggle: function( fn ) {
// Save reference to arguments for access in closure
- var args = arguments, i = 1;
+ var args = arguments,
+ i = 1;
// link all the functions, so any of them can unbind this click handler
while ( i < args.length ) {
@@ -2448,8 +3059,8 @@
return this.click( jQuery.proxy( fn, function( event ) {
// Figure out which function to execute
- var lastToggle = ( jQuery.data( this, "lastToggle" + fn.guid ) || 0 ) % i;
- jQuery.data( this, "lastToggle" + fn.guid, lastToggle + 1 );
+ var lastToggle = ( jQuery._data( this, "lastToggle" + fn.guid ) || 0 ) % i;
+ jQuery._data( this, "lastToggle" + fn.guid, lastToggle + 1 );
// Make sure that clicks stop
event.preventDefault();
@@ -2477,6 +3088,14 @@
selector = origSelector || this.selector,
context = origSelector ? this : jQuery( this.context );
+ if ( typeof types === "object" && !types.preventDefault ) {
+ for ( var key in types ) {
+ context[ name ]( key, data, types[key], selector );
+ }
+
+ return this;
+ }
+
if ( jQuery.isFunction( data ) ) {
fn = data;
data = undefined;
@@ -2510,31 +3129,40 @@
if ( name === "live" ) {
// bind live handler
- context.each(function(){
- jQuery.event.add( this, liveConvert( type, selector ),
+ for ( var j = 0, l = context.length; j < l; j++ ) {
+ jQuery.event.add( context[j], "live." + liveConvert( type, selector ),
{ data: data, selector: selector, handler: fn, origType: type, origHandler: fn, preType: preType } );
- });
+ }
} else {
// unbind live handler
- context.unbind( liveConvert( type, selector ), fn );
- }
- }
-
+ context.unbind( "live." + liveConvert( type, selector ), fn );
+ }
+ }
+
return this;
+ };
+});
+
+function liveHandler( event ) {
+ var stop, maxLevel, related, match, handleObj, elem, j, i, l, data, close, namespace, ret,
+ elems = [],
+ selectors = [],
+ events = jQuery._data( this, eventKey );
+
+ if ( typeof events === "function" ) {
+ events = events.events;
}
-});
-
-function liveHandler( event ) {
- var stop, elems = [], selectors = [], args = arguments,
- related, match, handleObj, elem, j, i, l, data,
- events = jQuery.data( this, "events" );
-
- // Make sure we avoid non-left-click bubbling in Firefox (#3861)
- if ( event.liveFired === this || !events || !events.live || event.button && event.type === "click" ) {
+
+ // Make sure we avoid non-left-click bubbling in Firefox (#3861) and disabled elements in IE (#6911)
+ if ( event.liveFired === this || !events || !events.live || event.target.disabled || event.button && event.type === "click" ) {
return;
}
+ if ( event.namespace ) {
+ namespace = new RegExp("(^|\\.)" + event.namespace.split(".").join("\\.(?:.*\\.)?") + "(\\.|$)");
+ }
+
event.liveFired = this;
var live = events.live.slice(0);
@@ -2553,20 +3181,23 @@
match = jQuery( event.target ).closest( selectors, event.currentTarget );
for ( i = 0, l = match.length; i < l; i++ ) {
+ close = match[i];
+
for ( j = 0; j < live.length; j++ ) {
handleObj = live[j];
- if ( match[i].selector === handleObj.selector ) {
- elem = match[i].elem;
+ if ( close.selector === handleObj.selector && (!namespace || namespace.test( handleObj.namespace )) ) {
+ elem = close.elem;
related = null;
// Those two events require additional checking
if ( handleObj.preType === "mouseenter" || handleObj.preType === "mouseleave" ) {
+ event.type = handleObj.preType;
related = jQuery( event.relatedTarget ).closest( handleObj.selector )[0];
}
if ( !related || related !== elem ) {
- elems.push({ elem: elem, handleObj: handleObj });
+ elems.push({ elem: elem, handleObj: handleObj, level: close.level });
}
}
}
@@ -2574,13 +3205,26 @@
for ( i = 0, l = elems.length; i < l; i++ ) {
match = elems[i];
+
+ if ( maxLevel && match.level > maxLevel ) {
+ break;
+ }
+
event.currentTarget = match.elem;
event.data = match.handleObj.data;
event.handleObj = match.handleObj;
- if ( match.handleObj.origHandler.apply( match.elem, args ) === false ) {
- stop = false;
- break;
+ ret = match.handleObj.origHandler.apply( match.elem, arguments );
+
+ if ( ret === false || event.isPropagationStopped() ) {
+ maxLevel = match.level;
+
+ if ( ret === false ) {
+ stop = false;
+ }
+ if ( event.isImmediatePropagationStopped() ) {
+ break;
+ }
}
}
@@ -2588,7 +3232,7 @@
}
function liveConvert( type, selector ) {
- return "live." + (type && type !== "*" ? type + "." : "") + selector.replace(/\./g, "`").replace(/ /g, "&");
+ return (type && type !== "*" ? type + "." : "") + selector.replace(rperiod, "`").replace(rspace, "&");
}
jQuery.each( ("blur focus focusin focusout load resize scroll unload click dblclick " +
@@ -2596,8 +3240,15 @@
"change select submit keydown keypress keyup error").split(" "), function( i, name ) {
// Handle event binding
- jQuery.fn[ name ] = function( fn ) {
- return fn ? this.bind( name, fn ) : this.trigger( name );
+ jQuery.fn[ name ] = function( data, fn ) {
+ if ( fn == null ) {
+ fn = data;
+ data = null;
+ }
+
+ return arguments.length > 0 ?
+ this.bind( name, data, fn ) :
+ this.trigger( name );
};
if ( jQuery.attrFn ) {
@@ -2605,31 +3256,16 @@
}
});
-// Prevent memory leaks in IE
-// Window isn't included so as not to unbind existing unload events
-// More info:
-// - http://isaacschlueter.com/2006/10/msie-memory-leaks/
-if ( window.attachEvent && !window.addEventListener ) {
- window.attachEvent("onunload", function() {
- for ( var id in jQuery.cache ) {
- if ( jQuery.cache[ id ].handle ) {
- // Try/Catch is to handle iframes being unloaded, see #4280
- try {
- jQuery.event.remove( jQuery.cache[ id ].handle.elem );
- } catch(e) {}
- }
- }
- });
-}
+
/*!
- * Sizzle CSS Selector Engine - v1.0
- * Copyright 2009, The Dojo Foundation
+ * Sizzle CSS Selector Engine
+ * Copyright 2011, The Dojo Foundation
* Released under the MIT, BSD, and GPL Licenses.
* More information: http://sizzlejs.com/
*/
(function(){
-var chunker = /((?:\((?:\([^()]+\)|[^()]+)+\)|\[(?:\[[^[\]]*\]|['"][^'"]*['"]|[^[\]'"]+)+\]|\\.|[^ >+~,(\[\\]+)+|[>+~])(\s*,\s*)?((?:.|\r|\n)*)/g,
+var chunker = /((?:\((?:\([^()]+\)|[^()]+)+\)|\[(?:\[[^\[\]]*\]|['"][^'"]*['"]|[^\[\]'"]+)+\]|\\.|[^ >+~,(\[\\]+)+|[>+~])(\s*,\s*)?((?:.|\r|\n)*)/g,
done = 0,
toString = Object.prototype.toString,
hasDuplicate = false,
@@ -2639,14 +3275,16 @@
// optimization where it does not always call our comparision
// function. If that is the case, discard the hasDuplicate value.
// Thus far that includes Google Chrome.
-[0, 0].sort(function(){
+[0, 0].sort(function() {
baseHasDuplicate = false;
return 0;
});
-var Sizzle = function(selector, context, results, seed) {
+var Sizzle = function( selector, context, results, seed ) {
results = results || [];
- var origContext = context = context || document;
+ context = context || document;
+
+ var origContext = context;
if ( context.nodeType !== 1 && context.nodeType !== 9 ) {
return [];
@@ -2656,24 +3294,34 @@
return results;
}
- var parts = [], m, set, checkSet, extra, prune = true, contextXML = isXML(context),
+ var m, set, checkSet, extra, ret, cur, pop, i,
+ prune = true,
+ contextXML = Sizzle.isXML( context ),
+ parts = [],
soFar = selector;
// Reset the position of the chunker regexp (start from head)
- while ( (chunker.exec(""), m = chunker.exec(soFar)) !== null ) {
- soFar = m[3];
+ do {
+ chunker.exec( "" );
+ m = chunker.exec( soFar );
+
+ if ( m ) {
+ soFar = m[3];
- parts.push( m[1] );
+ parts.push( m[1] );
- if ( m[2] ) {
- extra = m[3];
- break;
- }
- }
+ if ( m[2] ) {
+ extra = m[3];
+ break;
+ }
+ }
+ } while ( m );
if ( parts.length > 1 && origPOS.exec( selector ) ) {
+
if ( parts.length === 2 && Expr.relative[ parts[0] ] ) {
set = posProcess( parts[0] + parts[1], context );
+
} else {
set = Expr.relative[ parts[0] ] ?
[ context ] :
@@ -2689,29 +3337,38 @@
set = posProcess( selector, set );
}
}
+
} else {
// Take a shortcut and set the context if the root selector is an ID
// (but not if it'll be faster if the inner selector is an ID)
if ( !seed && parts.length > 1 && context.nodeType === 9 && !contextXML &&
Expr.match.ID.test(parts[0]) && !Expr.match.ID.test(parts[parts.length - 1]) ) {
- var ret = Sizzle.find( parts.shift(), context, contextXML );
- context = ret.expr ? Sizzle.filter( ret.expr, ret.set )[0] : ret.set[0];
+
+ ret = Sizzle.find( parts.shift(), context, contextXML );
+ context = ret.expr ?
+ Sizzle.filter( ret.expr, ret.set )[0] :
+ ret.set[0];
}
if ( context ) {
- var ret = seed ?
+ ret = seed ?
{ expr: parts.pop(), set: makeArray(seed) } :
Sizzle.find( parts.pop(), parts.length === 1 && (parts[0] === "~" || parts[0] === "+") && context.parentNode ? context.parentNode : context, contextXML );
- set = ret.expr ? Sizzle.filter( ret.expr, ret.set ) : ret.set;
+
+ set = ret.expr ?
+ Sizzle.filter( ret.expr, ret.set ) :
+ ret.set;
if ( parts.length > 0 ) {
- checkSet = makeArray(set);
+ checkSet = makeArray( set );
+
} else {
prune = false;
}
while ( parts.length ) {
- var cur = parts.pop(), pop = cur;
+ cur = parts.pop();
+ pop = cur;
if ( !Expr.relative[ cur ] ) {
cur = "";
@@ -2725,6 +3382,7 @@
Expr.relative[ cur ]( checkSet, pop, contextXML );
}
+
} else {
checkSet = parts = [];
}
@@ -2741,19 +3399,22 @@
if ( toString.call(checkSet) === "[object Array]" ) {
if ( !prune ) {
results.push.apply( results, checkSet );
+
} else if ( context && context.nodeType === 1 ) {
- for ( var i = 0; checkSet[i] != null; i++ ) {
- if ( checkSet[i] && (checkSet[i] === true || checkSet[i].nodeType === 1 && contains(context, checkSet[i])) ) {
+ for ( i = 0; checkSet[i] != null; i++ ) {
+ if ( checkSet[i] && (checkSet[i] === true || checkSet[i].nodeType === 1 && Sizzle.contains(context, checkSet[i])) ) {
results.push( set[i] );
}
}
+
} else {
- for ( var i = 0; checkSet[i] != null; i++ ) {
+ for ( i = 0; checkSet[i] != null; i++ ) {
if ( checkSet[i] && checkSet[i].nodeType === 1 ) {
results.push( set[i] );
}
}
}
+
} else {
makeArray( checkSet, results );
}
@@ -2766,15 +3427,15 @@
return results;
};
-Sizzle.uniqueSort = function(results){
+Sizzle.uniqueSort = function( results ) {
if ( sortOrder ) {
hasDuplicate = baseHasDuplicate;
- results.sort(sortOrder);
+ results.sort( sortOrder );
if ( hasDuplicate ) {
for ( var i = 1; i < results.length; i++ ) {
- if ( results[i] === results[i-1] ) {
- results.splice(i--, 1);
+ if ( results[i] === results[ i - 1 ] ) {
+ results.splice( i--, 1 );
}
}
}
@@ -2783,27 +3444,33 @@
return results;
};
-Sizzle.matches = function(expr, set){
- return Sizzle(expr, null, null, set);
+Sizzle.matches = function( expr, set ) {
+ return Sizzle( expr, null, null, set );
};
-Sizzle.find = function(expr, context, isXML){
- var set, match;
+Sizzle.matchesSelector = function( node, expr ) {
+ return Sizzle( expr, null, null, [node] ).length > 0;
+};
+
+Sizzle.find = function( expr, context, isXML ) {
+ var set;
if ( !expr ) {
return [];
}
for ( var i = 0, l = Expr.order.length; i < l; i++ ) {
- var type = Expr.order[i], match;
+ var match,
+ type = Expr.order[i];
if ( (match = Expr.leftMatch[ type ].exec( expr )) ) {
var left = match[1];
- match.splice(1,1);
+ match.splice( 1, 1 );
if ( left.substr( left.length - 1 ) !== "\\" ) {
match[1] = (match[1] || "").replace(/\\/g, "");
set = Expr.find[ type ]( match, context, isXML );
+
if ( set != null ) {
expr = expr.replace( Expr.match[ type ], "" );
break;
@@ -2813,20 +3480,28 @@
}
if ( !set ) {
- set = context.getElementsByTagName("*");
+ set = typeof context.getElementsByTagName !== "undefined" ?
+ context.getElementsByTagName( "*" ) :
+ [];
}
- return {set: set, expr: expr};
+ return { set: set, expr: expr };
};
-Sizzle.filter = function(expr, set, inplace, not){
- var old = expr, result = [], curLoop = set, match, anyFound,
- isXMLFilter = set && set[0] && isXML(set[0]);
+Sizzle.filter = function( expr, set, inplace, not ) {
+ var match, anyFound,
+ old = expr,
+ result = [],
+ curLoop = set,
+ isXMLFilter = set && set[0] && Sizzle.isXML( set[0] );
while ( expr && set.length ) {
for ( var type in Expr.filter ) {
if ( (match = Expr.leftMatch[ type ].exec( expr )) != null && match[2] ) {
- var filter = Expr.filter[ type ], found, item, left = match[1];
+ var found, item,
+ filter = Expr.filter[ type ],
+ left = match[1];
+
anyFound = false;
match.splice(1,1);
@@ -2844,6 +3519,7 @@
if ( !match ) {
anyFound = found = true;
+
} else if ( match === true ) {
continue;
}
@@ -2858,9 +3534,11 @@
if ( inplace && found != null ) {
if ( pass ) {
anyFound = true;
+
} else {
curLoop[i] = false;
}
+
} else if ( pass ) {
result.push( item );
anyFound = true;
@@ -2889,6 +3567,7 @@
if ( expr === old ) {
if ( anyFound == null ) {
Sizzle.error( expr );
+
} else {
break;
}
@@ -2906,30 +3585,35 @@
var Expr = Sizzle.selectors = {
order: [ "ID", "NAME", "TAG" ],
+
match: {
- ID: /#((?:[\w\u00c0-\uFFFF-]|\\.)+)/,
- CLASS: /\.((?:[\w\u00c0-\uFFFF-]|\\.)+)/,
- NAME: /\[name=['"]*((?:[\w\u00c0-\uFFFF-]|\\.)+)['"]*\]/,
- ATTR: /\[\s*((?:[\w\u00c0-\uFFFF-]|\\.)+)\s*(?:(\S?=)\s*(['"]*)(.*?)\3|)\s*\]/,
- TAG: /^((?:[\w\u00c0-\uFFFF\*-]|\\.)+)/,
- CHILD: /:(only|nth|last|first)-child(?:\((even|odd|[\dn+-]*)\))?/,
- POS: /:(nth|eq|gt|lt|first|last|even|odd)(?:\((\d*)\))?(?=[^-]|$)/,
- PSEUDO: /:((?:[\w\u00c0-\uFFFF-]|\\.)+)(?:\((['"]?)((?:\([^\)]+\)|[^\(\)]*)+)\2\))?/
- },
+ ID: /#((?:[\w\u00c0-\uFFFF\-]|\\.)+)/,
+ CLASS: /\.((?:[\w\u00c0-\uFFFF\-]|\\.)+)/,
+ NAME: /\[name=['"]*((?:[\w\u00c0-\uFFFF\-]|\\.)+)['"]*\]/,
+ ATTR: /\[\s*((?:[\w\u00c0-\uFFFF\-]|\\.)+)\s*(?:(\S?=)\s*(?:(['"])(.*?)\3|(#?(?:[\w\u00c0-\uFFFF\-]|\\.)*)|)|)\s*\]/,
+ TAG: /^((?:[\w\u00c0-\uFFFF\*\-]|\\.)+)/,
+ CHILD: /:(only|nth|last|first)-child(?:\(\s*(even|odd|(?:[+\-]?\d+|(?:[+\-]?\d*)?n\s*(?:[+\-]\s*\d+)?))\s*\))?/,
+ POS: /:(nth|eq|gt|lt|first|last|even|odd)(?:\((\d*)\))?(?=[^\-]|$)/,
+ PSEUDO: /:((?:[\w\u00c0-\uFFFF\-]|\\.)+)(?:\((['"]?)((?:\([^\)]+\)|[^\(\)]*)+)\2\))?/
+ },
+
leftMatch: {},
+
attrMap: {
"class": "className",
"for": "htmlFor"
},
+
attrHandle: {
- href: function(elem){
- return elem.getAttribute("href");
- }
- },
+ href: function( elem ) {
+ return elem.getAttribute( "href" );
+ }
+ },
+
relative: {
"+": function(checkSet, part){
var isPartStr = typeof part === "string",
- isTag = isPartStr && !/\W/.test(part),
+ isTag = isPartStr && !/\W/.test( part ),
isPartStrNotTag = isPartStr && !isTag;
if ( isTag ) {
@@ -2950,22 +3634,29 @@
Sizzle.filter( part, checkSet, true );
}
},
- ">": function(checkSet, part){
- var isPartStr = typeof part === "string";
-
- if ( isPartStr && !/\W/.test(part) ) {
+
+ ">": function( checkSet, part ) {
+ var elem,
+ isPartStr = typeof part === "string",
+ i = 0,
+ l = checkSet.length;
+
+ if ( isPartStr && !/\W/.test( part ) ) {
part = part.toLowerCase();
- for ( var i = 0, l = checkSet.length; i < l; i++ ) {
- var elem = checkSet[i];
+ for ( ; i < l; i++ ) {
+ elem = checkSet[i];
+
if ( elem ) {
var parent = elem.parentNode;
checkSet[i] = parent.nodeName.toLowerCase() === part ? parent : false;
}
}
+
} else {
- for ( var i = 0, l = checkSet.length; i < l; i++ ) {
- var elem = checkSet[i];
+ for ( ; i < l; i++ ) {
+ elem = checkSet[i];
+
if ( elem ) {
checkSet[i] = isPartStr ?
elem.parentNode :
@@ -2978,37 +3669,50 @@
}
}
},
+
"": function(checkSet, part, isXML){
- var doneName = done++, checkFn = dirCheck;
+ var nodeCheck,
+ doneName = done++,
+ checkFn = dirCheck;
if ( typeof part === "string" && !/\W/.test(part) ) {
- var nodeCheck = part = part.toLowerCase();
+ part = part.toLowerCase();
+ nodeCheck = part;
checkFn = dirNodeCheck;
}
- checkFn("parentNode", part, doneName, checkSet, nodeCheck, isXML);
+ checkFn( "parentNode", part, doneName, checkSet, nodeCheck, isXML );
},
- "~": function(checkSet, part, isXML){
- var doneName = done++, checkFn = dirCheck;
-
- if ( typeof part === "string" && !/\W/.test(part) ) {
- var nodeCheck = part = part.toLowerCase();
+
+ "~": function( checkSet, part, isXML ) {
+ var nodeCheck,
+ doneName = done++,
+ checkFn = dirCheck;
+
+ if ( typeof part === "string" && !/\W/.test( part ) ) {
+ part = part.toLowerCase();
+ nodeCheck = part;
checkFn = dirNodeCheck;
}
- checkFn("previousSibling", part, doneName, checkSet, nodeCheck, isXML);
- }
- },
+ checkFn( "previousSibling", part, doneName, checkSet, nodeCheck, isXML );
+ }
+ },
+
find: {
- ID: function(match, context, isXML){
+ ID: function( match, context, isXML ) {
if ( typeof context.getElementById !== "undefined" && !isXML ) {
var m = context.getElementById(match[1]);
- return m ? [m] : [];
+ // Check parentNode to catch when Blackberry 4.6 returns
+ // nodes that are no longer in the document #6963
+ return m && m.parentNode ? [m] : [];
}
},
- NAME: function(match, context){
+
+ NAME: function( match, context ) {
if ( typeof context.getElementsByName !== "undefined" ) {
- var ret = [], results = context.getElementsByName(match[1]);
+ var ret = [],
+ results = context.getElementsByName( match[1] );
for ( var i = 0, l = results.length; i < l; i++ ) {
if ( results[i].getAttribute("name") === match[1] ) {
@@ -3019,12 +3723,15 @@
return ret.length === 0 ? null : ret;
}
},
- TAG: function(match, context){
- return context.getElementsByTagName(match[1]);
+
+ TAG: function( match, context ) {
+ if ( typeof context.getElementsByTagName !== "undefined" ) {
+ return context.getElementsByTagName( match[1] );
+ }
}
},
preFilter: {
- CLASS: function(match, curLoop, inplace, result, not, isXML){
+ CLASS: function( match, curLoop, inplace, result, not, isXML ) {
match = " " + match[1].replace(/\\/g, "") + " ";
if ( isXML ) {
@@ -3033,10 +3740,11 @@
for ( var i = 0, elem; (elem = curLoop[i]) != null; i++ ) {
if ( elem ) {
- if ( not ^ (elem.className && (" " + elem.className + " ").replace(/[\t\n]/g, " ").indexOf(match) >= 0) ) {
+ if ( not ^ (elem.className && (" " + elem.className + " ").replace(/[\t\n\r]/g, " ").indexOf(match) >= 0) ) {
if ( !inplace ) {
result.push( elem );
}
+
} else if ( inplace ) {
curLoop[i] = false;
}
@@ -3045,16 +3753,25 @@
return false;
},
- ID: function(match){
+
+ ID: function( match ) {
return match[1].replace(/\\/g, "");
},
- TAG: function(match, curLoop){
+
+ TAG: function( match, curLoop ) {
return match[1].toLowerCase();
},
- CHILD: function(match){
+
+ CHILD: function( match ) {
if ( match[1] === "nth" ) {
+ if ( !match[2] ) {
+ Sizzle.error( match[0] );
+ }
+
+ match[2] = match[2].replace(/^\+|\s*/g, '');
+
// parse equations like 'even', 'odd', '5', '2n', '3n+2', '4n-1', '-n+6'
- var test = /(-?)(\d*)n((?:\+|-)?\d*)/.exec(
+ var test = /(-?)(\d*)(?:n([+\-]?\d*))?/.exec(
match[2] === "even" && "2n" || match[2] === "odd" && "2n+1" ||
!/\D/.test( match[2] ) && "0n+" + match[2] || match[2]);
@@ -3062,178 +3779,229 @@
match[2] = (test[1] + (test[2] || 1)) - 0;
match[3] = test[3] - 0;
}
+ else if ( match[2] ) {
+ Sizzle.error( match[0] );
+ }
// TODO: Move to normal caching system
match[0] = done++;
return match;
},
- ATTR: function(match, curLoop, inplace, result, not, isXML){
- var name = match[1].replace(/\\/g, "");
+
+ ATTR: function( match, curLoop, inplace, result, not, isXML ) {
+ var name = match[1] = match[1].replace(/\\/g, "");
if ( !isXML && Expr.attrMap[name] ) {
match[1] = Expr.attrMap[name];
}
+ // Handle if an un-quoted value was used
+ match[4] = ( match[4] || match[5] || "" ).replace(/\\/g, "");
+
if ( match[2] === "~=" ) {
match[4] = " " + match[4] + " ";
}
return match;
},
- PSEUDO: function(match, curLoop, inplace, result, not){
+
+ PSEUDO: function( match, curLoop, inplace, result, not ) {
if ( match[1] === "not" ) {
// If we're dealing with a complex expression, or a simple one
if ( ( chunker.exec(match[3]) || "" ).length > 1 || /^\w/.test(match[3]) ) {
match[3] = Sizzle(match[3], null, null, curLoop);
+
} else {
var ret = Sizzle.filter(match[3], curLoop, inplace, true ^ not);
+
if ( !inplace ) {
result.push.apply( result, ret );
}
+
return false;
}
+
} else if ( Expr.match.POS.test( match[0] ) || Expr.match.CHILD.test( match[0] ) ) {
return true;
}
return match;
},
- POS: function(match){
+
+ POS: function( match ) {
match.unshift( true );
+
return match;
}
},
+
filters: {
- enabled: function(elem){
+ enabled: function( elem ) {
return elem.disabled === false && elem.type !== "hidden";
},
- disabled: function(elem){
+
+ disabled: function( elem ) {
return elem.disabled === true;
},
- checked: function(elem){
+
+ checked: function( elem ) {
return elem.checked === true;
},
- selected: function(elem){
+
+ selected: function( elem ) {
// Accessing this property makes selected-by-default
// options in Safari work properly
elem.parentNode.selectedIndex;
+
return elem.selected === true;
},
- parent: function(elem){
+
+ parent: function( elem ) {
return !!elem.firstChild;
},
- empty: function(elem){
+
+ empty: function( elem ) {
return !elem.firstChild;
},
- has: function(elem, i, match){
+
+ has: function( elem, i, match ) {
return !!Sizzle( match[3], elem ).length;
},
- header: function(elem){
- return /h\d/i.test( elem.nodeName );
+
+ header: function( elem ) {
+ return (/h\d/i).test( elem.nodeName );
},
- text: function(elem){
+
+ text: function( elem ) {
return "text" === elem.type;
},
- radio: function(elem){
+ radio: function( elem ) {
return "radio" === elem.type;
},
- checkbox: function(elem){
+
+ checkbox: function( elem ) {
return "checkbox" === elem.type;
},
- file: function(elem){
+
+ file: function( elem ) {
return "file" === elem.type;
},
- password: function(elem){
+ password: function( elem ) {
return "password" === elem.type;
},
- submit: function(elem){
+
+ submit: function( elem ) {
return "submit" === elem.type;
},
- image: function(elem){
+
+ image: function( elem ) {
return "image" === elem.type;
},
- reset: function(elem){
+
+ reset: function( elem ) {
return "reset" === elem.type;
},
- button: function(elem){
+
+ button: function( elem ) {
return "button" === elem.type || elem.nodeName.toLowerCase() === "button";
},
- input: function(elem){
- return /input|select|textarea|button/i.test(elem.nodeName);
+
+ input: function( elem ) {
+ return (/input|select|textarea|button/i).test( elem.nodeName );
}
},
setFilters: {
- first: function(elem, i){
+ first: function( elem, i ) {
return i === 0;
},
- last: function(elem, i, match, array){
+
+ last: function( elem, i, match, array ) {
return i === array.length - 1;
},
- even: function(elem, i){
+
+ even: function( elem, i ) {
return i % 2 === 0;
},
- odd: function(elem, i){
+
+ odd: function( elem, i ) {
return i % 2 === 1;
},
- lt: function(elem, i, match){
+
+ lt: function( elem, i, match ) {
return i < match[3] - 0;
},
- gt: function(elem, i, match){
+
+ gt: function( elem, i, match ) {
return i > match[3] - 0;
},
- nth: function(elem, i, match){
+
+ nth: function( elem, i, match ) {
return match[3] - 0 === i;
},
- eq: function(elem, i, match){
+
+ eq: function( elem, i, match ) {
return match[3] - 0 === i;
}
},
filter: {
- PSEUDO: function(elem, match, i, array){
- var name = match[1], filter = Expr.filters[ name ];
+ PSEUDO: function( elem, match, i, array ) {
+ var name = match[1],
+ filter = Expr.filters[ name ];
if ( filter ) {
return filter( elem, i, match, array );
+
} else if ( name === "contains" ) {
- return (elem.textContent || elem.innerText || getText([ elem ]) || "").indexOf(match[3]) >= 0;
+ return (elem.textContent || elem.innerText || Sizzle.getText([ elem ]) || "").indexOf(match[3]) >= 0;
+
} else if ( name === "not" ) {
var not = match[3];
- for ( var i = 0, l = not.length; i < l; i++ ) {
- if ( not[i] === elem ) {
+ for ( var j = 0, l = not.length; j < l; j++ ) {
+ if ( not[j] === elem ) {
return false;
}
}
return true;
+
} else {
- Sizzle.error( "Syntax error, unrecognized expression: " + name );
+ Sizzle.error( name );
}
},
- CHILD: function(elem, match){
- var type = match[1], node = elem;
- switch (type) {
- case 'only':
- case 'first':
+
+ CHILD: function( elem, match ) {
+ var type = match[1],
+ node = elem;
+
+ switch ( type ) {
+ case "only":
+ case "first":
while ( (node = node.previousSibling) ) {
if ( node.nodeType === 1 ) {
return false;
}
}
+
if ( type === "first" ) {
return true;
}
+
node = elem;
- case 'last':
+
+ case "last":
while ( (node = node.nextSibling) ) {
if ( node.nodeType === 1 ) {
return false;
}
}
+
return true;
- case 'nth':
- var first = match[2], last = match[3];
+
+ case "nth":
+ var first = match[2],
+ last = match[3];
if ( first === 1 && last === 0 ) {
return true;
@@ -3244,33 +4012,41 @@
if ( parent && (parent.sizcache !== doneName || !elem.nodeIndex) ) {
var count = 0;
+
for ( node = parent.firstChild; node; node = node.nextSibling ) {
if ( node.nodeType === 1 ) {
node.nodeIndex = ++count;
}
}
+
parent.sizcache = doneName;
}
var diff = elem.nodeIndex - last;
+
if ( first === 0 ) {
return diff === 0;
+
} else {
return ( diff % first === 0 && diff / first >= 0 );
}
}
},
- ID: function(elem, match){
+
+ ID: function( elem, match ) {
return elem.nodeType === 1 && elem.getAttribute("id") === match;
},
- TAG: function(elem, match){
+
+ TAG: function( elem, match ) {
return (match === "*" && elem.nodeType === 1) || elem.nodeName.toLowerCase() === match;
},
- CLASS: function(elem, match){
+
+ CLASS: function( elem, match ) {
return (" " + (elem.className || elem.getAttribute("class")) + " ")
.indexOf( match ) > -1;
},
- ATTR: function(elem, match){
+
+ ATTR: function( elem, match ) {
var name = match[1],
result = Expr.attrHandle[ name ] ?
Expr.attrHandle[ name ]( elem ) :
@@ -3301,8 +4077,10 @@
value === check || value.substr(0, check.length + 1) === check + "-" :
false;
},
- POS: function(elem, match, i, array){
- var name = match[2], filter = Expr.setFilters[ name ];
+
+ POS: function( elem, match, i, array ) {
+ var name = match[2],
+ filter = Expr.setFilters[ name ];
if ( filter ) {
return filter( elem, i, match, array );
@@ -3311,16 +4089,17 @@
}
};
-var origPOS = Expr.match.POS;
+var origPOS = Expr.match.POS,
+ fescape = function(all, num){
+ return "\\" + (num - 0 + 1);
+ };
for ( var type in Expr.match ) {
- Expr.match[ type ] = new RegExp( Expr.match[ type ].source + /(?![^\[]*\])(?![^\(]*\))/.source );
- Expr.leftMatch[ type ] = new RegExp( /(^(?:.|\r|\n)*?)/.source + Expr.match[ type ].source.replace(/\\(\d+)/g, function(all, num){
- return "\\" + (num - 0 + 1);
- }));
+ Expr.match[ type ] = new RegExp( Expr.match[ type ].source + (/(?![^\[]*\])(?![^\(]*\))/.source) );
+ Expr.leftMatch[ type ] = new RegExp( /(^(?:.|\r|\n)*?)/.source + Expr.match[ type ].source.replace(/\\(\d+)/g, fescape) );
}
-var makeArray = function(array, results) {
+var makeArray = function( array, results ) {
array = Array.prototype.slice.call( array, 0 );
if ( results ) {
@@ -3339,19 +4118,22 @@
Array.prototype.slice.call( document.documentElement.childNodes, 0 )[0].nodeType;
// Provide a fallback method if it does not work
-} catch(e){
- makeArray = function(array, results) {
- var ret = results || [];
+} catch( e ) {
+ makeArray = function( array, results ) {
+ var i = 0,
+ ret = results || [];
if ( toString.call(array) === "[object Array]" ) {
Array.prototype.push.apply( ret, array );
+
} else {
if ( typeof array.length === "number" ) {
- for ( var i = 0, l = array.length; i < l; i++ ) {
+ for ( var l = array.length; i < l; i++ ) {
ret.push( array[i] );
}
+
} else {
- for ( var i = 0; array[i]; i++ ) {
+ for ( ; array[i]; i++ ) {
ret.push( array[i] );
}
}
@@ -3361,62 +4143,99 @@
};
}
-var sortOrder;
+var sortOrder, siblingCheck;
if ( document.documentElement.compareDocumentPosition ) {
sortOrder = function( a, b ) {
+ if ( a === b ) {
+ hasDuplicate = true;
+ return 0;
+ }
+
if ( !a.compareDocumentPosition || !b.compareDocumentPosition ) {
- if ( a == b ) {
- hasDuplicate = true;
- }
return a.compareDocumentPosition ? -1 : 1;
}
- var ret = a.compareDocumentPosition(b) & 4 ? -1 : a === b ? 0 : 1;
- if ( ret === 0 ) {
+ return a.compareDocumentPosition(b) & 4 ? -1 : 1;
+ };
+
+} else {
+ sortOrder = function( a, b ) {
+ var al, bl,
+ ap = [],
+ bp = [],
+ aup = a.parentNode,
+ bup = b.parentNode,
+ cur = aup;
+
+ // The nodes are identical, we can exit early
+ if ( a === b ) {
hasDuplicate = true;
- }
- return ret;
+ return 0;
+
+ // If the nodes are siblings (or identical) we can do a quick check
+ } else if ( aup === bup ) {
+ return siblingCheck( a, b );
+
+ // If no parents were found then the nodes are disconnected
+ } else if ( !aup ) {
+ return -1;
+
+ } else if ( !bup ) {
+ return 1;
+ }
+
+ // Otherwise they're somewhere else in the tree so we need
+ // to build up a full list of the parentNodes for comparison
+ while ( cur ) {
+ ap.unshift( cur );
+ cur = cur.parentNode;
+ }
+
+ cur = bup;
+
+ while ( cur ) {
+ bp.unshift( cur );
+ cur = cur.parentNode;
+ }
+
+ al = ap.length;
+ bl = bp.length;
+
+ // Start walking down the tree looking for a discrepancy
+ for ( var i = 0; i < al && i < bl; i++ ) {
+ if ( ap[i] !== bp[i] ) {
+ return siblingCheck( ap[i], bp[i] );
+ }
+ }
+
+ // We ended someplace up the tree so do a sibling check
+ return i === al ?
+ siblingCheck( a, bp[i], -1 ) :
+ siblingCheck( ap[i], b, 1 );
};
-} else if ( "sourceIndex" in document.documentElement ) {
- sortOrder = function( a, b ) {
- if ( !a.sourceIndex || !b.sourceIndex ) {
- if ( a == b ) {
- hasDuplicate = true;
- }
- return a.sourceIndex ? -1 : 1;
- }
-
- var ret = a.sourceIndex - b.sourceIndex;
- if ( ret === 0 ) {
- hasDuplicate = true;
- }
- return ret;
- };
-} else if ( document.createRange ) {
- sortOrder = function( a, b ) {
- if ( !a.ownerDocument || !b.ownerDocument ) {
- if ( a == b ) {
- hasDuplicate = true;
- }
- return a.ownerDocument ? -1 : 1;
- }
-
- var aRange = a.ownerDocument.createRange(), bRange = b.ownerDocument.createRange();
- aRange.setStart(a, 0);
- aRange.setEnd(a, 0);
- bRange.setStart(b, 0);
- bRange.setEnd(b, 0);
- var ret = aRange.compareBoundaryPoints(Range.START_TO_END, bRange);
- if ( ret === 0 ) {
- hasDuplicate = true;
- }
- return ret;
+
+ siblingCheck = function( a, b, ret ) {
+ if ( a === b ) {
+ return ret;
+ }
+
+ var cur = a.nextSibling;
+
+ while ( cur ) {
+ if ( cur === b ) {
+ return -1;
+ }
+
+ cur = cur.nextSibling;
+ }
+
+ return 1;
};
}
// Utility function for retreiving the text value of an array of DOM nodes
-function getText( elems ) {
+Sizzle.getText = function( elems ) {
var ret = "", elem;
for ( var i = 0; elems[i]; i++ ) {
@@ -3428,43 +4247,52 @@
// Traverse everything else, except comment nodes
} else if ( elem.nodeType !== 8 ) {
- ret += getText( elem.childNodes );
+ ret += Sizzle.getText( elem.childNodes );
}
}
return ret;
-}
+};
// Check to see if the browser returns elements by name when
// querying by getElementById (and provide a workaround)
(function(){
// We're going to inject a fake input element with a specified name
var form = document.createElement("div"),
- id = "script" + (new Date).getTime();
+ id = "script" + (new Date()).getTime(),
+ root = document.documentElement;
+
form.innerHTML = "<a name='" + id + "'/>";
// Inject it into the root element, check its status, and remove it quickly
- var root = document.documentElement;
root.insertBefore( form, root.firstChild );
// The workaround has to do additional checks after a getElementById
// Which slows things down for other browsers (hence the branching)
if ( document.getElementById( id ) ) {
- Expr.find.ID = function(match, context, isXML){
+ Expr.find.ID = function( match, context, isXML ) {
if ( typeof context.getElementById !== "undefined" && !isXML ) {
var m = context.getElementById(match[1]);
- return m ? m.id === match[1] || typeof m.getAttributeNode !== "undefined" && m.getAttributeNode("id").nodeValue === match[1] ? [m] : undefined : [];
+
+ return m ?
+ m.id === match[1] || typeof m.getAttributeNode !== "undefined" && m.getAttributeNode("id").nodeValue === match[1] ?
+ [m] :
+ undefined :
+ [];
}
};
- Expr.filter.ID = function(elem, match){
+ Expr.filter.ID = function( elem, match ) {
var node = typeof elem.getAttributeNode !== "undefined" && elem.getAttributeNode("id");
+
return elem.nodeType === 1 && node && node.nodeValue === match;
};
}
root.removeChild( form );
- root = form = null; // release memory in IE
+
+ // release memory in IE
+ root = form = null;
})();
(function(){
@@ -3477,8 +4305,8 @@
// Make sure no comments are found
if ( div.getElementsByTagName("*").length > 0 ) {
- Expr.find.TAG = function(match, context){
- var results = context.getElementsByTagName(match[1]);
+ Expr.find.TAG = function( match, context ) {
+ var results = context.getElementsByTagName( match[1] );
// Filter out possible comments
if ( match[1] === "*" ) {
@@ -3499,19 +4327,25 @@
// Check to see if an attribute returns normalized href attributes
div.innerHTML = "<a href='#'></a>";
+
if ( div.firstChild && typeof div.firstChild.getAttribute !== "undefined" &&
div.firstChild.getAttribute("href") !== "#" ) {
- Expr.attrHandle.href = function(elem){
- return elem.getAttribute("href", 2);
+
+ Expr.attrHandle.href = function( elem ) {
+ return elem.getAttribute( "href", 2 );
};
}
- div = null; // release memory in IE
+ // release memory in IE
+ div = null;
})();
if ( document.querySelectorAll ) {
(function(){
- var oldSizzle = Sizzle, div = document.createElement("div");
+ var oldSizzle = Sizzle,
+ div = document.createElement("div"),
+ id = "__sizzle__";
+
div.innerHTML = "<p class='TEST'></p>";
// Safari can't handle uppercase or unicode characters when
@@ -3520,15 +4354,85 @@
return;
}
- Sizzle = function(query, context, extra, seed){
+ Sizzle = function( query, context, extra, seed ) {
context = context || document;
// Only use querySelectorAll on non-XML documents
// (ID selectors don't work in non-HTML documents)
- if ( !seed && context.nodeType === 9 && !isXML(context) ) {
- try {
- return makeArray( context.querySelectorAll(query), extra );
- } catch(e){}
+ if ( !seed && !Sizzle.isXML(context) ) {
+ // See if we find a selector to speed up
+ var match = /^(\w+$)|^\.([\w\-]+$)|^#([\w\-]+$)/.exec( query );
+
+ if ( match && (context.nodeType === 1 || context.nodeType === 9) ) {
+ // Speed-up: Sizzle("TAG")
+ if ( match[1] ) {
+ return makeArray( context.getElementsByTagName( query ), extra );
+
+ // Speed-up: Sizzle(".CLASS")
+ } else if ( match[2] && Expr.find.CLASS && context.getElementsByClassName ) {
+ return makeArray( context.getElementsByClassName( match[2] ), extra );
+ }
+ }
+
+ if ( context.nodeType === 9 ) {
+ // Speed-up: Sizzle("body")
+ // The body element only exists once, optimize finding it
+ if ( query === "body" && context.body ) {
+ return makeArray( [ context.body ], extra );
+
+ // Speed-up: Sizzle("#ID")
+ } else if ( match && match[3] ) {
+ var elem = context.getElementById( match[3] );
+
+ // Check parentNode to catch when Blackberry 4.6 returns
+ // nodes that are no longer in the document #6963
+ if ( elem && elem.parentNode ) {
+ // Handle the case where IE and Opera return items
+ // by name instead of ID
+ if ( elem.id === match[3] ) {
+ return makeArray( [ elem ], extra );
+ }
+
+ } else {
+ return makeArray( [], extra );
+ }
+ }
+
+ try {
+ return makeArray( context.querySelectorAll(query), extra );
+ } catch(qsaError) {}
+
+ // qSA works strangely on Element-rooted queries
+ // We can work around this by specifying an extra ID on the root
+ // and working up from there (Thanks to Andrew Dupont for the technique)
+ // IE 8 doesn't work on object elements
+ } else if ( context.nodeType === 1 && context.nodeName.toLowerCase() !== "object" ) {
+ var old = context.getAttribute( "id" ),
+ nid = old || id,
+ hasParent = context.parentNode,
+ relativeHierarchySelector = /^\s*[+~]/.test( query );
+
+ if ( !old ) {
+ context.setAttribute( "id", nid );
+ } else {
+ nid = nid.replace( /'/g, "\\$&" );
+ }
+ if ( relativeHierarchySelector && hasParent ) {
+ context = context.parentNode;
+ }
+
+ try {
+ if ( !relativeHierarchySelector || hasParent ) {
+ return makeArray( context.querySelectorAll( "[id='" + nid + "'] " + query ), extra );
+ }
+
+ } catch(pseudoError) {
+ } finally {
+ if ( !old ) {
+ context.removeAttribute( "id" );
+ }
+ }
+ }
}
return oldSizzle(query, context, extra, seed);
@@ -3538,11 +4442,44 @@
Sizzle[ prop ] = oldSizzle[ prop ];
}
- div = null; // release memory in IE
+ // release memory in IE
+ div = null;
})();
}
(function(){
+ var html = document.documentElement,
+ matches = html.matchesSelector || html.mozMatchesSelector || html.webkitMatchesSelector || html.msMatchesSelector,
+ pseudoWorks = false;
+
+ try {
+ // This should fail with an exception
+ // Gecko does not error, returns false instead
+ matches.call( document.documentElement, "[test!='']:sizzle" );
+
+ } catch( pseudoError ) {
+ pseudoWorks = true;
+ }
+
+ if ( matches ) {
+ Sizzle.matchesSelector = function( node, expr ) {
+ // Make sure that attribute selectors are quoted
+ expr = expr.replace(/\=\s*([^'"\]]*)\s*\]/g, "='$1']");
+
+ if ( !Sizzle.isXML( node ) ) {
+ try {
+ if ( pseudoWorks || !Expr.match.PSEUDO.test( expr ) && !/!=/.test( expr ) ) {
+ return matches.call( node, expr );
+ }
+ } catch(e) {}
+ }
+
+ return Sizzle(expr, null, null, [node]).length > 0;
+ };
+ }
+})();
+
+(function(){
var div = document.createElement("div");
div.innerHTML = "<div class='test e'></div><div class='test'></div>";
@@ -3561,21 +4498,24 @@
}
Expr.order.splice(1, 0, "CLASS");
- Expr.find.CLASS = function(match, context, isXML) {
+ Expr.find.CLASS = function( match, context, isXML ) {
if ( typeof context.getElementsByClassName !== "undefined" && !isXML ) {
return context.getElementsByClassName(match[1]);
}
};
- div = null; // release memory in IE
+ // release memory in IE
+ div = null;
})();
function dirNodeCheck( dir, cur, doneName, checkSet, nodeCheck, isXML ) {
for ( var i = 0, l = checkSet.length; i < l; i++ ) {
var elem = checkSet[i];
+
if ( elem ) {
+ var match = false;
+
elem = elem[dir];
- var match = false;
while ( elem ) {
if ( elem.sizcache === doneName ) {
@@ -3604,9 +4544,11 @@
function dirCheck( dir, cur, doneName, checkSet, nodeCheck, isXML ) {
for ( var i = 0, l = checkSet.length; i < l; i++ ) {
var elem = checkSet[i];
+
if ( elem ) {
+ var match = false;
+
elem = elem[dir];
- var match = false;
while ( elem ) {
if ( elem.sizcache === doneName ) {
@@ -3619,6 +4561,7 @@
elem.sizcache = doneName;
elem.sizset = i;
}
+
if ( typeof cur !== "string" ) {
if ( elem === cur ) {
match = true;
@@ -3639,21 +4582,34 @@
}
}
-var contains = document.compareDocumentPosition ? function(a, b){
- return !!(a.compareDocumentPosition(b) & 16);
-} : function(a, b){
- return a !== b && (a.contains ? a.contains(b) : true);
-};
-
-var isXML = function(elem){
+if ( document.documentElement.contains ) {
+ Sizzle.contains = function( a, b ) {
+ return a !== b && (a.contains ? a.contains(b) : true);
+ };
+
+} else if ( document.documentElement.compareDocumentPosition ) {
+ Sizzle.contains = function( a, b ) {
+ return !!(a.compareDocumentPosition(b) & 16);
+ };
+
+} else {
+ Sizzle.contains = function() {
+ return false;
+ };
+}
+
+Sizzle.isXML = function( elem ) {
// documentElement is verified for cases where it doesn't yet exist
// (such as loading iframes in IE - #4833)
var documentElement = (elem ? elem.ownerDocument || elem : 0).documentElement;
+
return documentElement ? documentElement.nodeName !== "HTML" : false;
};
-var posProcess = function(selector, context){
- var tmpSet = [], later = "", match,
+var posProcess = function( selector, context ) {
+ var match,
+ tmpSet = [],
+ later = "",
root = context.nodeType ? [context] : context;
// Position selectors must be done after the filter
@@ -3677,53 +4633,33 @@
jQuery.expr = Sizzle.selectors;
jQuery.expr[":"] = jQuery.expr.filters;
jQuery.unique = Sizzle.uniqueSort;
-jQuery.text = getText;
-jQuery.isXMLDoc = isXML;
-jQuery.contains = contains;
-
-return;
-
-window.Sizzle = Sizzle;
+jQuery.text = Sizzle.getText;
+jQuery.isXMLDoc = Sizzle.isXML;
+jQuery.contains = Sizzle.contains;
+
})();
+
+
var runtil = /Until$/,
rparentsprev = /^(?:parents|prevUntil|prevAll)/,
// Note: This RegExp should be improved, or likely pulled from Sizzle
rmultiselector = /,/,
- slice = Array.prototype.slice;
-
-// Implement the identical functionality for filter and not
-var winnow = function( elements, qualifier, keep ) {
- if ( jQuery.isFunction( qualifier ) ) {
- return jQuery.grep(elements, function( elem, i ) {
- return !!qualifier.call( elem, i, elem ) === keep;
- });
-
- } else if ( qualifier.nodeType ) {
- return jQuery.grep(elements, function( elem, i ) {
- return (elem === qualifier) === keep;
- });
-
- } else if ( typeof qualifier === "string" ) {
- var filtered = jQuery.grep(elements, function( elem ) {
- return elem.nodeType === 1;
- });
-
- if ( isSimple.test( qualifier ) ) {
- return jQuery.filter(qualifier, filtered, !keep);
- } else {
- qualifier = jQuery.filter( qualifier, filtered );
- }
- }
-
- return jQuery.grep(elements, function( elem, i ) {
- return (jQuery.inArray( elem, qualifier ) >= 0) === keep;
- });
-};
+ isSimple = /^.[^:#\[\.,]*$/,
+ slice = Array.prototype.slice,
+ POS = jQuery.expr.match.POS,
+ // methods guaranteed to produce a unique set when starting from a unique set
+ guaranteedUnique = {
+ children: true,
+ contents: true,
+ next: true,
+ prev: true
+ };
jQuery.fn.extend({
find: function( selector ) {
- var ret = this.pushStack( "", "find", selector ), length = 0;
+ var ret = this.pushStack( "", "find", selector ),
+ length = 0;
for ( var i = 0, l = this.length; i < l; i++ ) {
length = ret.length;
@@ -3763,21 +4699,25 @@
filter: function( selector ) {
return this.pushStack( winnow(this, selector, true), "filter", selector );
},
-
+
is: function( selector ) {
return !!selector && jQuery.filter( selector, this ).length > 0;
},
closest: function( selectors, context ) {
+ var ret = [], i, l, cur = this[0];
+
if ( jQuery.isArray( selectors ) ) {
- var ret = [], cur = this[0], match, matches = {}, selector;
+ var match, selector,
+ matches = {},
+ level = 1;
if ( cur && selectors.length ) {
- for ( var i = 0, l = selectors.length; i < l; i++ ) {
+ for ( i = 0, l = selectors.length; i < l; i++ ) {
selector = selectors[i];
if ( !matches[selector] ) {
- matches[selector] = jQuery.expr.match.POS.test( selector ) ?
+ matches[selector] = jQuery.expr.match.POS.test( selector ) ?
jQuery( selector, context || this.context ) :
selector;
}
@@ -3788,31 +4728,43 @@
match = matches[selector];
if ( match.jquery ? match.index(cur) > -1 : jQuery(cur).is(match) ) {
- ret.push({ selector: selector, elem: cur });
- delete matches[selector];
+ ret.push({ selector: selector, elem: cur, level: level });
}
}
+
cur = cur.parentNode;
+ level++;
}
}
return ret;
}
- var pos = jQuery.expr.match.POS.test( selectors ) ?
+ var pos = POS.test( selectors ) ?
jQuery( selectors, context || this.context ) : null;
- return this.map(function( i, cur ) {
- while ( cur && cur.ownerDocument && cur !== context ) {
- if ( pos ? pos.index(cur) > -1 : jQuery(cur).is(selectors) ) {
- return cur;
- }
- cur = cur.parentNode;
- }
- return null;
- });
- },
-
+ for ( i = 0, l = this.length; i < l; i++ ) {
+ cur = this[i];
+
+ while ( cur ) {
+ if ( pos ? pos.index(cur) > -1 : jQuery.find.matchesSelector(cur, selectors) ) {
+ ret.push( cur );
+ break;
+
+ } else {
+ cur = cur.parentNode;
+ if ( !cur || !cur.ownerDocument || cur === context ) {
+ break;
+ }
+ }
+ }
+ }
+
+ ret = ret.length > 1 ? jQuery.unique(ret) : ret;
+
+ return this.pushStack( ret, "closest", selectors );
+ },
+
// Determine the position of an element within
// the matched set of elements
index: function( elem ) {
@@ -3830,7 +4782,7 @@
add: function( selector, context ) {
var set = typeof selector === "string" ?
- jQuery( selector, context || this.context ) :
+ jQuery( selector, context ) :
jQuery.makeArray( selector ),
all = jQuery.merge( this.get(), set );
@@ -3892,8 +4844,13 @@
}
}, function( name, fn ) {
jQuery.fn[ name ] = function( until, selector ) {
- var ret = jQuery.map( this, fn, until );
-
+ var ret = jQuery.map( this, fn, until ),
+ // The variable 'args' was introduced in
+ // https://github.com/jquery/jquery/commit/52a0238
+ // to work around a bug in Chrome 10 (Dev) and should be removed when the bug is fixed.
+ // http://code.google.com/p/v8/issues/detail?id=1050
+ args = slice.call(arguments);
+
if ( !runtil.test( name ) ) {
selector = until;
}
@@ -3902,13 +4859,13 @@
ret = jQuery.filter( selector, ret );
}
- ret = this.length > 1 ? jQuery.unique( ret ) : ret;
+ ret = this.length > 1 && !guaranteedUnique[ name ] ? jQuery.unique( ret ) : ret;
if ( (this.length > 1 || rmultiselector.test( selector )) && rparentsprev.test( name ) ) {
ret = ret.reverse();
}
- return this.pushStack( ret, name, slice.call(arguments).join(",") );
+ return this.pushStack( ret, name, args.join(",") );
};
});
@@ -3918,11 +4875,15 @@
expr = ":not(" + expr + ")";
}
- return jQuery.find.matches(expr, elems);
- },
-
+ return elems.length === 1 ?
+ jQuery.find.matchesSelector(elems[0], expr) ? [ elems[0] ] : [] :
+ jQuery.find.matches(expr, elems);
+ },
+
dir: function( elem, dir, until ) {
- var matched = [], cur = elem[dir];
+ var matched = [],
+ cur = elem[ dir ];
+
while ( cur && cur.nodeType !== 9 && (until === undefined || cur.nodeType !== 1 || !jQuery( cur ).is( until )) ) {
if ( cur.nodeType === 1 ) {
matched.push( cur );
@@ -3957,20 +4918,49 @@
return r;
}
});
+
+// Implement the identical functionality for filter and not
+function winnow( elements, qualifier, keep ) {
+ if ( jQuery.isFunction( qualifier ) ) {
+ return jQuery.grep(elements, function( elem, i ) {
+ var retVal = !!qualifier.call( elem, i, elem );
+ return retVal === keep;
+ });
+
+ } else if ( qualifier.nodeType ) {
+ return jQuery.grep(elements, function( elem, i ) {
+ return (elem === qualifier) === keep;
+ });
+
+ } else if ( typeof qualifier === "string" ) {
+ var filtered = jQuery.grep(elements, function( elem ) {
+ return elem.nodeType === 1;
+ });
+
+ if ( isSimple.test( qualifier ) ) {
+ return jQuery.filter(qualifier, filtered, !keep);
+ } else {
+ qualifier = jQuery.filter( qualifier, filtered );
+ }
+ }
+
+ return jQuery.grep(elements, function( elem, i ) {
+ return (jQuery.inArray( elem, qualifier ) >= 0) === keep;
+ });
+}
+
+
+
+
var rinlinejQuery = / jQuery\d+="(?:\d+|null)"/g,
rleadingWhitespace = /^\s+/,
- rxhtmlTag = /(<([\w:]+)[^>]*?)\/>/g,
- rselfClosing = /^(?:area|br|col|embed|hr|img|input|link|meta|param)$/i,
+ rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([\w:]+)[^>]*)\/>/ig,
rtagName = /<([\w:]+)/,
rtbody = /<tbody/i,
rhtml = /<|&#?\w+;/,
- rnocache = /<script|<object|<embed|<option|<style/i,
- rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i, // checked="checked" or checked (html5)
- fcloseTag = function( all, front, tag ) {
- return rselfClosing.test( tag ) ?
- all :
- front + "></" + tag + ">";
- },
+ rnocache = /<(?:script|object|embed|option|style)/i,
+ // checked="checked" or checked (html5)
+ rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
wrapMap = {
option: [ 1, "<select multiple='multiple'>", "</select>" ],
legend: [ 1, "<fieldset>", "</fieldset>" ],
@@ -3995,7 +4985,8 @@
text: function( text ) {
if ( jQuery.isFunction(text) ) {
return this.each(function(i) {
- var self = jQuery(this);
+ var self = jQuery( this );
+
self.text( text.call(this, i, self.text()) );
});
}
@@ -4044,7 +5035,8 @@
}
return this.each(function() {
- var self = jQuery( this ), contents = self.contents();
+ var self = jQuery( this ),
+ contents = self.contents();
if ( contents.length ) {
contents.wrapAll( html );
@@ -4108,7 +5100,7 @@
return set;
}
},
-
+
// keepData is for internal use only--do not document
remove: function( selector, keepData ) {
for ( var i = 0, elem; (elem = this[i]) != null; i++ ) {
@@ -4123,7 +5115,7 @@
}
}
}
-
+
return this;
},
@@ -4139,46 +5131,17 @@
elem.removeChild( elem.firstChild );
}
}
-
+
return this;
},
- clone: function( events ) {
- // Do the clone
- var ret = this.map(function() {
- if ( !jQuery.support.noCloneEvent && !jQuery.isXMLDoc(this) ) {
- // IE copies events bound via attachEvent when
- // using cloneNode. Calling detachEvent on the
- // clone will also remove the events from the orignal
- // In order to get around this, we use innerHTML.
- // Unfortunately, this means some modifications to
- // attributes in IE that are actually only stored
- // as properties will not be copied (such as the
- // the name attribute on an input).
- var html = this.outerHTML, ownerDocument = this.ownerDocument;
- if ( !html ) {
- var div = ownerDocument.createElement("div");
- div.appendChild( this.cloneNode(true) );
- html = div.innerHTML;
- }
-
- return jQuery.clean([html.replace(rinlinejQuery, "")
- // Handle the case in IE 8 where action=/test/> self-closes a tag
- .replace(/=([^="'>\s]+\/)>/g, '="$1">')
- .replace(rleadingWhitespace, "")], ownerDocument)[0];
- } else {
- return this.cloneNode(true);
- }
+ clone: function( dataAndEvents, deepDataAndEvents ) {
+ dataAndEvents = dataAndEvents == null ? true : dataAndEvents;
+ deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
+
+ return this.map( function () {
+ return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
});
-
- // Copy the events from the original to the clone
- if ( events === true ) {
- cloneCopyEvent( this, ret );
- cloneCopyEvent( this.find("*"), ret.find("*") );
- }
-
- // Return the cloned set
- return ret;
},
html: function( value ) {
@@ -4192,7 +5155,7 @@
(jQuery.support.leadingWhitespace || !rleadingWhitespace.test( value )) &&
!wrapMap[ (rtagName.exec( value ) || ["", ""])[1].toLowerCase() ] ) {
- value = value.replace(rxhtmlTag, fcloseTag);
+ value = value.replace(rxhtmlTag, "<$1></$2>");
try {
for ( var i = 0, l = this.length; i < l; i++ ) {
@@ -4210,10 +5173,9 @@
} else if ( jQuery.isFunction( value ) ) {
this.each(function(i){
- var self = jQuery(this), old = self.html();
- self.empty().append(function(){
- return value.call( this, i, old );
- });
+ var self = jQuery( this );
+
+ self.html( value.call(this, i, self.html()) );
});
} else {
@@ -4235,13 +5197,14 @@
}
if ( typeof value !== "string" ) {
- value = jQuery(value).detach();
+ value = jQuery( value ).detach();
}
return this.each(function() {
- var next = this.nextSibling, parent = this.parentNode;
-
- jQuery(this).remove();
+ var next = this.nextSibling,
+ parent = this.parentNode;
+
+ jQuery( this ).remove();
if ( next ) {
jQuery(next).before( value );
@@ -4259,7 +5222,9 @@
},
domManip: function( args, table, callback ) {
- var results, first, value = args[0], scripts = [], fragment, parent;
+ var results, first, fragment, parent,
+ value = args[0],
+ scripts = [];
// We can't cloneNode fragments that contain checked, in WebKit
if ( !jQuery.support.checkClone && arguments.length === 3 && typeof value === "string" && rchecked.test( value ) ) {
@@ -4284,11 +5249,11 @@
results = { fragment: parent };
} else {
- results = buildFragment( args, this, scripts );
- }
-
+ results = jQuery.buildFragment( args, this, scripts );
+ }
+
fragment = results.fragment;
-
+
if ( fragment.childNodes.length === 1 ) {
first = fragment = fragment.firstChild;
} else {
@@ -4298,13 +5263,20 @@
if ( first ) {
table = table && jQuery.nodeName( first, "tr" );
- for ( var i = 0, l = this.length; i < l; i++ ) {
+ for ( var i = 0, l = this.length, lastIndex = l - 1; i < l; i++ ) {
callback.call(
table ?
root(this[i], first) :
this[i],
- i > 0 || results.cacheable || this.length > 1 ?
- fragment.cloneNode(true) :
+ // Make sure that we do not leak memory by inadvertently discarding
+ // the original fragment (which might have attached data) instead of
+ // using it; in addition, use the original fragment object for the last
+ // item instead of first because it can end up being emptied incorrectly
+ // in certain situations (Bug #8070).
+ // Fragments from the fragment cache must always be cloned and never used
+ // in place.
+ results.cacheable || (l > 1 && i < lastIndex) ?
+ jQuery.clone( fragment, true, true ) :
fragment
);
}
@@ -4316,49 +5288,107 @@
}
return this;
-
- function root( elem, cur ) {
- return jQuery.nodeName(elem, "table") ?
- (elem.getElementsByTagName("tbody")[0] ||
- elem.appendChild(elem.ownerDocument.createElement("tbody"))) :
- elem;
- }
}
});
-function cloneCopyEvent(orig, ret) {
- var i = 0;
-
- ret.each(function() {
- if ( this.nodeName !== (orig[i] && orig[i].nodeName) ) {
- return;
- }
-
- var oldData = jQuery.data( orig[i++] ), curData = jQuery.data( this, oldData ), events = oldData && oldData.events;
+function root( elem, cur ) {
+ return jQuery.nodeName(elem, "table") ?
+ (elem.getElementsByTagName("tbody")[0] ||
+ elem.appendChild(elem.ownerDocument.createElement("tbody"))) :
+ elem;
+}
+
+function cloneCopyEvent( src, dest ) {
+
+ if ( dest.nodeType !== 1 || !jQuery.hasData( src ) ) {
+ return;
+ }
+
+ var internalKey = jQuery.expando,
+ oldData = jQuery.data( src ),
+ curData = jQuery.data( dest, oldData );
+
+ // Switch to use the internal data object, if it exists, for the next
+ // stage of data copying
+ if ( (oldData = oldData[ internalKey ]) ) {
+ var events = oldData.events;
+ curData = curData[ internalKey ] = jQuery.extend({}, oldData);
if ( events ) {
delete curData.handle;
curData.events = {};
for ( var type in events ) {
- for ( var handler in events[ type ] ) {
- jQuery.event.add( this, type, events[ type ][ handler ], events[ type ][ handler ].data );
- }
- }
- }
- });
+ for ( var i = 0, l = events[ type ].length; i < l; i++ ) {
+ jQuery.event.add( dest, type, events[ type ][ i ], events[ type ][ i ].data );
+ }
+ }
+ }
+ }
}
-function buildFragment( args, nodes, scripts ) {
+function cloneFixAttributes(src, dest) {
+ // We do not need to do anything for non-Elements
+ if ( dest.nodeType !== 1 ) {
+ return;
+ }
+
+ var nodeName = dest.nodeName.toLowerCase();
+
+ // clearAttributes removes the attributes, which we don't want,
+ // but also removes the attachEvent events, which we *do* want
+ dest.clearAttributes();
+
+ // mergeAttributes, in contrast, only merges back on the
+ // original attributes, not the events
+ dest.mergeAttributes(src);
+
+ // IE6-8 fail to clone children inside object elements that use
+ // the proprietary classid attribute value (rather than the type
+ // attribute) to identify the type of content to display
+ if ( nodeName === "object" ) {
+ dest.outerHTML = src.outerHTML;
+
+ } else if ( nodeName === "input" && (src.type === "checkbox" || src.type === "radio") ) {
+ // IE6-8 fails to persist the checked state of a cloned checkbox
+ // or radio button. Worse, IE6-7 fail to give the cloned element
+ // a checked appearance if the defaultChecked value isn't also set
+ if ( src.checked ) {
+ dest.defaultChecked = dest.checked = src.checked;
+ }
+
+ // IE6-7 get confused and end up setting the value of a cloned
+ // checkbox/radio button to an empty string instead of "on"
+ if ( dest.value !== src.value ) {
+ dest.value = src.value;
+ }
+
+ // IE6-8 fails to return the selected option to the default selected
+ // state when cloning options
+ } else if ( nodeName === "option" ) {
+ dest.selected = src.defaultSelected;
+
+ // IE6-8 fails to set the defaultValue to the correct value when
+ // cloning other types of input fields
+ } else if ( nodeName === "input" || nodeName === "textarea" ) {
+ dest.defaultValue = src.defaultValue;
+ }
+
+ // Event data gets referenced instead of copied if the expando
+ // gets copied too
+ dest.removeAttribute( jQuery.expando );
+}
+
+jQuery.buildFragment = function( args, nodes, scripts ) {
var fragment, cacheable, cacheresults,
doc = (nodes && nodes[0] ? nodes[0].ownerDocument || nodes[0] : document);
- // Only cache "small" (1/2 KB) strings that are associated with the main document
+ // Only cache "small" (1/2 KB) HTML strings that are associated with the main document
// Cloning options loses the selected state, so don't cache them
// IE 6 doesn't like it when you put <object> or <embed> elements in a fragment
// Also, WebKit does not clone 'checked' attributes on cloneNode, so don't cache
if ( args.length === 1 && typeof args[0] === "string" && args[0].length < 512 && doc === document &&
- !rnocache.test( args[0] ) && (jQuery.support.checkClone || !rchecked.test( args[0] )) ) {
+ args[0].charAt(0) === "<" && !rnocache.test( args[0] ) && (jQuery.support.checkClone || !rchecked.test( args[0] )) ) {
cacheable = true;
cacheresults = jQuery.fragments[ args[0] ];
@@ -4379,7 +5409,7 @@
}
return { fragment: fragment, cacheable: cacheable };
-}
+};
jQuery.fragments = {};
@@ -4391,26 +5421,75 @@
replaceAll: "replaceWith"
}, function( name, original ) {
jQuery.fn[ name ] = function( selector ) {
- var ret = [], insert = jQuery( selector ),
+ var ret = [],
+ insert = jQuery( selector ),
parent = this.length === 1 && this[0].parentNode;
-
+
if ( parent && parent.nodeType === 11 && parent.childNodes.length === 1 && insert.length === 1 ) {
insert[ original ]( this[0] );
return this;
-
+
} else {
for ( var i = 0, l = insert.length; i < l; i++ ) {
var elems = (i > 0 ? this.clone(true) : this).get();
- jQuery.fn[ original ].apply( jQuery(insert[i]), elems );
+ jQuery( insert[i] )[ original ]( elems );
ret = ret.concat( elems );
}
-
+
return this.pushStack( ret, name, insert.selector );
}
};
});
jQuery.extend({
+ clone: function( elem, dataAndEvents, deepDataAndEvents ) {
+ var clone = elem.cloneNode(true),
+ srcElements,
+ destElements,
+ i;
+
+ if ( !jQuery.support.noCloneEvent && (elem.nodeType === 1 || elem.nodeType === 11) && !jQuery.isXMLDoc(elem) ) {
+ // IE copies events bound via attachEvent when using cloneNode.
+ // Calling detachEvent on the clone will also remove the events
+ // from the original. In order to get around this, we use some
+ // proprietary methods to clear the events. Thanks to MooTools
+ // guys for this hotness.
+
+ // Using Sizzle here is crazy slow, so we use getElementsByTagName
+ // instead
+ srcElements = elem.getElementsByTagName("*");
+ destElements = clone.getElementsByTagName("*");
+
+ // Weird iteration because IE will replace the length property
+ // with an element if you are cloning the body and one of the
+ // elements on the page has a name or id of "length"
+ for ( i = 0; srcElements[i]; ++i ) {
+ cloneFixAttributes( srcElements[i], destElements[i] );
+ }
+
+ cloneFixAttributes( elem, clone );
+ }
+
+ // Copy the events from the original to the clone
+ if ( dataAndEvents ) {
+
+ cloneCopyEvent( elem, clone );
+
+ if ( deepDataAndEvents && "getElementsByTagName" in elem ) {
+
+ srcElements = elem.getElementsByTagName("*");
+ destElements = clone.getElementsByTagName("*");
+
+ if ( srcElements.length ) {
+ for ( i = 0; srcElements[i]; ++i ) {
+ cloneCopyEvent( srcElements[i], destElements[i] );
+ }
+ }
+ }
+ }
+ // Return the cloned set
+ return clone;
+ },
clean: function( elems, context, fragment, scripts ) {
context = context || document;
@@ -4436,7 +5515,7 @@
} else if ( typeof elem === "string" ) {
// Fix "XHTML"-style tags in all browsers
- elem = elem.replace(rxhtmlTag, fcloseTag);
+ elem = elem.replace(rxhtmlTag, "<$1></$2>");
// Trim whitespace, otherwise indexOf won't work as expected
var tag = (rtagName.exec( elem ) || ["", ""])[1].toLowerCase(),
@@ -4489,10 +5568,10 @@
}
if ( fragment ) {
- for ( var i = 0; ret[i]; i++ ) {
+ for ( i = 0; ret[i]; i++ ) {
if ( scripts && jQuery.nodeName( ret[i], "script" ) && (!ret[i].type || ret[i].type.toLowerCase() === "text/javascript") ) {
scripts.push( ret[i].parentNode ? ret[i].parentNode.removeChild( ret[i] ) : ret[i] );
-
+
} else {
if ( ret[i].nodeType === 1 ) {
ret.splice.apply( ret, [i + 1, 0].concat(jQuery.makeArray(ret[i].getElementsByTagName("script"))) );
@@ -4504,233 +5583,196 @@
return ret;
},
-
+
cleanData: function( elems ) {
- var data, id, cache = jQuery.cache,
- special = jQuery.event.special,
+ var data, id, cache = jQuery.cache, internalKey = jQuery.expando, special = jQuery.event.special,
deleteExpando = jQuery.support.deleteExpando;
-
+
for ( var i = 0, elem; (elem = elems[i]) != null; i++ ) {
+ if ( elem.nodeName && jQuery.noData[elem.nodeName.toLowerCase()] ) {
+ continue;
+ }
+
id = elem[ jQuery.expando ];
-
+
if ( id ) {
- data = cache[ id ];
-
- if ( data.events ) {
+ data = cache[ id ] && cache[ id ][ internalKey ];
+
+ if ( data && data.events ) {
for ( var type in data.events ) {
if ( special[ type ] ) {
jQuery.event.remove( elem, type );
+ // This is a shortcut to avoid jQuery.event.remove's overhead
} else {
- removeEvent( elem, type, data.handle );
+ jQuery.removeEvent( elem, type, data.handle );
}
}
- }
-
+
+ // Null the DOM reference to avoid IE6/7/8 leak (#7054)
+ if ( data.handle ) {
+ data.handle.elem = null;
+ }
+ }
+
if ( deleteExpando ) {
delete elem[ jQuery.expando ];
} else if ( elem.removeAttribute ) {
elem.removeAttribute( jQuery.expando );
}
-
+
delete cache[ id ];
}
}
}
});
-// exclude the following css properties to add px
-var rexclude = /z-?index|font-?weight|opacity|zoom|line-?height/i,
- ralpha = /alpha\([^)]*\)/,
+
+function evalScript( i, elem ) {
+ if ( elem.src ) {
+ jQuery.ajax({
+ url: elem.src,
+ async: false,
+ dataType: "script"
+ });
+ } else {
+ jQuery.globalEval( elem.text || elem.textContent || elem.innerHTML || "" );
+ }
+
+ if ( elem.parentNode ) {
+ elem.parentNode.removeChild( elem );
+ }
+}
+
+
+
+
+var ralpha = /alpha\([^)]*\)/i,
ropacity = /opacity=([^)]*)/,
- rfloat = /float/i,
rdashAlpha = /-([a-z])/ig,
rupper = /([A-Z])/g,
rnumpx = /^-?\d+(?:px)?$/i,
rnum = /^-?\d/,
- cssShow = { position: "absolute", visibility: "hidden", display:"block" },
+ cssShow = { position: "absolute", visibility: "hidden", display: "block" },
cssWidth = [ "Left", "Right" ],
cssHeight = [ "Top", "Bottom" ],
-
- // cache check for defaultView.getComputedStyle
- getComputedStyle = document.defaultView && document.defaultView.getComputedStyle,
- // normalize float css property
- styleFloat = jQuery.support.cssFloat ? "cssFloat" : "styleFloat",
+ curCSS,
+
+ getComputedStyle,
+ currentStyle,
+
fcamelCase = function( all, letter ) {
return letter.toUpperCase();
};
jQuery.fn.css = function( name, value ) {
- return access( this, name, value, true, function( elem, name, value ) {
- if ( value === undefined ) {
- return jQuery.curCSS( elem, name );
- }
-
- if ( typeof value === "number" && !rexclude.test(name) ) {
- value += "px";
- }
-
- jQuery.style( elem, name, value );
+ // Setting 'undefined' is a no-op
+ if ( arguments.length === 2 && value === undefined ) {
+ return this;
+ }
+
+ return jQuery.access( this, name, value, true, function( elem, name, value ) {
+ return value !== undefined ?
+ jQuery.style( elem, name, value ) :
+ jQuery.css( elem, name );
});
};
jQuery.extend({
- style: function( elem, name, value ) {
- // don't set styles on text and comment nodes
- if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 ) {
- return undefined;
- }
-
- // ignore negative width and height values #1599
- if ( (name === "width" || name === "height") && parseFloat(value) < 0 ) {
- value = undefined;
- }
-
- var style = elem.style || elem, set = value !== undefined;
-
- // IE uses filters for opacity
- if ( !jQuery.support.opacity && name === "opacity" ) {
- if ( set ) {
- // IE has trouble with opacity if it does not have layout
- // Force it by setting the zoom level
- style.zoom = 1;
-
- // Set the alpha filter to set the opacity
- var opacity = parseInt( value, 10 ) + "" === "NaN" ? "" : "alpha(opacity=" + value * 100 + ")";
- var filter = style.filter || jQuery.curCSS( elem, "filter" ) || "";
- style.filter = ralpha.test(filter) ? filter.replace(ralpha, opacity) : opacity;
- }
-
- return style.filter && style.filter.indexOf("opacity=") >= 0 ?
- (parseFloat( ropacity.exec(style.filter)[1] ) / 100) + "":
- "";
- }
-
- // Make sure we're using the right name for getting the float value
- if ( rfloat.test( name ) ) {
- name = styleFloat;
- }
-
- name = name.replace(rdashAlpha, fcamelCase);
-
- if ( set ) {
- style[ name ] = value;
- }
-
- return style[ name ];
- },
-
- css: function( elem, name, force, extra ) {
- if ( name === "width" || name === "height" ) {
- var val, props = cssShow, which = name === "width" ? cssWidth : cssHeight;
-
- function getWH() {
- val = name === "width" ? elem.offsetWidth : elem.offsetHeight;
-
- if ( extra === "border" ) {
- return;
- }
-
- jQuery.each( which, function() {
- if ( !extra ) {
- val -= parseFloat(jQuery.curCSS( elem, "padding" + this, true)) || 0;
- }
-
- if ( extra === "margin" ) {
- val += parseFloat(jQuery.curCSS( elem, "margin" + this, true)) || 0;
- } else {
- val -= parseFloat(jQuery.curCSS( elem, "border" + this + "Width", true)) || 0;
- }
- });
- }
-
- if ( elem.offsetWidth !== 0 ) {
- getWH();
- } else {
- jQuery.swap( elem, props, getWH );
- }
-
- return Math.max(0, Math.round(val));
- }
-
- return jQuery.curCSS( elem, name, force );
- },
-
- curCSS: function( elem, name, force ) {
- var ret, style = elem.style, filter;
-
- // IE uses filters for opacity
- if ( !jQuery.support.opacity && name === "opacity" && elem.currentStyle ) {
- ret = ropacity.test(elem.currentStyle.filter || "") ?
- (parseFloat(RegExp.$1) / 100) + "" :
- "";
-
- return ret === "" ?
- "1" :
- ret;
- }
-
- // Make sure we're using the right name for getting the float value
- if ( rfloat.test( name ) ) {
- name = styleFloat;
- }
-
- if ( !force && style && style[ name ] ) {
- ret = style[ name ];
-
- } else if ( getComputedStyle ) {
-
- // Only "float" is needed here
- if ( rfloat.test( name ) ) {
- name = "float";
- }
-
- name = name.replace( rupper, "-$1" ).toLowerCase();
-
- var defaultView = elem.ownerDocument.defaultView;
-
- if ( !defaultView ) {
- return null;
- }
-
- var computedStyle = defaultView.getComputedStyle( elem, null );
-
- if ( computedStyle ) {
- ret = computedStyle.getPropertyValue( name );
- }
-
- // We should always get a number back from opacity
- if ( name === "opacity" && ret === "" ) {
- ret = "1";
- }
-
- } else if ( elem.currentStyle ) {
- var camelCase = name.replace(rdashAlpha, fcamelCase);
-
- ret = elem.currentStyle[ name ] || elem.currentStyle[ camelCase ];
-
- // From the awesome hack by Dean Edwards
- // http://erik.eae.net/archives/2007/07/27/18.54.15/#comment-102291
-
- // If we're not dealing with a regular pixel number
- // but a number that has a weird ending, we need to convert it to pixels
- if ( !rnumpx.test( ret ) && rnum.test( ret ) ) {
- // Remember the original values
- var left = style.left, rsLeft = elem.runtimeStyle.left;
-
- // Put in the new values to get a computed value out
- elem.runtimeStyle.left = elem.currentStyle.left;
- style.left = camelCase === "fontSize" ? "1em" : (ret || 0);
- ret = style.pixelLeft + "px";
-
- // Revert the changed values
- style.left = left;
- elem.runtimeStyle.left = rsLeft;
- }
- }
-
- return ret;
+ // Add in style property hooks for overriding the default
+ // behavior of getting and setting a style property
+ cssHooks: {
+ opacity: {
+ get: function( elem, computed ) {
+ if ( computed ) {
+ // We should always get a number back from opacity
+ var ret = curCSS( elem, "opacity", "opacity" );
+ return ret === "" ? "1" : ret;
+
+ } else {
+ return elem.style.opacity;
+ }
+ }
+ }
+ },
+
+ // Exclude the following css properties to add px
+ cssNumber: {
+ "zIndex": true,
+ "fontWeight": true,
+ "opacity": true,
+ "zoom": true,
+ "lineHeight": true
+ },
+
+ // Add in properties whose names you wish to fix before
+ // setting or getting the value
+ cssProps: {
+ // normalize float css property
+ "float": jQuery.support.cssFloat ? "cssFloat" : "styleFloat"
+ },
+
+ // Get and set the style property on a DOM Node
+ style: function( elem, name, value, extra ) {
+ // Don't set styles on text and comment nodes
+ if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
+ return;
+ }
+
+ // Make sure that we're working with the right name
+ var ret, origName = jQuery.camelCase( name ),
+ style = elem.style, hooks = jQuery.cssHooks[ origName ];
+
+ name = jQuery.cssProps[ origName ] || origName;
+
+ // Check if we're setting a value
+ if ( value !== undefined ) {
+ // Make sure that NaN and null values aren't set. See: #7116
+ if ( typeof value === "number" && isNaN( value ) || value == null ) {
+ return;
+ }
+
+ // If a number was passed in, add 'px' to the (except for certain CSS properties)
+ if ( typeof value === "number" && !jQuery.cssNumber[ origName ] ) {
+ value += "px";
+ }
+
+ // If a hook was provided, use that value, otherwise just set the specified value
+ if ( !hooks || !("set" in hooks) || (value = hooks.set( elem, value )) !== undefined ) {
+ // Wrapped to prevent IE from throwing errors when 'invalid' values are provided
+ // Fixes bug #5509
+ try {
+ style[ name ] = value;
+ } catch(e) {}
+ }
+
+ } else {
+ // If a hook was provided get the non-computed value from there
+ if ( hooks && "get" in hooks && (ret = hooks.get( elem, false, extra )) !== undefined ) {
+ return ret;
+ }
+
+ // Otherwise just get the value from the style object
+ return style[ name ];
+ }
+ },
+
+ css: function( elem, name, extra ) {
+ // Make sure that we're working with the right name
+ var ret, origName = jQuery.camelCase( name ),
+ hooks = jQuery.cssHooks[ origName ];
+
+ name = jQuery.cssProps[ origName ] || origName;
+
+ // If a hook was provided get the computed value from there
+ if ( hooks && "get" in hooks && (ret = hooks.get( elem, true, extra )) !== undefined ) {
+ return ret;
+
+ // Otherwise, if a way to get the computed value exists, use that
+ } else if ( curCSS ) {
+ return curCSS( elem, name, origName );
+ }
},
// A method for quickly swapping in/out CSS properties to get correct calculations
@@ -4746,55 +5788,328 @@
callback.call( elem );
// Revert the old values
- for ( var name in options ) {
+ for ( name in options ) {
elem.style[ name ] = old[ name ];
}
+ },
+
+ camelCase: function( string ) {
+ return string.replace( rdashAlpha, fcamelCase );
}
});
+// DEPRECATED, Use jQuery.css() instead
+jQuery.curCSS = jQuery.css;
+
+jQuery.each(["height", "width"], function( i, name ) {
+ jQuery.cssHooks[ name ] = {
+ get: function( elem, computed, extra ) {
+ var val;
+
+ if ( computed ) {
+ if ( elem.offsetWidth !== 0 ) {
+ val = getWH( elem, name, extra );
+
+ } else {
+ jQuery.swap( elem, cssShow, function() {
+ val = getWH( elem, name, extra );
+ });
+ }
+
+ if ( val <= 0 ) {
+ val = curCSS( elem, name, name );
+
+ if ( val === "0px" && currentStyle ) {
+ val = currentStyle( elem, name, name );
+ }
+
+ if ( val != null ) {
+ // Should return "auto" instead of 0, use 0 for
+ // temporary backwards-compat
+ return val === "" || val === "auto" ? "0px" : val;
+ }
+ }
+
+ if ( val < 0 || val == null ) {
+ val = elem.style[ name ];
+
+ // Should return "auto" instead of 0, use 0 for
+ // temporary backwards-compat
+ return val === "" || val === "auto" ? "0px" : val;
+ }
+
+ return typeof val === "string" ? val : val + "px";
+ }
+ },
+
+ set: function( elem, value ) {
+ if ( rnumpx.test( value ) ) {
+ // ignore negative width and height values #1599
+ value = parseFloat(value);
+
+ if ( value >= 0 ) {
+ return value + "px";
+ }
+
+ } else {
+ return value;
+ }
+ }
+ };
+});
+
+if ( !jQuery.support.opacity ) {
+ jQuery.cssHooks.opacity = {
+ get: function( elem, computed ) {
+ // IE uses filters for opacity
+ return ropacity.test((computed && elem.currentStyle ? elem.currentStyle.filter : elem.style.filter) || "") ?
+ (parseFloat(RegExp.$1) / 100) + "" :
+ computed ? "1" : "";
+ },
+
+ set: function( elem, value ) {
+ var style = elem.style;
+
+ // IE has trouble with opacity if it does not have layout
+ // Force it by setting the zoom level
+ style.zoom = 1;
+
+ // Set the alpha filter to set the opacity
+ var opacity = jQuery.isNaN(value) ?
+ "" :
+ "alpha(opacity=" + value * 100 + ")",
+ filter = style.filter || "";
+
+ style.filter = ralpha.test(filter) ?
+ filter.replace(ralpha, opacity) :
+ style.filter + ' ' + opacity;
+ }
+ };
+}
+
+if ( document.defaultView && document.defaultView.getComputedStyle ) {
+ getComputedStyle = function( elem, newName, name ) {
+ var ret, defaultView, computedStyle;
+
+ name = name.replace( rupper, "-$1" ).toLowerCase();
+
+ if ( !(defaultView = elem.ownerDocument.defaultView) ) {
+ return undefined;
+ }
+
+ if ( (computedStyle = defaultView.getComputedStyle( elem, null )) ) {
+ ret = computedStyle.getPropertyValue( name );
+ if ( ret === "" && !jQuery.contains( elem.ownerDocument.documentElement, elem ) ) {
+ ret = jQuery.style( elem, name );
+ }
+ }
+
+ return ret;
+ };
+}
+
+if ( document.documentElement.currentStyle ) {
+ currentStyle = function( elem, name ) {
+ var left,
+ ret = elem.currentStyle && elem.currentStyle[ name ],
+ rsLeft = elem.runtimeStyle && elem.runtimeStyle[ name ],
+ style = elem.style;
+
+ // From the awesome hack by Dean Edwards
+ // http://erik.eae.net/archives/2007/07/27/18.54.15/#comment-102291
+
+ // If we're not dealing with a regular pixel number
+ // but a number that has a weird ending, we need to convert it to pixels
+ if ( !rnumpx.test( ret ) && rnum.test( ret ) ) {
+ // Remember the original values
+ left = style.left;
+
+ // Put in the new values to get a computed value out
+ if ( rsLeft ) {
+ elem.runtimeStyle.left = elem.currentStyle.left;
+ }
+ style.left = name === "fontSize" ? "1em" : (ret || 0);
+ ret = style.pixelLeft + "px";
+
+ // Revert the changed values
+ style.left = left;
+ if ( rsLeft ) {
+ elem.runtimeStyle.left = rsLeft;
+ }
+ }
+
+ return ret === "" ? "auto" : ret;
+ };
+}
+
+curCSS = getComputedStyle || currentStyle;
+
+function getWH( elem, name, extra ) {
+ var which = name === "width" ? cssWidth : cssHeight,
+ val = name === "width" ? elem.offsetWidth : elem.offsetHeight;
+
+ if ( extra === "border" ) {
+ return val;
+ }
+
+ jQuery.each( which, function() {
+ if ( !extra ) {
+ val -= parseFloat(jQuery.css( elem, "padding" + this )) || 0;
+ }
+
+ if ( extra === "margin" ) {
+ val += parseFloat(jQuery.css( elem, "margin" + this )) || 0;
+
+ } else {
+ val -= parseFloat(jQuery.css( elem, "border" + this + "Width" )) || 0;
+ }
+ });
+
+ return val;
+}
+
if ( jQuery.expr && jQuery.expr.filters ) {
jQuery.expr.filters.hidden = function( elem ) {
- var width = elem.offsetWidth, height = elem.offsetHeight,
- skip = elem.nodeName.toLowerCase() === "tr";
-
- return width === 0 && height === 0 && !skip ?
- true :
- width > 0 && height > 0 && !skip ?
- false :
- jQuery.curCSS(elem, "display") === "none";
+ var width = elem.offsetWidth,
+ height = elem.offsetHeight;
+
+ return (width === 0 && height === 0) || (!jQuery.support.reliableHiddenOffsets && (elem.style.display || jQuery.css( elem, "display" )) === "none");
};
jQuery.expr.filters.visible = function( elem ) {
return !jQuery.expr.filters.hidden( elem );
};
}
-var jsc = now(),
- rscript = /<script(.|\s)*?\/script>/gi,
- rselectTextarea = /select|textarea/i,
- rinput = /color|date|datetime|email|hidden|month|number|password|range|search|tel|text|time|url|week/i,
- jsre = /=\?(&|$)/,
+
+
+
+
+var r20 = /%20/g,
+ rbracket = /\[\]$/,
+ rCRLF = /\r?\n/g,
+ rhash = /#.*$/,
+ rheaders = /^(.*?):\s*(.*?)\r?$/mg, // IE leaves an \r character at EOL
+ rinput = /^(?:color|date|datetime|email|hidden|month|number|password|range|search|tel|text|time|url|week)$/i,
+ rnoContent = /^(?:GET|HEAD)$/,
+ rprotocol = /^\/\//,
rquery = /\?/,
- rts = /(\?|&)_=.*?(&|$)/,
- rurl = /^(\w+:)?\/\/([^\/?#]+)/,
- r20 = /%20/g,
+ rscript = /<script\b[^<]*(?:(?!<\/script>)<[^<]*)*<\/script>/gi,
+ rselectTextarea = /^(?:select|textarea)/i,
+ rspacesAjax = /\s+/,
+ rts = /([?&])_=[^&]*/,
+ rurl = /^(\w+:)\/\/([^\/?#:]+)(?::(\d+))?/,
// Keep a copy of the old load method
- _load = jQuery.fn.load;
+ _load = jQuery.fn.load,
+
+ /* Prefilters
+ * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
+ * 2) These are called:
+ * - BEFORE asking for a transport
+ * - AFTER param serialization (s.data is a string if s.processData is true)
+ * 3) key is the dataType
+ * 4) the catchall symbol "*" can be used
+ * 5) execution will start with transport dataType and THEN continue down to "*" if needed
+ */
+ prefilters = {},
+
+ /* Transports bindings
+ * 1) key is the dataType
+ * 2) the catchall symbol "*" can be used
+ * 3) selection will start with transport dataType and THEN go to "*" if needed
+ */
+ transports = {};
+
+// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
+function addToPrefiltersOrTransports( structure ) {
+
+ // dataTypeExpression is optional and defaults to "*"
+ return function( dataTypeExpression, func ) {
+
+ if ( typeof dataTypeExpression !== "string" ) {
+ func = dataTypeExpression;
+ dataTypeExpression = "*";
+ }
+
+ if ( jQuery.isFunction( func ) ) {
+ var dataTypes = dataTypeExpression.toLowerCase().split( rspacesAjax ),
+ i = 0,
+ length = dataTypes.length,
+ dataType,
+ list,
+ placeBefore;
+
+ // For each dataType in the dataTypeExpression
+ for(; i < length; i++ ) {
+ dataType = dataTypes[ i ];
+ // We control if we're asked to add before
+ // any existing element
+ placeBefore = /^\+/.test( dataType );
+ if ( placeBefore ) {
+ dataType = dataType.substr( 1 ) || "*";
+ }
+ list = structure[ dataType ] = structure[ dataType ] || [];
+ // then we add to the structure accordingly
+ list[ placeBefore ? "unshift" : "push" ]( func );
+ }
+ }
+ };
+}
+
+//Base inspection function for prefilters and transports
+function inspectPrefiltersOrTransports( structure, options, originalOptions, jXHR,
+ dataType /* internal */, inspected /* internal */ ) {
+
+ dataType = dataType || options.dataTypes[ 0 ];
+ inspected = inspected || {};
+
+ inspected[ dataType ] = true;
+
+ var list = structure[ dataType ],
+ i = 0,
+ length = list ? list.length : 0,
+ executeOnly = ( structure === prefilters ),
+ selection;
+
+ for(; i < length && ( executeOnly || !selection ); i++ ) {
+ selection = list[ i ]( options, originalOptions, jXHR );
+ // If we got redirected to another dataType
+ // we try there if not done already
+ if ( typeof selection === "string" ) {
+ if ( inspected[ selection ] ) {
+ selection = undefined;
+ } else {
+ options.dataTypes.unshift( selection );
+ selection = inspectPrefiltersOrTransports(
+ structure, options, originalOptions, jXHR, selection, inspected );
+ }
+ }
+ }
+ // If we're only executing or nothing was selected
+ // we try the catchall dataType if not done already
+ if ( ( executeOnly || !selection ) && !inspected[ "*" ] ) {
+ selection = inspectPrefiltersOrTransports(
+ structure, options, originalOptions, jXHR, "*", inspected );
+ }
+ // unnecessary when only executing (prefilters)
+ // but it'll be ignored by the caller in that case
+ return selection;
+}
jQuery.fn.extend({
load: function( url, params, callback ) {
- if ( typeof url !== "string" ) {
- return _load.call( this, url );
+ if ( typeof url !== "string" && _load ) {
+ return _load.apply( this, arguments );
// Don't do a request if no elements are being requested
} else if ( !this.length ) {
return this;
}
- var off = url.indexOf(" ");
+ var off = url.indexOf( " " );
if ( off >= 0 ) {
- var selector = url.slice(off, url.length);
- url = url.slice(0, off);
+ var selector = url.slice( off, url.length );
+ url = url.slice( 0, off );
}
// Default to a GET request
@@ -4823,26 +6138,34 @@
type: type,
dataType: "html",
data: params,
- complete: function( res, status ) {
+ // Complete callback (responseText is used internally)
+ complete: function( jXHR, status, responseText ) {
+ // Store the response as specified by the jXHR object
+ responseText = jXHR.responseText;
// If successful, inject the HTML into all the matched elements
- if ( status === "success" || status === "notmodified" ) {
+ if ( jXHR.isResolved() ) {
+ // #4825: Get the actual response in case
+ // a dataFilter is present in ajaxSettings
+ jXHR.done(function( r ) {
+ responseText = r;
+ });
// See if a selector was specified
self.html( selector ?
// Create a dummy div to hold the results
- jQuery("<div />")
+ jQuery("<div>")
// inject the contents of the document in, removing the scripts
// to avoid any 'Permission Denied' errors in IE
- .append(res.responseText.replace(rscript, ""))
+ .append(responseText.replace(rscript, ""))
// Locate the specified elements
.find(selector) :
// If not, just inject the full result
- res.responseText );
+ responseText );
}
if ( callback ) {
- self.each( callback, [res.responseText, status, res] );
+ self.each( callback, [ responseText, status, jXHR ] );
}
}
});
@@ -4851,42 +6174,42 @@
},
serialize: function() {
- return jQuery.param(this.serializeArray());
- },
+ return jQuery.param( this.serializeArray() );
+ },
+
serializeArray: function() {
- return this.map(function() {
- return this.elements ? jQuery.makeArray(this.elements) : this;
+ return this.map(function(){
+ return this.elements ? jQuery.makeArray( this.elements ) : this;
})
- .filter(function() {
+ .filter(function(){
return this.name && !this.disabled &&
- (this.checked || rselectTextarea.test(this.nodeName) ||
- rinput.test(this.type));
+ ( this.checked || rselectTextarea.test( this.nodeName ) ||
+ rinput.test( this.type ) );
})
- .map(function( i, elem ) {
- var val = jQuery(this).val();
+ .map(function( i, elem ){
+ var val = jQuery( this ).val();
return val == null ?
null :
- jQuery.isArray(val) ?
- jQuery.map( val, function( val, i ) {
- return { name: elem.name, value: val };
+ jQuery.isArray( val ) ?
+ jQuery.map( val, function( val, i ){
+ return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
}) :
- { name: elem.name, value: val };
+ { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
}).get();
}
});
// Attach a bunch of functions for handling common AJAX events
-jQuery.each( "ajaxStart ajaxStop ajaxComplete ajaxError ajaxSuccess ajaxSend".split(" "), function( i, o ) {
- jQuery.fn[o] = function( f ) {
- return this.bind(o, f);
+jQuery.each( "ajaxStart ajaxStop ajaxComplete ajaxError ajaxSuccess ajaxSend".split( " " ), function( i, o ){
+ jQuery.fn[ o ] = function( f ){
+ return this.bind( o, f );
};
-});
-
-jQuery.extend({
-
- get: function( url, data, callback, type ) {
- // shift arguments if data argument was omited
+} );
+
+jQuery.each( [ "get", "post" ], function( i, method ) {
+ jQuery[ method ] = function( url, data, callback, type ) {
+ // shift arguments if data argument was omitted
if ( jQuery.isFunction( data ) ) {
type = type || callback;
callback = data;
@@ -4894,41 +6217,30 @@
}
return jQuery.ajax({
- type: "GET",
+ type: method,
url: url,
data: data,
success: callback,
dataType: type
});
- },
+ };
+} );
+
+jQuery.extend({
getScript: function( url, callback ) {
- return jQuery.get(url, null, callback, "script");
+ return jQuery.get( url, null, callback, "script" );
},
getJSON: function( url, data, callback ) {
- return jQuery.get(url, data, callback, "json");
- },
-
- post: function( url, data, callback, type ) {
- // shift arguments if data argument was omited
- if ( jQuery.isFunction( data ) ) {
- type = type || callback;
- callback = data;
- data = {};
- }
-
- return jQuery.ajax({
- type: "POST",
- url: url,
- data: data,
- success: callback,
- dataType: type
- });
+ return jQuery.get( url, data, callback, "json" );
},
ajaxSetup: function( settings ) {
- jQuery.extend( jQuery.ajaxSettings, settings );
+ jQuery.extend( true, jQuery.ajaxSettings, settings );
+ if ( settings.context ) {
+ jQuery.ajaxSettings.context = settings.context;
+ }
},
ajaxSettings: {
@@ -4941,507 +6253,1035 @@
/*
timeout: 0,
data: null,
+ dataType: null,
username: null,
password: null,
+ cache: null,
traditional: false,
+ headers: {},
+ crossDomain: null,
*/
- // Create the request object; Microsoft failed to properly
- // implement the XMLHttpRequest in IE7 (can't request local files),
- // so we use the ActiveXObject when it is available
- // This function can be overriden by calling jQuery.ajaxSetup
- xhr: window.XMLHttpRequest && (window.location.protocol !== "file:" || !window.ActiveXObject) ?
- function() {
- return new window.XMLHttpRequest();
- } :
- function() {
- try {
- return new window.ActiveXObject("Microsoft.XMLHTTP");
- } catch(e) {}
- },
+
accepts: {
xml: "application/xml, text/xml",
html: "text/html",
- script: "text/javascript, application/javascript",
+ text: "text/plain",
json: "application/json, text/javascript",
- text: "text/plain",
- _default: "*/*"
- }
- },
-
- // Last-Modified header cache for next request
- lastModified: {},
- etag: {},
-
- ajax: function( origSettings ) {
- var s = jQuery.extend(true, {}, jQuery.ajaxSettings, origSettings);
-
- var jsonp, status, data,
- callbackContext = origSettings && origSettings.context || s,
- type = s.type.toUpperCase();
-
- // convert data if not already a string
+ "*": "*/*"
+ },
+
+ contents: {
+ xml: /xml/,
+ html: /html/,
+ json: /json/
+ },
+
+ responseFields: {
+ xml: "responseXML",
+ text: "responseText"
+ },
+
+ // List of data converters
+ // 1) key format is "source_type destination_type" (a single space in-between)
+ // 2) the catchall symbol "*" can be used for source_type
+ converters: {
+
+ // Convert anything to text
+ "* text": window.String,
+
+ // Text to html (true = no transformation)
+ "text html": true,
+
+ // Evaluate text as a json expression
+ "text json": jQuery.parseJSON,
+
+ // Parse text as xml
+ "text xml": jQuery.parseXML
+ }
+ },
+
+ ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
+ ajaxTransport: addToPrefiltersOrTransports( transports ),
+
+ // Main method
+ ajax: function( url, options ) {
+
+ // If options is not an object,
+ // we simulate pre-1.5 signature
+ if ( typeof options !== "object" ) {
+ options = url;
+ url = undefined;
+ }
+
+ // Force options to be an object
+ options = options || {};
+
+ var // Create the final options object
+ s = jQuery.extend( true, {}, jQuery.ajaxSettings, options ),
+ // Callbacks contexts
+ // We force the original context if it exists
+ // or take it from jQuery.ajaxSettings otherwise
+ // (plain objects used as context get extended)
+ callbackContext =
+ ( s.context = ( "context" in options ? options : jQuery.ajaxSettings ).context ) || s,
+ globalEventContext = callbackContext === s ? jQuery.event : jQuery( callbackContext ),
+ // Deferreds
+ deferred = jQuery.Deferred(),
+ completeDeferred = jQuery._Deferred(),
+ // Status-dependent callbacks
+ statusCode = s.statusCode || {},
+ // Headers (they are sent all at once)
+ requestHeaders = {},
+ // Response headers
+ responseHeadersString,
+ responseHeaders,
+ // transport
+ transport,
+ // timeout handle
+ timeoutTimer,
+ // Cross-domain detection vars
+ loc = document.location,
+ protocol = loc.protocol || "http:",
+ parts,
+ // The jXHR state
+ state = 0,
+ // Loop variable
+ i,
+ // Fake xhr
+ jXHR = {
+
+ readyState: 0,
+
+ // Caches the header
+ setRequestHeader: function( name, value ) {
+ if ( state === 0 ) {
+ requestHeaders[ name.toLowerCase() ] = value;
+ }
+ return this;
+ },
+
+ // Raw string
+ getAllResponseHeaders: function() {
+ return state === 2 ? responseHeadersString : null;
+ },
+
+ // Builds headers hashtable if needed
+ getResponseHeader: function( key ) {
+ var match;
+ if ( state === 2 ) {
+ if ( !responseHeaders ) {
+ responseHeaders = {};
+ while( ( match = rheaders.exec( responseHeadersString ) ) ) {
+ responseHeaders[ match[1].toLowerCase() ] = match[ 2 ];
+ }
+ }
+ match = responseHeaders[ key.toLowerCase() ];
+ }
+ return match || null;
+ },
+
+ // Cancel the request
+ abort: function( statusText ) {
+ statusText = statusText || "abort";
+ if ( transport ) {
+ transport.abort( statusText );
+ }
+ done( 0, statusText );
+ return this;
+ }
+ };
+
+ // Callback for when everything is done
+ // It is defined here because jslint complains if it is declared
+ // at the end of the function (which would be more logical and readable)
+ function done( status, statusText, responses, headers) {
+
+ // Called once
+ if ( state === 2 ) {
+ return;
+ }
+
+ // State is "done" now
+ state = 2;
+
+ // Clear timeout if it exists
+ if ( timeoutTimer ) {
+ clearTimeout( timeoutTimer );
+ }
+
+ // Dereference transport for early garbage collection
+ // (no matter how long the jXHR object will be used)
+ transport = undefined;
+
+ // Cache response headers
+ responseHeadersString = headers || "";
+
+ // Set readyState
+ jXHR.readyState = status ? 4 : 0;
+
+ var isSuccess,
+ success,
+ error,
+ response = responses ? ajaxHandleResponses( s, jXHR, responses ) : undefined,
+ lastModified,
+ etag;
+
+ // If successful, handle type chaining
+ if ( status >= 200 && status < 300 || status === 304 ) {
+
+ // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+ if ( s.ifModified ) {
+
+ if ( ( lastModified = jXHR.getResponseHeader( "Last-Modified" ) ) ) {
+ jQuery.lastModified[ s.url ] = lastModified;
+ }
+ if ( ( etag = jXHR.getResponseHeader( "Etag" ) ) ) {
+ jQuery.etag[ s.url ] = etag;
+ }
+ }
+
+ // If not modified
+ if ( status === 304 ) {
+
+ statusText = "notmodified";
+ isSuccess = true;
+
+ // If we have data
+ } else {
+
+ try {
+ success = ajaxConvert( s, response );
+ statusText = "success";
+ isSuccess = true;
+ } catch(e) {
+ // We have a parsererror
+ statusText = "parsererror";
+ error = e;
+ }
+ }
+ } else {
+ // We extract error from statusText
+ // then normalize statusText and status for non-aborts
+ error = statusText;
+ if( status ) {
+ statusText = "error";
+ if ( status < 0 ) {
+ status = 0;
+ }
+ }
+ }
+
+ // Set data for the fake xhr object
+ jXHR.status = status;
+ jXHR.statusText = statusText;
+
+ // Success/Error
+ if ( isSuccess ) {
+ deferred.resolveWith( callbackContext, [ success, statusText, jXHR ] );
+ } else {
+ deferred.rejectWith( callbackContext, [ jXHR, statusText, error ] );
+ }
+
+ // Status-dependent callbacks
+ jXHR.statusCode( statusCode );
+ statusCode = undefined;
+
+ if ( s.global ) {
+ globalEventContext.trigger( "ajax" + ( isSuccess ? "Success" : "Error" ),
+ [ jXHR, s, isSuccess ? success : error ] );
+ }
+
+ // Complete
+ completeDeferred.resolveWith( callbackContext, [ jXHR, statusText ] );
+
+ if ( s.global ) {
+ globalEventContext.trigger( "ajaxComplete", [ jXHR, s] );
+ // Handle the global AJAX counter
+ if ( !( --jQuery.active ) ) {
+ jQuery.event.trigger( "ajaxStop" );
+ }
+ }
+ }
+
+ // Attach deferreds
+ deferred.promise( jXHR );
+ jXHR.success = jXHR.done;
+ jXHR.error = jXHR.fail;
+ jXHR.complete = completeDeferred.done;
+
+ // Status-dependent callbacks
+ jXHR.statusCode = function( map ) {
+ if ( map ) {
+ var tmp;
+ if ( state < 2 ) {
+ for( tmp in map ) {
+ statusCode[ tmp ] = [ statusCode[tmp], map[tmp] ];
+ }
+ } else {
+ tmp = map[ jXHR.status ];
+ jXHR.then( tmp, tmp );
+ }
+ }
+ return this;
+ };
+
+ // Remove hash character (#7531: and string promotion)
+ // Add protocol if not provided (#5866: IE7 issue with protocol-less urls)
+ // We also use the url parameter if available
+ s.url = ( "" + ( url || s.url ) ).replace( rhash, "" ).replace( rprotocol, protocol + "//" );
+
+ // Extract dataTypes list
+ s.dataTypes = jQuery.trim( s.dataType || "*" ).toLowerCase().split( rspacesAjax );
+
+ // Determine if a cross-domain request is in order
+ if ( !s.crossDomain ) {
+ parts = rurl.exec( s.url.toLowerCase() );
+ s.crossDomain = !!( parts &&
+ ( parts[ 1 ] != protocol || parts[ 2 ] != loc.hostname ||
+ ( parts[ 3 ] || ( parts[ 1 ] === "http:" ? 80 : 443 ) ) !=
+ ( loc.port || ( protocol === "http:" ? 80 : 443 ) ) )
+ );
+ }
+
+ // Convert data if not already a string
if ( s.data && s.processData && typeof s.data !== "string" ) {
s.data = jQuery.param( s.data, s.traditional );
}
- // Handle JSONP Parameter Callbacks
- if ( s.dataType === "jsonp" ) {
- if ( type === "GET" ) {
- if ( !jsre.test( s.url ) ) {
- s.url += (rquery.test( s.url ) ? "&" : "?") + (s.jsonp || "callback") + "=?";
- }
- } else if ( !s.data || !jsre.test(s.data) ) {
- s.data = (s.data ? s.data + "&" : "") + (s.jsonp || "callback") + "=?";
- }
- s.dataType = "json";
- }
-
- // Build temporary JSONP function
- if ( s.dataType === "json" && (s.data && jsre.test(s.data) || jsre.test(s.url)) ) {
- jsonp = s.jsonpCallback || ("jsonp" + jsc++);
-
- // Replace the =? sequence both in the query string and the data
+ // Apply prefilters
+ inspectPrefiltersOrTransports( prefilters, s, options, jXHR );
+
+ // Uppercase the type
+ s.type = s.type.toUpperCase();
+
+ // Determine if request has content
+ s.hasContent = !rnoContent.test( s.type );
+
+ // Watch for a new set of requests
+ if ( s.global && jQuery.active++ === 0 ) {
+ jQuery.event.trigger( "ajaxStart" );
+ }
+
+ // More options handling for requests with no content
+ if ( !s.hasContent ) {
+
+ // If data is available, append data to url
if ( s.data ) {
- s.data = (s.data + "").replace(jsre, "=" + jsonp + "$1");
- }
-
- s.url = s.url.replace(jsre, "=" + jsonp + "$1");
-
- // We need to make sure
- // that a JSONP style response is executed properly
- s.dataType = "script";
-
- // Handle JSONP-style loading
- window[ jsonp ] = window[ jsonp ] || function( tmp ) {
- data = tmp;
- success();
- complete();
- // Garbage collect
- window[ jsonp ] = undefined;
+ s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.data;
+ }
+
+ // Add anti-cache in url if needed
+ if ( s.cache === false ) {
+
+ var ts = jQuery.now(),
+ // try replacing _= if it is there
+ ret = s.url.replace( rts, "$1_=" + ts );
+
+ // if nothing was replaced, add timestamp to the end
+ s.url = ret + ( (ret === s.url ) ? ( rquery.test( s.url ) ? "&" : "?" ) + "_=" + ts : "" );
+ }
+ }
+
+ // Set the correct header, if data is being sent
+ if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
+ requestHeaders[ "content-type" ] = s.contentType;
+ }
+
+ // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+ if ( s.ifModified ) {
+ if ( jQuery.lastModified[ s.url ] ) {
+ requestHeaders[ "if-modified-since" ] = jQuery.lastModified[ s.url ];
+ }
+ if ( jQuery.etag[ s.url ] ) {
+ requestHeaders[ "if-none-match" ] = jQuery.etag[ s.url ];
+ }
+ }
+
+ // Set the Accepts header for the server, depending on the dataType
+ requestHeaders.accept = s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[0] ] ?
+ s.accepts[ s.dataTypes[0] ] + ( s.dataTypes[ 0 ] !== "*" ? ", */*; q=0.01" : "" ) :
+ s.accepts[ "*" ];
+
+ // Check for headers option
+ for ( i in s.headers ) {
+ requestHeaders[ i.toLowerCase() ] = s.headers[ i ];
+ }
+
+ // Allow custom headers/mimetypes and early abort
+ if ( s.beforeSend && ( s.beforeSend.call( callbackContext, jXHR, s ) === false || state === 2 ) ) {
+ // Abort if not done already
+ done( 0, "abort" );
+ // Return false
+ jXHR = false;
+
+ } else {
+
+ // Install callbacks on deferreds
+ for ( i in { success: 1, error: 1, complete: 1 } ) {
+ jXHR[ i ]( s[ i ] );
+ }
+
+ // Get transport
+ transport = inspectPrefiltersOrTransports( transports, s, options, jXHR );
+
+ // If no transport, we auto-abort
+ if ( !transport ) {
+ done( -1, "No Transport" );
+ } else {
+ // Set state as sending
+ state = jXHR.readyState = 1;
+ // Send global event
+ if ( s.global ) {
+ globalEventContext.trigger( "ajaxSend", [ jXHR, s ] );
+ }
+ // Timeout
+ if ( s.async && s.timeout > 0 ) {
+ timeoutTimer = setTimeout( function(){
+ jXHR.abort( "timeout" );
+ }, s.timeout );
+ }
try {
- delete window[ jsonp ];
- } catch(e) {}
-
- if ( head ) {
- head.removeChild( script );
- }
- };
- }
-
- if ( s.dataType === "script" && s.cache === null ) {
- s.cache = false;
- }
-
- if ( s.cache === false && type === "GET" ) {
- var ts = now();
-
- // try replacing _= if it is there
- var ret = s.url.replace(rts, "$1_=" + ts + "$2");
-
- // if nothing was replaced, add timestamp to the end
- s.url = ret + ((ret === s.url) ? (rquery.test(s.url) ? "&" : "?") + "_=" + ts : "");
- }
-
- // If data is available, append data to url for get requests
- if ( s.data && type === "GET" ) {
- s.url += (rquery.test(s.url) ? "&" : "?") + s.data;
- }
-
- // Watch for a new set of requests
- if ( s.global && ! jQuery.active++ ) {
- jQuery.event.trigger( "ajaxStart" );
- }
-
- // Matches an absolute URL, and saves the domain
- var parts = rurl.exec( s.url ),
- remote = parts && (parts[1] && parts[1] !== location.protocol || parts[2] !== location.host);
-
- // If we're requesting a remote document
- // and trying to load JSON or Script with a GET
- if ( s.dataType === "script" && type === "GET" && remote ) {
- var head = document.getElementsByTagName("head")[0] || document.documentElement;
- var script = document.createElement("script");
- script.src = s.url;
- if ( s.scriptCharset ) {
- script.charset = s.scriptCharset;
- }
-
- // Handle Script loading
- if ( !jsonp ) {
- var done = false;
-
- // Attach handlers for all browsers
- script.onload = script.onreadystatechange = function() {
- if ( !done && (!this.readyState ||
- this.readyState === "loaded" || this.readyState === "complete") ) {
- done = true;
- success();
- complete();
-
- // Handle memory leak in IE
- script.onload = script.onreadystatechange = null;
- if ( head && script.parentNode ) {
- head.removeChild( script );
- }
+ transport.send( requestHeaders, done );
+ } catch (e) {
+ // Propagate exception as error if not done
+ if ( status < 2 ) {
+ done( -1, e );
+ // Simply rethrow otherwise
+ } else {
+ jQuery.error( e );
}
- };
- }
-
- // Use insertBefore instead of appendChild to circumvent an IE6 bug.
- // This arises when a base node is used (#2709 and #4378).
- head.insertBefore( script, head.firstChild );
-
- // We handle everything using the script element injection
- return undefined;
- }
-
- var requestDone = false;
-
- // Create the request object
- var xhr = s.xhr();
-
- if ( !xhr ) {
- return;
- }
-
- // Open the socket
- // Passing null username, generates a login popup on Opera (#2865)
- if ( s.username ) {
- xhr.open(type, s.url, s.async, s.username, s.password);
- } else {
- xhr.open(type, s.url, s.async);
- }
-
- // Need an extra try/catch for cross domain requests in Firefox 3
- try {
- // Set the correct header, if data is being sent
- if ( s.data || origSettings && origSettings.contentType ) {
- xhr.setRequestHeader("Content-Type", s.contentType);
- }
-
- // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
- if ( s.ifModified ) {
- if ( jQuery.lastModified[s.url] ) {
- xhr.setRequestHeader("If-Modified-Since", jQuery.lastModified[s.url]);
- }
-
- if ( jQuery.etag[s.url] ) {
- xhr.setRequestHeader("If-None-Match", jQuery.etag[s.url]);
- }
- }
-
- // Set header so the called script knows that it's an XMLHttpRequest
- // Only send the header if it's not a remote XHR
- if ( !remote ) {
- xhr.setRequestHeader("X-Requested-With", "XMLHttpRequest");
- }
-
- // Set the Accepts header for the server, depending on the dataType
- xhr.setRequestHeader("Accept", s.dataType && s.accepts[ s.dataType ] ?
- s.accepts[ s.dataType ] + ", */*" :
- s.accepts._default );
- } catch(e) {}
-
- // Allow custom headers/mimetypes and early abort
- if ( s.beforeSend && s.beforeSend.call(callbackContext, xhr, s) === false ) {
- // Handle the global AJAX counter
- if ( s.global && ! --jQuery.active ) {
- jQuery.event.trigger( "ajaxStop" );
- }
-
- // close opended socket
- xhr.abort();
- return false;
- }
-
- if ( s.global ) {
- trigger("ajaxSend", [xhr, s]);
- }
-
- // Wait for a response to come back
- var onreadystatechange = xhr.onreadystatechange = function( isTimeout ) {
- // The request was aborted
- if ( !xhr || xhr.readyState === 0 || isTimeout === "abort" ) {
- // Opera doesn't call onreadystatechange before this point
- // so we simulate the call
- if ( !requestDone ) {
- complete();
- }
-
- requestDone = true;
- if ( xhr ) {
- xhr.onreadystatechange = jQuery.noop;
- }
-
- // The transfer is complete and the data is available, or the request timed out
- } else if ( !requestDone && xhr && (xhr.readyState === 4 || isTimeout === "timeout") ) {
- requestDone = true;
- xhr.onreadystatechange = jQuery.noop;
-
- status = isTimeout === "timeout" ?
- "timeout" :
- !jQuery.httpSuccess( xhr ) ?
- "error" :
- s.ifModified && jQuery.httpNotModified( xhr, s.url ) ?
- "notmodified" :
- "success";
-
- var errMsg;
-
- if ( status === "success" ) {
- // Watch for, and catch, XML document parse errors
- try {
- // process the data (runs the xml through httpData regardless of callback)
- data = jQuery.httpData( xhr, s.dataType, s );
- } catch(err) {
- status = "parsererror";
- errMsg = err;
- }
- }
-
- // Make sure that the request was successful or notmodified
- if ( status === "success" || status === "notmodified" ) {
- // JSONP handles its own success callback
- if ( !jsonp ) {
- success();
- }
- } else {
- jQuery.handleError(s, xhr, status, errMsg);
- }
-
- // Fire the complete handlers
- complete();
-
- if ( isTimeout === "timeout" ) {
- xhr.abort();
- }
-
- // Stop memory leaks
- if ( s.async ) {
- xhr = null;
- }
- }
- };
-
- // Override the abort handler, if we can (IE doesn't allow it, but that's OK)
- // Opera doesn't fire onreadystatechange at all on abort
- try {
- var oldAbort = xhr.abort;
- xhr.abort = function() {
- if ( xhr ) {
- oldAbort.call( xhr );
- }
-
- onreadystatechange( "abort" );
- };
- } catch(e) { }
-
- // Timeout checker
- if ( s.async && s.timeout > 0 ) {
- setTimeout(function() {
- // Check to see if the request is still happening
- if ( xhr && !requestDone ) {
- onreadystatechange( "timeout" );
- }
- }, s.timeout);
- }
-
- // Send the data
- try {
- xhr.send( type === "POST" || type === "PUT" || type === "DELETE" ? s.data : null );
- } catch(e) {
- jQuery.handleError(s, xhr, null, e);
- // Fire the complete handlers
- complete();
- }
-
- // firefox 1.5 doesn't fire statechange for sync requests
- if ( !s.async ) {
- onreadystatechange();
- }
-
- function success() {
- // If a local callback was specified, fire it and pass it the data
- if ( s.success ) {
- s.success.call( callbackContext, data, status, xhr );
- }
-
- // Fire the global callback
- if ( s.global ) {
- trigger( "ajaxSuccess", [xhr, s] );
- }
- }
-
- function complete() {
- // Process result
- if ( s.complete ) {
- s.complete.call( callbackContext, xhr, status);
- }
-
- // The request was completed
- if ( s.global ) {
- trigger( "ajaxComplete", [xhr, s] );
- }
-
- // Handle the global AJAX counter
- if ( s.global && ! --jQuery.active ) {
- jQuery.event.trigger( "ajaxStop" );
- }
- }
-
- function trigger(type, args) {
- (s.context ? jQuery(s.context) : jQuery.event).trigger(type, args);
- }
-
- // return XMLHttpRequest to allow aborting the request etc.
- return xhr;
- },
-
- handleError: function( s, xhr, status, e ) {
- // If a local callback was specified, fire it
- if ( s.error ) {
- s.error.call( s.context || s, xhr, status, e );
- }
-
- // Fire the global callback
- if ( s.global ) {
- (s.context ? jQuery(s.context) : jQuery.event).trigger( "ajaxError", [xhr, s, e] );
- }
- },
-
- // Counter for holding the number of active queries
- active: 0,
-
- // Determines if an XMLHttpRequest was successful or not
- httpSuccess: function( xhr ) {
- try {
- // IE error sometimes returns 1223 when it should be 204 so treat it as success, see #1450
- return !xhr.status && location.protocol === "file:" ||
- // Opera returns 0 when status is 304
- ( xhr.status >= 200 && xhr.status < 300 ) ||
- xhr.status === 304 || xhr.status === 1223 || xhr.status === 0;
- } catch(e) {}
-
- return false;
- },
-
- // Determines if an XMLHttpRequest returns NotModified
- httpNotModified: function( xhr, url ) {
- var lastModified = xhr.getResponseHeader("Last-Modified"),
- etag = xhr.getResponseHeader("Etag");
-
- if ( lastModified ) {
- jQuery.lastModified[url] = lastModified;
- }
-
- if ( etag ) {
- jQuery.etag[url] = etag;
- }
-
- // Opera returns 0 when status is 304
- return xhr.status === 304 || xhr.status === 0;
- },
-
- httpData: function( xhr, type, s ) {
- var ct = xhr.getResponseHeader("content-type") || "",
- xml = type === "xml" || !type && ct.indexOf("xml") >= 0,
- data = xml ? xhr.responseXML : xhr.responseText;
-
- if ( xml && data.documentElement.nodeName === "parsererror" ) {
- jQuery.error( "parsererror" );
- }
-
- // Allow a pre-filtering function to sanitize the response
- // s is checked to keep backwards compatibility
- if ( s && s.dataFilter ) {
- data = s.dataFilter( data, type );
- }
-
- // The filter can actually parse the response
- if ( typeof data === "string" ) {
- // Get the JavaScript object, if JSON is used.
- if ( type === "json" || !type && ct.indexOf("json") >= 0 ) {
- data = jQuery.parseJSON( data );
-
- // If the type is "script", eval it in global context
- } else if ( type === "script" || !type && ct.indexOf("javascript") >= 0 ) {
- jQuery.globalEval( data );
- }
- }
-
- return data;
+ }
+ }
+ }
+ return jXHR;
},
// Serialize an array of form elements or a set of
// key/values into a query string
param: function( a, traditional ) {
- var s = [];
-
+ var s = [],
+ add = function( key, value ) {
+ // If value is a function, invoke it and return its value
+ value = jQuery.isFunction( value ) ? value() : value;
+ s[ s.length ] = encodeURIComponent( key ) + "=" + encodeURIComponent( value );
+ };
+
// Set traditional to true for jQuery <= 1.3.2 behavior.
if ( traditional === undefined ) {
traditional = jQuery.ajaxSettings.traditional;
}
-
+
// If an array was passed in, assume that it is an array of form elements.
- if ( jQuery.isArray(a) || a.jquery ) {
+ if ( jQuery.isArray( a ) || a.jquery ) {
// Serialize the form elements
jQuery.each( a, function() {
add( this.name, this.value );
- });
-
+ } );
+
} else {
// If traditional, encode the "old" way (the way 1.3.2 or older
// did it), otherwise encode params recursively.
for ( var prefix in a ) {
- buildParams( prefix, a[prefix] );
+ buildParams( prefix, a[ prefix ], traditional, add );
}
}
// Return the resulting serialization
- return s.join("&").replace(r20, "+");
-
- function buildParams( prefix, obj ) {
- if ( jQuery.isArray(obj) ) {
- // Serialize array item.
- jQuery.each( obj, function( i, v ) {
- if ( traditional || /\[\]$/.test( prefix ) ) {
- // Treat each array item as a scalar.
- add( prefix, v );
- } else {
- // If array item is non-scalar (array or object), encode its
- // numeric index to resolve deserialization ambiguity issues.
- // Note that rack (as of 1.0.0) can't currently deserialize
- // nested arrays properly, and attempting to do so may cause
- // a server error. Possible fixes are to modify rack's
- // deserialization algorithm or to provide an option or flag
- // to force array serialization to be shallow.
- buildParams( prefix + "[" + ( typeof v === "object" || jQuery.isArray(v) ? i : "" ) + "]", v );
- }
- });
-
- } else if ( !traditional && obj != null && typeof obj === "object" ) {
- // Serialize object item.
- jQuery.each( obj, function( k, v ) {
- buildParams( prefix + "[" + k + "]", v );
- });
-
- } else {
- // Serialize scalar item.
- add( prefix, obj );
- }
- }
-
- function add( key, value ) {
- // If value is a function, invoke it and return its value
- value = jQuery.isFunction(value) ? value() : value;
- s[ s.length ] = encodeURIComponent(key) + "=" + encodeURIComponent(value);
- }
+ return s.join( "&" ).replace( r20, "+" );
}
});
+
+function buildParams( prefix, obj, traditional, add ) {
+ if ( jQuery.isArray( obj ) && obj.length ) {
+ // Serialize array item.
+ jQuery.each( obj, function( i, v ) {
+ if ( traditional || rbracket.test( prefix ) ) {
+ // Treat each array item as a scalar.
+ add( prefix, v );
+
+ } else {
+ // If array item is non-scalar (array or object), encode its
+ // numeric index to resolve deserialization ambiguity issues.
+ // Note that rack (as of 1.0.0) can't currently deserialize
+ // nested arrays properly, and attempting to do so may cause
+ // a server error. Possible fixes are to modify rack's
+ // deserialization algorithm or to provide an option or flag
+ // to force array serialization to be shallow.
+ buildParams( prefix + "[" + ( typeof v === "object" || jQuery.isArray(v) ? i : "" ) + "]", v, traditional, add );
+ }
+ });
+
+ } else if ( !traditional && obj != null && typeof obj === "object" ) {
+ // If we see an array here, it is empty and should be treated as an empty
+ // object
+ if ( jQuery.isArray( obj ) || jQuery.isEmptyObject( obj ) ) {
+ add( prefix, "" );
+
+ // Serialize object item.
+ } else {
+ jQuery.each( obj, function( k, v ) {
+ buildParams( prefix + "[" + k + "]", v, traditional, add );
+ });
+ }
+
+ } else {
+ // Serialize scalar item.
+ add( prefix, obj );
+ }
+}
+
+// This is still on the jQuery object... for now
+// Want to move this to jQuery.ajax some day
+jQuery.extend({
+
+ // Counter for holding the number of active queries
+ active: 0,
+
+ // Last-Modified header cache for next request
+ lastModified: {},
+ etag: {}
+
+});
+
+/* Handles responses to an ajax request:
+ * - sets all responseXXX fields accordingly
+ * - finds the right dataType (mediates between content-type and expected dataType)
+ * - returns the corresponding response
+ */
+function ajaxHandleResponses( s, jXHR, responses ) {
+
+ var contents = s.contents,
+ dataTypes = s.dataTypes,
+ responseFields = s.responseFields,
+ ct,
+ type,
+ finalDataType,
+ firstDataType;
+
+ // Fill responseXXX fields
+ for( type in responseFields ) {
+ if ( type in responses ) {
+ jXHR[ responseFields[type] ] = responses[ type ];
+ }
+ }
+
+ // Remove auto dataType and get content-type in the process
+ while( dataTypes[ 0 ] === "*" ) {
+ dataTypes.shift();
+ if ( ct === undefined ) {
+ ct = jXHR.getResponseHeader( "content-type" );
+ }
+ }
+
+ // Check if we're dealing with a known content-type
+ if ( ct ) {
+ for ( type in contents ) {
+ if ( contents[ type ] && contents[ type ].test( ct ) ) {
+ dataTypes.unshift( type );
+ break;
+ }
+ }
+ }
+
+ // Check to see if we have a response for the expected dataType
+ if ( dataTypes[ 0 ] in responses ) {
+ finalDataType = dataTypes[ 0 ];
+ } else {
+ // Try convertible dataTypes
+ for ( type in responses ) {
+ if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[0] ] ) {
+ finalDataType = type;
+ break;
+ }
+ if ( !firstDataType ) {
+ firstDataType = type;
+ }
+ }
+ // Or just use first one
+ finalDataType = finalDataType || firstDataType;
+ }
+
+ // If we found a dataType
+ // We add the dataType to the list if needed
+ // and return the corresponding response
+ if ( finalDataType ) {
+ if ( finalDataType !== dataTypes[ 0 ] ) {
+ dataTypes.unshift( finalDataType );
+ }
+ return responses[ finalDataType ];
+ }
+}
+
+// Chain conversions given the request and the original response
+function ajaxConvert( s, response ) {
+
+ // Apply the dataFilter if provided
+ if ( s.dataFilter ) {
+ response = s.dataFilter( response, s.dataType );
+ }
+
+ var dataTypes = s.dataTypes,
+ converters = s.converters,
+ i,
+ length = dataTypes.length,
+ tmp,
+ // Current and previous dataTypes
+ current = dataTypes[ 0 ],
+ prev,
+ // Conversion expression
+ conversion,
+ // Conversion function
+ conv,
+ // Conversion functions (transitive conversion)
+ conv1,
+ conv2;
+
+ // For each dataType in the chain
+ for( i = 1; i < length; i++ ) {
+
+ // Get the dataTypes
+ prev = current;
+ current = dataTypes[ i ];
+
+ // If current is auto dataType, update it to prev
+ if( current === "*" ) {
+ current = prev;
+ // If no auto and dataTypes are actually different
+ } else if ( prev !== "*" && prev !== current ) {
+
+ // Get the converter
+ conversion = prev + " " + current;
+ conv = converters[ conversion ] || converters[ "* " + current ];
+
+ // If there is no direct converter, search transitively
+ if ( !conv ) {
+ conv2 = undefined;
+ for( conv1 in converters ) {
+ tmp = conv1.split( " " );
+ if ( tmp[ 0 ] === prev || tmp[ 0 ] === "*" ) {
+ conv2 = converters[ tmp[1] + " " + current ];
+ if ( conv2 ) {
+ conv1 = converters[ conv1 ];
+ if ( conv1 === true ) {
+ conv = conv2;
+ } else if ( conv2 === true ) {
+ conv = conv1;
+ }
+ break;
+ }
+ }
+ }
+ }
+ // If we found no converter, dispatch an error
+ if ( !( conv || conv2 ) ) {
+ jQuery.error( "No conversion from " + conversion.replace(" "," to ") );
+ }
+ // If found converter is not an equivalence
+ if ( conv !== true ) {
+ // Convert with 1 or 2 converters accordingly
+ response = conv ? conv( response ) : conv2( conv1(response) );
+ }
+ }
+ }
+ return response;
+}
+
+
+
+
+var jsc = jQuery.now(),
+ jsre = /(\=)\?(&|$)|()\?\?()/i;
+
+// Default jsonp settings
+jQuery.ajaxSetup({
+ jsonp: "callback",
+ jsonpCallback: function() {
+ return jQuery.expando + "_" + ( jsc++ );
+ }
+});
+
+// Detect, normalize options and install callbacks for jsonp requests
+jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, dataIsString /* internal */ ) {
+
+ dataIsString = ( typeof s.data === "string" );
+
+ if ( s.dataTypes[ 0 ] === "jsonp" ||
+ originalSettings.jsonpCallback ||
+ originalSettings.jsonp != null ||
+ s.jsonp !== false && ( jsre.test( s.url ) ||
+ dataIsString && jsre.test( s.data ) ) ) {
+
+ var responseContainer,
+ jsonpCallback = s.jsonpCallback =
+ jQuery.isFunction( s.jsonpCallback ) ? s.jsonpCallback() : s.jsonpCallback,
+ previous = window[ jsonpCallback ],
+ url = s.url,
+ data = s.data,
+ replace = "$1" + jsonpCallback + "$2";
+
+ if ( s.jsonp !== false ) {
+ url = url.replace( jsre, replace );
+ if ( s.url === url ) {
+ if ( dataIsString ) {
+ data = data.replace( jsre, replace );
+ }
+ if ( s.data === data ) {
+ // Add callback manually
+ url += (/\?/.test( url ) ? "&" : "?") + s.jsonp + "=" + jsonpCallback;
+ }
+ }
+ }
+
+ s.url = url;
+ s.data = data;
+
+ window[ jsonpCallback ] = function( response ) {
+ responseContainer = [ response ];
+ };
+
+ s.complete = [ function() {
+
+ // Set callback back to previous value
+ window[ jsonpCallback ] = previous;
+
+ // Call if it was a function and we have a response
+ if ( previous) {
+ if ( responseContainer && jQuery.isFunction( previous ) ) {
+ window[ jsonpCallback ] ( responseContainer[ 0 ] );
+ }
+ } else {
+ // else, more memory leak avoidance
+ try{
+ delete window[ jsonpCallback ];
+ } catch( e ) {}
+ }
+
+ }, s.complete ];
+
+ // Use data converter to retrieve json after script execution
+ s.converters["script json"] = function() {
+ if ( ! responseContainer ) {
+ jQuery.error( jsonpCallback + " was not called" );
+ }
+ return responseContainer[ 0 ];
+ };
+
+ // force json dataType
+ s.dataTypes[ 0 ] = "json";
+
+ // Delegate to script
+ return "script";
+ }
+} );
+
+
+
+
+// Install script dataType
+jQuery.ajaxSetup({
+ accepts: {
+ script: "text/javascript, application/javascript"
+ },
+ contents: {
+ script: /javascript/
+ },
+ converters: {
+ "text script": function( text ) {
+ jQuery.globalEval( text );
+ return text;
+ }
+ }
+});
+
+// Handle cache's special case and global
+jQuery.ajaxPrefilter( "script", function( s ) {
+ if ( s.cache === undefined ) {
+ s.cache = false;
+ }
+ if ( s.crossDomain ) {
+ s.type = "GET";
+ s.global = false;
+ }
+} );
+
+// Bind script tag hack transport
+jQuery.ajaxTransport( "script", function(s) {
+
+ // This transport only deals with cross domain requests
+ if ( s.crossDomain ) {
+
+ var script,
+ head = document.getElementsByTagName( "head" )[ 0 ] || document.documentElement;
+
+ return {
+
+ send: function( _, callback ) {
+
+ script = document.createElement( "script" );
+
+ script.async = "async";
+
+ if ( s.scriptCharset ) {
+ script.charset = s.scriptCharset;
+ }
+
+ script.src = s.url;
+
+ // Attach handlers for all browsers
+ script.onload = script.onreadystatechange = function( _, isAbort ) {
+
+ if ( !script.readyState || /loaded|complete/.test( script.readyState ) ) {
+
+ // Handle memory leak in IE
+ script.onload = script.onreadystatechange = null;
+
+ // Remove the script
+ if ( head && script.parentNode ) {
+ head.removeChild( script );
+ }
+
+ // Dereference the script
+ script = undefined;
+
+ // Callback if not abort
+ if ( !isAbort ) {
+ callback( 200, "success" );
+ }
+ }
+ };
+ // Use insertBefore instead of appendChild to circumvent an IE6 bug.
+ // This arises when a base node is used (#2709 and #4378).
+ head.insertBefore( script, head.firstChild );
+ },
+
+ abort: function() {
+ if ( script ) {
+ script.onload( 0, 1 );
+ }
+ }
+ };
+ }
+} );
+
+
+
+
+var // Next active xhr id
+ xhrId = jQuery.now(),
+
+ // active xhrs
+ xhrs = {},
+
+ // #5280: see below
+ xhrUnloadAbortInstalled,
+
+ // XHR used to determine supports properties
+ testXHR;
+
+// Create the request object
+// (This is still attached to ajaxSettings for backward compatibility)
+jQuery.ajaxSettings.xhr = window.ActiveXObject ?
+ /* Microsoft failed to properly
+ * implement the XMLHttpRequest in IE7 (can't request local files),
+ * so we use the ActiveXObject when it is available
+ * Additionally XMLHttpRequest can be disabled in IE7/IE8 so
+ * we need a fallback.
+ */
+ function() {
+ if ( window.location.protocol !== "file:" ) {
+ try {
+ return new window.XMLHttpRequest();
+ } catch( xhrError ) {}
+ }
+
+ try {
+ return new window.ActiveXObject("Microsoft.XMLHTTP");
+ } catch( activeError ) {}
+ } :
+ // For all other browsers, use the standard XMLHttpRequest object
+ function() {
+ return new window.XMLHttpRequest();
+ };
+
+// Test if we can create an xhr object
+try {
+ testXHR = jQuery.ajaxSettings.xhr();
+} catch( xhrCreationException ) {}
+
+//Does this browser support XHR requests?
+jQuery.support.ajax = !!testXHR;
+
+// Does this browser support crossDomain XHR requests
+jQuery.support.cors = testXHR && ( "withCredentials" in testXHR );
+
+// No need for the temporary xhr anymore
+testXHR = undefined;
+
+// Create transport if the browser can provide an xhr
+if ( jQuery.support.ajax ) {
+
+ jQuery.ajaxTransport(function( s ) {
+ // Cross domain only allowed if supported through XMLHttpRequest
+ if ( !s.crossDomain || jQuery.support.cors ) {
+
+ var callback;
+
+ return {
+ send: function( headers, complete ) {
+
+ // #5280: we need to abort on unload or IE will keep connections alive
+ if ( !xhrUnloadAbortInstalled ) {
+
+ xhrUnloadAbortInstalled = 1;
+
+ jQuery(window).bind( "unload", function() {
+
+ // Abort all pending requests
+ jQuery.each( xhrs, function( _, xhr ) {
+ if ( xhr.onreadystatechange ) {
+ xhr.onreadystatechange( 1 );
+ }
+ } );
+
+ } );
+ }
+
+ // Get a new xhr
+ var xhr = s.xhr(),
+ handle;
+
+ // Open the socket
+ // Passing null username, generates a login popup on Opera (#2865)
+ if ( s.username ) {
+ xhr.open( s.type, s.url, s.async, s.username, s.password );
+ } else {
+ xhr.open( s.type, s.url, s.async );
+ }
+
+ // Requested-With header
+ // Not set for crossDomain requests with no content
+ // (see why at http://trac.dojotoolkit.org/ticket/9486)
+ // Won't change header if already provided
+ if ( !( s.crossDomain && !s.hasContent ) && !headers["x-requested-with"] ) {
+ headers[ "x-requested-with" ] = "XMLHttpRequest";
+ }
+
+ // Need an extra try/catch for cross domain requests in Firefox 3
+ try {
+ jQuery.each( headers, function( key, value ) {
+ xhr.setRequestHeader( key, value );
+ } );
+ } catch( _ ) {}
+
+ // Do send the request
+ // This may raise an exception which is actually
+ // handled in jQuery.ajax (so no try/catch here)
+ xhr.send( ( s.hasContent && s.data ) || null );
+
+ // Listener
+ callback = function( _, isAbort ) {
+
+ // Was never called and is aborted or complete
+ if ( callback && ( isAbort || xhr.readyState === 4 ) ) {
+
+ // Only called once
+ callback = 0;
+
+ // Do not keep as active anymore
+ if ( handle ) {
+ xhr.onreadystatechange = jQuery.noop;
+ delete xhrs[ handle ];
+ }
+
+ // If it's an abort
+ if ( isAbort ) {
+ // Abort it manually if needed
+ if ( xhr.readyState !== 4 ) {
+ xhr.abort();
+ }
+ } else {
+ // Get info
+ var status = xhr.status,
+ statusText,
+ responseHeaders = xhr.getAllResponseHeaders(),
+ responses = {},
+ xml = xhr.responseXML;
+
+ // Construct response list
+ if ( xml && xml.documentElement /* #4958 */ ) {
+ responses.xml = xml;
+ }
+ responses.text = xhr.responseText;
+
+ // Firefox throws an exception when accessing
+ // statusText for faulty cross-domain requests
+ try {
+ statusText = xhr.statusText;
+ } catch( e ) {
+ // We normalize with Webkit giving an empty statusText
+ statusText = "";
+ }
+
+ // Filter status for non standard behaviours
+ status =
+ // Opera returns 0 when it should be 304
+ // Webkit returns 0 for failing cross-domain no matter the real status
+ status === 0 ?
+ (
+ // Webkit, Firefox: filter out faulty cross-domain requests
+ !s.crossDomain || statusText ?
+ (
+ // Opera: filter out real aborts #6060
+ responseHeaders ?
+ 304 :
+ 0
+ ) :
+ // We assume 302 but could be anything cross-domain related
+ 302
+ ) :
+ (
+ // IE sometimes returns 1223 when it should be 204 (see #1450)
+ status == 1223 ?
+ 204 :
+ status
+ );
+
+ // Call complete
+ complete( status, statusText, responses, responseHeaders );
+ }
+ }
+ };
+
+ // if we're in sync mode or it's in cache
+ // and has been retrieved directly (IE6 & IE7)
+ // we need to manually fire the callback
+ if ( !s.async || xhr.readyState === 4 ) {
+ callback();
+ } else {
+ // Add to list of active xhrs
+ handle = xhrId++;
+ xhrs[ handle ] = xhr;
+ xhr.onreadystatechange = callback;
+ }
+ },
+
+ abort: function() {
+ if ( callback ) {
+ callback(0,1);
+ }
+ }
+ };
+ }
+ });
+}
+
+
+
+
var elemdisplay = {},
- rfxtypes = /toggle|show|hide/,
- rfxnum = /^([+-]=)?([\d+-.]+)(.*)$/,
+ rfxtypes = /^(?:toggle|show|hide)$/,
+ rfxnum = /^([+\-]=)?([\d+.\-]+)([a-z%]*)$/i,
timerId,
fxAttrs = [
// height animations
@@ -5453,66 +7293,63 @@
];
jQuery.fn.extend({
- show: function( speed, callback ) {
- if ( speed || speed === 0) {
- return this.animate( genFx("show", 3), speed, callback);
+ show: function( speed, easing, callback ) {
+ var elem, display;
+
+ if ( speed || speed === 0 ) {
+ return this.animate( genFx("show", 3), speed, easing, callback);
} else {
- for ( var i = 0, l = this.length; i < l; i++ ) {
- var old = jQuery.data(this[i], "olddisplay");
-
- this[i].style.display = old || "";
-
- if ( jQuery.css(this[i], "display") === "none" ) {
- var nodeName = this[i].nodeName, display;
-
- if ( elemdisplay[ nodeName ] ) {
- display = elemdisplay[ nodeName ];
-
- } else {
- var elem = jQuery("<" + nodeName + " />").appendTo("body");
-
- display = elem.css("display");
-
- if ( display === "none" ) {
- display = "block";
- }
-
- elem.remove();
-
- elemdisplay[ nodeName ] = display;
- }
-
- jQuery.data(this[i], "olddisplay", display);
+ for ( var i = 0, j = this.length; i < j; i++ ) {
+ elem = this[i];
+ display = elem.style.display;
+
+ // Reset the inline display of this element to learn if it is
+ // being hidden by cascaded rules or not
+ if ( !jQuery._data(elem, "olddisplay") && display === "none" ) {
+ display = elem.style.display = "";
+ }
+
+ // Set elements which have been overridden with display: none
+ // in a stylesheet to whatever the default browser style is
+ // for such an element
+ if ( display === "" && jQuery.css( elem, "display" ) === "none" ) {
+ jQuery._data(elem, "olddisplay", defaultDisplay(elem.nodeName));
+ }
+ }
+
+ // Set the display of most of the elements in a second loop
+ // to avoid the constant reflow
+ for ( i = 0; i < j; i++ ) {
+ elem = this[i];
+ display = elem.style.display;
+
+ if ( display === "" || display === "none" ) {
+ elem.style.display = jQuery._data(elem, "olddisplay") || "";
+ }
+ }
+
+ return this;
+ }
+ },
+
+ hide: function( speed, easing, callback ) {
+ if ( speed || speed === 0 ) {
+ return this.animate( genFx("hide", 3), speed, easing, callback);
+
+ } else {
+ for ( var i = 0, j = this.length; i < j; i++ ) {
+ var display = jQuery.css( this[i], "display" );
+
+ if ( display !== "none" && !jQuery._data( this[i], "olddisplay" ) ) {
+ jQuery._data( this[i], "olddisplay", display );
}
}
// Set the display of the elements in a second loop
// to avoid the constant reflow
- for ( var j = 0, k = this.length; j < k; j++ ) {
- this[j].style.display = jQuery.data(this[j], "olddisplay") || "";
- }
-
- return this;
- }
- },
-
- hide: function( speed, callback ) {
- if ( speed || speed === 0 ) {
- return this.animate( genFx("hide", 3), speed, callback);
-
- } else {
- for ( var i = 0, l = this.length; i < l; i++ ) {
- var old = jQuery.data(this[i], "olddisplay");
- if ( !old && old !== "none" ) {
- jQuery.data(this[i], "olddisplay", jQuery.css(this[i], "display"));
- }
- }
-
- // Set the display of the elements in a second loop
- // to avoid the constant reflow
- for ( var j = 0, k = this.length; j < k; j++ ) {
- this[j].style.display = "none";
+ for ( i = 0; i < j; i++ ) {
+ this[i].style.display = "none";
}
return this;
@@ -5522,7 +7359,7 @@
// Save the old toggle function
_toggle: jQuery.fn.toggle,
- toggle: function( fn, fn2 ) {
+ toggle: function( fn, fn2, callback ) {
var bool = typeof fn === "boolean";
if ( jQuery.isFunction(fn) && jQuery.isFunction(fn2) ) {
@@ -5535,15 +7372,15 @@
});
} else {
- this.animate(genFx("toggle", 3), fn, fn2);
+ this.animate(genFx("toggle", 3), fn, fn2, callback);
}
return this;
},
- fadeTo: function( speed, to, callback ) {
+ fadeTo: function( speed, to, easing, callback ) {
return this.filter(":hidden").css("opacity", 0).show().end()
- .animate({opacity: to}, speed, callback);
+ .animate({opacity: to}, speed, easing, callback);
},
animate: function( prop, speed, easing, callback ) {
@@ -5554,12 +7391,16 @@
}
return this[ optall.queue === false ? "each" : "queue" ](function() {
+ // XXX 'this' does not always have a nodeName when running the
+ // test suite
+
var opt = jQuery.extend({}, optall), p,
- hidden = this.nodeType === 1 && jQuery(this).is(":hidden"),
+ isElement = this.nodeType === 1,
+ hidden = isElement && jQuery(this).is(":hidden"),
self = this;
for ( p in prop ) {
- var name = p.replace(rdashAlpha, fcamelCase);
+ var name = jQuery.camelCase( p );
if ( p !== name ) {
prop[ name ] = prop[ p ];
@@ -5571,12 +7412,35 @@
return opt.complete.call(this);
}
- if ( ( p === "height" || p === "width" ) && this.style ) {
- // Store display property
- opt.display = jQuery.css(this, "display");
-
+ if ( isElement && ( p === "height" || p === "width" ) ) {
// Make sure that nothing sneaks out
- opt.overflow = this.style.overflow;
+ // Record all 3 overflow attributes because IE does not
+ // change the overflow attribute when overflowX and
+ // overflowY are set to the same value
+ opt.overflow = [ this.style.overflow, this.style.overflowX, this.style.overflowY ];
+
+ // Set display property to inline-block for height/width
+ // animations on inline elements that are having width/height
+ // animated
+ if ( jQuery.css( this, "display" ) === "inline" &&
+ jQuery.css( this, "float" ) === "none" ) {
+ if ( !jQuery.support.inlineBlockNeedsLayout ) {
+ this.style.display = "inline-block";
+
+ } else {
+ var display = defaultDisplay(this.nodeName);
+
+ // inline-level elements accept inline-block;
+ // block-level elements need to be inline with layout
+ if ( display === "inline" ) {
+ this.style.display = "inline-block";
+
+ } else {
+ this.style.display = "inline";
+ this.style.zoom = 1;
+ }
+ }
+ }
}
if ( jQuery.isArray( prop[p] ) ) {
@@ -5600,7 +7464,7 @@
} else {
var parts = rfxnum.exec(val),
- start = e.cur(true) || 0;
+ start = e.cur() || 0;
if ( parts ) {
var end = parseFloat( parts[2] ),
@@ -5608,9 +7472,9 @@
// We need to compute starting value
if ( unit !== "px" ) {
- self.style[ name ] = (end || 1) + unit;
- start = ((end || 1) / e.cur(true)) * start;
- self.style[ name ] = start + unit;
+ jQuery.style( self, name, (end || 1) + unit);
+ start = ((end || 1) / e.cur()) * start;
+ jQuery.style( self, name, start + unit);
}
// If a +=/-= token was provided, we're doing a relative animation
@@ -5662,22 +7526,33 @@
});
+function genFx( type, num ) {
+ var obj = {};
+
+ jQuery.each( fxAttrs.concat.apply([], fxAttrs.slice(0,num)), function() {
+ obj[ this ] = type;
+ });
+
+ return obj;
+}
+
// Generate shortcuts for custom animations
jQuery.each({
slideDown: genFx("show", 1),
slideUp: genFx("hide", 1),
slideToggle: genFx("toggle", 1),
fadeIn: { opacity: "show" },
- fadeOut: { opacity: "hide" }
+ fadeOut: { opacity: "hide" },
+ fadeToggle: { opacity: "toggle" }
}, function( name, props ) {
- jQuery.fn[ name ] = function( speed, callback ) {
- return this.animate( props, speed, callback );
+ jQuery.fn[ name ] = function( speed, easing, callback ) {
+ return this.animate( props, speed, easing, callback );
};
});
jQuery.extend({
speed: function( speed, easing, fn ) {
- var opt = speed && typeof speed === "object" ? speed : {
+ var opt = speed && typeof speed === "object" ? jQuery.extend({}, speed) : {
complete: fn || !fn && easing ||
jQuery.isFunction( speed ) && speed,
duration: speed,
@@ -5685,7 +7560,7 @@
};
opt.duration = jQuery.fx.off ? 0 : typeof opt.duration === "number" ? opt.duration :
- jQuery.fx.speeds[opt.duration] || jQuery.fx.speeds._default;
+ opt.duration in jQuery.fx.speeds ? jQuery.fx.speeds[opt.duration] : jQuery.fx.speeds._default;
// Queueing
opt.old = opt.complete;
@@ -5732,33 +7607,30 @@
}
(jQuery.fx.step[this.prop] || jQuery.fx.step._default)( this );
-
- // Set display property to block for height/width animations
- if ( ( this.prop === "height" || this.prop === "width" ) && this.elem.style ) {
- this.elem.style.display = "block";
- }
},
// Get the current size
- cur: function( force ) {
+ cur: function() {
if ( this.elem[this.prop] != null && (!this.elem.style || this.elem.style[this.prop] == null) ) {
return this.elem[ this.prop ];
}
- var r = parseFloat(jQuery.css(this.elem, this.prop, force));
- return r && r > -10000 ? r : parseFloat(jQuery.curCSS(this.elem, this.prop)) || 0;
+ var r = parseFloat( jQuery.css( this.elem, this.prop ) );
+ return r || 0;
},
// Start an animation from one number to another
custom: function( from, to, unit ) {
- this.startTime = now();
+ var self = this,
+ fx = jQuery.fx;
+
+ this.startTime = jQuery.now();
this.start = from;
this.end = to;
this.unit = unit || this.unit || "px";
this.now = this.start;
this.pos = this.state = 0;
- var self = this;
function t( gotoEnd ) {
return self.step(gotoEnd);
}
@@ -5766,7 +7638,7 @@
t.elem = this.elem;
if ( t() && jQuery.timers.push(t) && !timerId ) {
- timerId = setInterval(jQuery.fx.tick, 13);
+ timerId = setInterval(fx.tick, fx.interval);
}
},
@@ -5797,7 +7669,7 @@
// Each step of an animation
step: function( gotoEnd ) {
- var t = now(), done = true;
+ var t = jQuery.now(), done = true;
if ( gotoEnd || t >= this.options.duration + this.startTime ) {
this.now = this.end;
@@ -5813,17 +7685,14 @@
}
if ( done ) {
- if ( this.options.display != null ) {
- // Reset the overflow
- this.elem.style.overflow = this.options.overflow;
-
- // Reset the display
- var old = jQuery.data(this.elem, "olddisplay");
- this.elem.style.display = old ? old : this.options.display;
-
- if ( jQuery.css(this.elem, "display") === "none" ) {
- this.elem.style.display = "block";
- }
+ // Reset the overflow
+ if ( this.options.overflow != null && !jQuery.support.shrinkWrapBlocks ) {
+ var elem = this.elem,
+ options = this.options;
+
+ jQuery.each( [ "", "X", "Y" ], function (index, value) {
+ elem.style[ "overflow" + value ] = options.overflow[index];
+ } );
}
// Hide the element if the "hide" operation was done
@@ -5834,7 +7703,7 @@
// Reset the properties, if the item has been hidden or shown
if ( this.options.hide || this.options.show ) {
for ( var p in this.options.curAnim ) {
- jQuery.style(this.elem, p, this.options.orig[p]);
+ jQuery.style( this.elem, p, this.options.orig[p] );
}
}
@@ -5876,22 +7745,24 @@
jQuery.fx.stop();
}
},
-
+
+ interval: 13,
+
stop: function() {
clearInterval( timerId );
timerId = null;
},
-
+
speeds: {
slow: 600,
- fast: 200,
- // Default speed
- _default: 400
+ fast: 200,
+ // Default speed
+ _default: 400
},
step: {
opacity: function( fx ) {
- jQuery.style(fx.elem, "opacity", fx.now);
+ jQuery.style( fx.elem, "opacity", fx.now );
},
_default: function( fx ) {
@@ -5912,20 +7783,34 @@
};
}
-function genFx( type, num ) {
- var obj = {};
-
- jQuery.each( fxAttrs.concat.apply([], fxAttrs.slice(0,num)), function() {
- obj[ this ] = type;
- });
-
- return obj;
+function defaultDisplay( nodeName ) {
+ if ( !elemdisplay[ nodeName ] ) {
+ var elem = jQuery("<" + nodeName + ">").appendTo("body"),
+ display = elem.css("display");
+
+ elem.remove();
+
+ if ( display === "none" || display === "" ) {
+ display = "block";
+ }
+
+ elemdisplay[ nodeName ] = display;
+ }
+
+ return elemdisplay[ nodeName ];
}
+
+
+
+
+var rtable = /^t(?:able|d|h)$/i,
+ rroot = /^(?:body|html)$/i;
+
if ( "getBoundingClientRect" in document.documentElement ) {
jQuery.fn.offset = function( options ) {
- var elem = this[0];
-
- if ( options ) {
+ var elem = this[0], box;
+
+ if ( options ) {
return this.each(function( i ) {
jQuery.offset.setOffset( this, options, i );
});
@@ -5939,10 +7824,26 @@
return jQuery.offset.bodyOffset( elem );
}
- var box = elem.getBoundingClientRect(), doc = elem.ownerDocument, body = doc.body, docElem = doc.documentElement,
- clientTop = docElem.clientTop || body.clientTop || 0, clientLeft = docElem.clientLeft || body.clientLeft || 0,
- top = box.top + (self.pageYOffset || jQuery.support.boxModel && docElem.scrollTop || body.scrollTop ) - clientTop,
- left = box.left + (self.pageXOffset || jQuery.support.boxModel && docElem.scrollLeft || body.scrollLeft) - clientLeft;
+ try {
+ box = elem.getBoundingClientRect();
+ } catch(e) {}
+
+ var doc = elem.ownerDocument,
+ docElem = doc.documentElement;
+
+ // Make sure we're not dealing with a disconnected DOM node
+ if ( !box || !jQuery.contains( docElem, elem ) ) {
+ return box ? { top: box.top, left: box.left } : { top: 0, left: 0 };
+ }
+
+ var body = doc.body,
+ win = getWindow(doc),
+ clientTop = docElem.clientTop || body.clientTop || 0,
+ clientLeft = docElem.clientLeft || body.clientLeft || 0,
+ scrollTop = (win.pageYOffset || jQuery.support.boxModel && docElem.scrollTop || body.scrollTop ),
+ scrollLeft = (win.pageXOffset || jQuery.support.boxModel && docElem.scrollLeft || body.scrollLeft),
+ top = box.top + scrollTop - clientTop,
+ left = box.left + scrollLeft - clientLeft;
return { top: top, left: left };
};
@@ -5951,7 +7852,7 @@
jQuery.fn.offset = function( options ) {
var elem = this[0];
- if ( options ) {
+ if ( options ) {
return this.each(function( i ) {
jQuery.offset.setOffset( this, options, i );
});
@@ -5967,11 +7868,16 @@
jQuery.offset.initialize();
- var offsetParent = elem.offsetParent, prevOffsetParent = elem,
- doc = elem.ownerDocument, computedStyle, docElem = doc.documentElement,
- body = doc.body, defaultView = doc.defaultView,
+ var computedStyle,
+ offsetParent = elem.offsetParent,
+ prevOffsetParent = elem,
+ doc = elem.ownerDocument,
+ docElem = doc.documentElement,
+ body = doc.body,
+ defaultView = doc.defaultView,
prevComputedStyle = defaultView ? defaultView.getComputedStyle( elem, null ) : elem.currentStyle,
- top = elem.offsetTop, left = elem.offsetLeft;
+ top = elem.offsetTop,
+ left = elem.offsetLeft;
while ( (elem = elem.parentNode) && elem !== body && elem !== docElem ) {
if ( jQuery.offset.supportsFixedPosition && prevComputedStyle.position === "fixed" ) {
@@ -5986,12 +7892,13 @@
top += elem.offsetTop;
left += elem.offsetLeft;
- if ( jQuery.offset.doesNotAddBorder && !(jQuery.offset.doesAddBorderForTableAndCells && /^t(able|d|h)$/i.test(elem.nodeName)) ) {
+ if ( jQuery.offset.doesNotAddBorder && !(jQuery.offset.doesAddBorderForTableAndCells && rtable.test(elem.nodeName)) ) {
top += parseFloat( computedStyle.borderTopWidth ) || 0;
left += parseFloat( computedStyle.borderLeftWidth ) || 0;
}
- prevOffsetParent = offsetParent, offsetParent = elem.offsetParent;
+ prevOffsetParent = offsetParent;
+ offsetParent = elem.offsetParent;
}
if ( jQuery.offset.subtractsBorderForOverflowNotVisible && computedStyle.overflow !== "visible" ) {
@@ -6018,7 +7925,7 @@
jQuery.offset = {
initialize: function() {
- var body = document.body, container = document.createElement("div"), innerDiv, checkDiv, table, td, bodyMarginTop = parseFloat( jQuery.curCSS(body, "marginTop", true) ) || 0,
+ var body = document.body, container = document.createElement("div"), innerDiv, checkDiv, table, td, bodyMarginTop = parseFloat( jQuery.css(body, "marginTop") ) || 0,
html = "<div style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;'><div></div></div><table style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;' cellpadding='0' cellspacing='0'><tr><td></td></tr></table>";
jQuery.extend( container.style, { position: "absolute", top: 0, left: 0, margin: 0, border: 0, width: "1px", height: "1px", visibility: "hidden" } );
@@ -6032,12 +7939,16 @@
this.doesNotAddBorder = (checkDiv.offsetTop !== 5);
this.doesAddBorderForTableAndCells = (td.offsetTop === 5);
- checkDiv.style.position = "fixed", checkDiv.style.top = "20px";
+ checkDiv.style.position = "fixed";
+ checkDiv.style.top = "20px";
+
// safari subtracts parent border width here which is 5px
this.supportsFixedPosition = (checkDiv.offsetTop === 20 || checkDiv.offsetTop === 15);
checkDiv.style.position = checkDiv.style.top = "";
- innerDiv.style.overflow = "hidden", innerDiv.style.position = "relative";
+ innerDiv.style.overflow = "hidden";
+ innerDiv.style.position = "relative";
+
this.subtractsBorderForOverflowNotVisible = (checkDiv.offsetTop === -5);
this.doesNotIncludeMarginInBodyOffset = (body.offsetTop !== bodyMarginTop);
@@ -6048,37 +7959,53 @@
},
bodyOffset: function( body ) {
- var top = body.offsetTop, left = body.offsetLeft;
+ var top = body.offsetTop,
+ left = body.offsetLeft;
jQuery.offset.initialize();
if ( jQuery.offset.doesNotIncludeMarginInBodyOffset ) {
- top += parseFloat( jQuery.curCSS(body, "marginTop", true) ) || 0;
- left += parseFloat( jQuery.curCSS(body, "marginLeft", true) ) || 0;
+ top += parseFloat( jQuery.css(body, "marginTop") ) || 0;
+ left += parseFloat( jQuery.css(body, "marginLeft") ) || 0;
}
return { top: top, left: left };
},
-
+
setOffset: function( elem, options, i ) {
+ var position = jQuery.css( elem, "position" );
+
// set position first, in-case top/left are set even on static elem
- if ( /static/.test( jQuery.curCSS( elem, "position" ) ) ) {
+ if ( position === "static" ) {
elem.style.position = "relative";
}
- var curElem = jQuery( elem ),
+
+ var curElem = jQuery( elem ),
curOffset = curElem.offset(),
- curTop = parseInt( jQuery.curCSS( elem, "top", true ), 10 ) || 0,
- curLeft = parseInt( jQuery.curCSS( elem, "left", true ), 10 ) || 0;
+ curCSSTop = jQuery.css( elem, "top" ),
+ curCSSLeft = jQuery.css( elem, "left" ),
+ calculatePosition = (position === "absolute" && jQuery.inArray('auto', [curCSSTop, curCSSLeft]) > -1),
+ props = {}, curPosition = {}, curTop, curLeft;
+
+ // need to be able to calculate position if either top or left is auto and position is absolute
+ if ( calculatePosition ) {
+ curPosition = curElem.position();
+ }
+
+ curTop = calculatePosition ? curPosition.top : parseInt( curCSSTop, 10 ) || 0;
+ curLeft = calculatePosition ? curPosition.left : parseInt( curCSSLeft, 10 ) || 0;
if ( jQuery.isFunction( options ) ) {
options = options.call( elem, i, curOffset );
}
- var props = {
- top: (options.top - curOffset.top) + curTop,
- left: (options.left - curOffset.left) + curLeft
- };
-
+ if (options.top != null) {
+ props.top = (options.top - curOffset.top) + curTop;
+ }
+ if (options.left != null) {
+ props.left = (options.left - curOffset.left) + curLeft;
+ }
+
if ( "using" in options ) {
options.using.call( elem, props );
} else {
@@ -6101,17 +8028,17 @@
// Get correct offsets
offset = this.offset(),
- parentOffset = /^body|html$/i.test(offsetParent[0].nodeName) ? { top: 0, left: 0 } : offsetParent.offset();
+ parentOffset = rroot.test(offsetParent[0].nodeName) ? { top: 0, left: 0 } : offsetParent.offset();
// Subtract element margins
// note: when an element has margin: auto the offsetLeft and marginLeft
// are the same in Safari causing offset.left to incorrectly be 0
- offset.top -= parseFloat( jQuery.curCSS(elem, "marginTop", true) ) || 0;
- offset.left -= parseFloat( jQuery.curCSS(elem, "marginLeft", true) ) || 0;
+ offset.top -= parseFloat( jQuery.css(elem, "marginTop") ) || 0;
+ offset.left -= parseFloat( jQuery.css(elem, "marginLeft") ) || 0;
// Add offsetParent borders
- parentOffset.top += parseFloat( jQuery.curCSS(offsetParent[0], "borderTopWidth", true) ) || 0;
- parentOffset.left += parseFloat( jQuery.curCSS(offsetParent[0], "borderLeftWidth", true) ) || 0;
+ parentOffset.top += parseFloat( jQuery.css(offsetParent[0], "borderTopWidth") ) || 0;
+ parentOffset.left += parseFloat( jQuery.css(offsetParent[0], "borderLeftWidth") ) || 0;
// Subtract the two offsets
return {
@@ -6123,7 +8050,7 @@
offsetParent: function() {
return this.map(function() {
var offsetParent = this.offsetParent || document.body;
- while ( offsetParent && (!/^body|html$/i.test(offsetParent.nodeName) && jQuery.css(offsetParent, "position") === "static") ) {
+ while ( offsetParent && (!rroot.test(offsetParent.nodeName) && jQuery.css(offsetParent, "position") === "static") ) {
offsetParent = offsetParent.offsetParent;
}
return offsetParent;
@@ -6138,7 +8065,7 @@
jQuery.fn[ method ] = function(val) {
var elem = this[0], win;
-
+
if ( !elem ) {
return null;
}
@@ -6171,12 +8098,16 @@
});
function getWindow( elem ) {
- return ("scrollTo" in elem && elem.document) ?
+ return jQuery.isWindow( elem ) ?
elem :
elem.nodeType === 9 ?
elem.defaultView || elem.parentWindow :
false;
}
+
+
+
+
// Create innerHeight, innerWidth, outerHeight and outerWidth methods
jQuery.each([ "Height", "Width" ], function( i, name ) {
@@ -6185,14 +8116,14 @@
// innerHeight and innerWidth
jQuery.fn["inner" + name] = function() {
return this[0] ?
- jQuery.css( this[0], type, false, "padding" ) :
+ parseFloat( jQuery.css( this[0], type, "padding" ) ) :
null;
};
// outerHeight and outerWidth
jQuery.fn["outer" + name] = function( margin ) {
return this[0] ?
- jQuery.css( this[0], type, false, margin ? "margin" : "border" ) :
+ parseFloat( jQuery.css( this[0], type, margin ? "margin" : "border" ) ) :
null;
};
@@ -6202,7 +8133,7 @@
if ( !elem ) {
return size == null ? null : this;
}
-
+
if ( jQuery.isFunction( size ) ) {
return this.each(function( i ) {
var self = jQuery( this );
@@ -6210,31 +8141,36 @@
});
}
- return ("scrollTo" in elem && elem.document) ? // does it walk and quack like a window?
+ if ( jQuery.isWindow( elem ) ) {
// Everyone else use document.documentElement or document.body depending on Quirks vs Standards mode
- elem.document.compatMode === "CSS1Compat" && elem.document.documentElement[ "client" + name ] ||
- elem.document.body[ "client" + name ] :
-
- // Get document width or height
- (elem.nodeType === 9) ? // is it a document
- // Either scroll[Width/Height] or offset[Width/Height], whichever is greater
- Math.max(
- elem.documentElement["client" + name],
- elem.body["scroll" + name], elem.documentElement["scroll" + name],
- elem.body["offset" + name], elem.documentElement["offset" + name]
- ) :
-
- // Get or set width or height on the element
- size === undefined ?
- // Get width or height on the element
- jQuery.css( elem, type ) :
-
- // Set the width or height on the element (default to pixels if value is unitless)
- this.css( type, typeof size === "string" ? size : size + "px" );
+ // 3rd condition allows Nokia support, as it supports the docElem prop but not CSS1Compat
+ var docElemProp = elem.document.documentElement[ "client" + name ];
+ return elem.document.compatMode === "CSS1Compat" && docElemProp ||
+ elem.document.body[ "client" + name ] || docElemProp;
+
+ // Get document width or height
+ } else if ( elem.nodeType === 9 ) {
+ // Either scroll[Width/Height] or offset[Width/Height], whichever is greater
+ return Math.max(
+ elem.documentElement["client" + name],
+ elem.body["scroll" + name], elem.documentElement["scroll" + name],
+ elem.body["offset" + name], elem.documentElement["offset" + name]
+ );
+
+ // Get or set width or height on the element
+ } else if ( size === undefined ) {
+ var orig = jQuery.css( elem, type ),
+ ret = parseFloat( orig );
+
+ return jQuery.isNaN( ret ) ? orig : ret;
+
+ // Set the width or height on the element (default to pixels if value is unitless)
+ } else {
+ return this.css( type, typeof size === "string" ? size : size + "px" );
+ }
};
});
-// Expose jQuery to the global object
-window.jQuery = window.$ = jQuery;
+
})(window);
--- a/static/scripts/packed/jquery.js Sun Feb 06 11:29:04 2011 -0500
+++ b/static/scripts/packed/jquery.js Sun Feb 06 14:42:11 2011 -0500
@@ -1,8 +1,8 @@
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- * Sizzle CSS Selector Engine - v1.0
- * Copyright 2009, The Dojo Foundation
+ * Sizzle CSS Selector Engine
+ * Copyright 2011, The Dojo Foundation
* Released under the MIT, BSD, and GPL Licenses.
* More information: http://sizzlejs.com/
*/
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a4+a5*a6},swing:function(a6,a7,a4,a5){return((-Math.cos(a6*Math.PI)/2)+0.5)*a5+a4}},timers:[],fx:function(a5,a4,a6){this.options=a4;this.elem=a5;this.prop=a6;if(!a4.orig){a4.orig={}}}});a.fx.prototype={update:function(){if(this.options.step){this.options.step.call(this.elem,this.now,this)}(a.fx.step[this.prop]||a.fx.step._default)(this)},cur:function(){if(this.elem[this.prop]!=null&&(!this.elem.style||this.elem.style[this.prop]==null)){return this.elem[this.prop]}var a4=parseFloat(a.css(this.elem,this.prop));return a4||0},custom:function(a9,a8,a7){var a4=this,a6=a.fx;this.startTime=a.now();this.start=a9;this.end=a8;this.unit=a7||this.unit||"px";this.now=this.start;this.pos=this.state=0;function a5(ba){return a4.step(ba)}a5.elem=this.elem;if(a5()&&a.timers.push(a5)&&!aJ){aJ=setInterval(a6.tick,a6.interval)}},show:function(){this.options.orig[this.prop]=a.style(this.elem,this.prop);this.options.show=true;this.custom(this.prop==="width"||this.prop==="height"?1:0,this.cur());a(this.elem).show()},hide:function(){this.options.orig[this.prop]=a.style(this.elem,this.prop);this.options.hide=true;this.custom(this.cur(),0)},step:function(a7){var bc=a.now(),a8=true;if(a7||bc>=this.options.duration+this.startTime){this.now=this.end;this.pos=this.state=1;this.update();this.options.curAnim[this.prop]=true;for(var a9 in this.options.curAnim){if(this.options.curAnim[a9]!==true){a8=false}}if(a8){if(this.options.overflow!=null&&!a.support.shrinkWrapBlocks){var a6=this.elem,bd=this.options;a.each(["","X","Y"],function(be,bf){a6.style["overflow"+bf]=bd.overflow[be]})}if(this.options.hide){a(this.elem).hide()}if(this.options.hide||this.options.show){for(var a4 in this.options.curAnim){a.style(this.elem,a4,this.options.orig[a4])}}this.options.complete.call(this.elem)}return false}else{var a5=bc-this.startTime;this.state=a5/this.options.duration;var ba=this.options.specialEasing&&this.options.specialEasing[this.prop];var bb=this.options.easing||(a.easing.swing?"swing":"linear");this.pos=a.easing[ba||bb](this.state,a5,0,1,this.options.duration);this.now=this.start+((this.end-this.start)*this.pos);this.update()}return true}};a.extend(a.fx,{tick:function(){var a5=a.timers;for(var a4=0;a4<a5.length;a4++){if(!a5[a4]()){a5.splice(a4--,1)}}if(!a5.length){a.fx.stop()}},interval:13,stop:function(){clearInterval(aJ);aJ=null},speeds:{slow:600,fast:200,_default:400},step:{opacity:function(a4){a.style(a4.elem,"opacity",a4.now)},_default:function(a4){if(a4.elem.style&&a4.elem.style[a4.prop]!=null){a4.elem.style[a4.prop]=(a4.prop==="width"||a4.prop==="height"?Math.max(0,a4.now):a4.now)+a4.unit}else{a4.elem[a4.prop]=a4.now}}}});if(a.expr&&a.expr.filters){a.expr.filters.animated=function(a4){return a.grep(a.timers,function(a5){return a4===a5.elem}).length}}function u(a6){if(!J[a6]){var a4=a("<"+a6+">").appendTo("body"),a5=a4.css("display");a4.remove();if(a5==="none"||a5===""){a5="block"}J[a6]=a5}return J[a6]}var M=/^t(?:able|d|h)$/i,S=/^(?:body|html)$/i;if("getBoundingClientRect" in ae.documentElement){a.fn.offset=function(bh){var a7=this[0],ba;if(bh){return this.each(function(bi){a.offset.setOffset(this,bh,bi)})}if(!a7||!a7.ownerDocument){return null}if(a7===a7.ownerDocument.body){return a.offset.bodyOffset(a7)}try{ba=a7.getBoundingClientRect()}catch(be){}var bg=a7.ownerDocument,a5=bg.documentElement;if(!ba||!a.contains(a5,a7)){return ba?{top:ba.top,left:ba.left}:{top:0,left:0}}var bb=bg.body,bc=ap(bg),a9=a5.clientTop||bb.clientTop||0,bd=a5.clientLeft||bb.clientLeft||0,a4=(bc.pageYOffset||a.support.boxModel&&a5.scrollTop||bb.scrollTop),a8=(bc.pageXOffset||a.support.boxModel&&a5.scrollLeft||bb.scrollLeft),bf=ba.top+a4-a9,a6=ba.left+a8-bd;return{top:bf,left:a6}}}else{a.fn.offset=function(bf){var a9=this[0];if(bf){return this.each(function(bg){a.offset.setOffset(this,bf,bg)})}if(!a9||!a9.ownerDocument){return null}if(a9===a9.ownerDocument.body){return a.offset.bodyOffset(a9)}a.offset.initialize();var bc,a6=a9.offsetParent,a5=a9,be=a9.ownerDocument,a7=be.documentElement,ba=be.body,bb=be.defaultView,a4=bb?bb.getComputedStyle(a9,null):a9.currentStyle,bd=a9.offsetTop,a8=a9.offsetLeft;while((a9=a9.parentNode)&&a9!==ba&&a9!==a7){if(a.offset.supportsFixedPosition&&a4.position==="fixed"){break}bc=bb?bb.getComputedStyle(a9,null):a9.currentStyle;bd-=a9.scrollTop;a8-=a9.scrollLeft;if(a9===a6){bd+=a9.offsetTop;a8+=a9.offsetLeft;if(a.offset.doesNotAddBorder&&!(a.offset.doesAddBorderForTableAndCells&&M.test(a9.nodeName))){bd+=parseFloat(bc.borderTopWidth)||0;a8+=parseFloat(bc.borderLeftWidth)||0}a5=a6;a6=a9.offsetParent}if(a.offset.subtractsBorderForOverflowNotVisible&&bc.overflow!=="visible"){bd+=parseFloat(bc.borderTopWidth)||0;a8+=parseFloat(bc.borderLeftWidth)||0}a4=bc}if(a4.position==="relative"||a4.position==="static"){bd+=ba.offsetTop;a8+=ba.offsetLeft}if(a.offset.supportsFixedPosition&&a4.position==="fixed"){bd+=Math.max(a7.scrollTop,ba.scrollTop);a8+=Math.max(a7.scrollLeft,ba.scrollLeft)}return{top:bd,left:a8}}}a.offset={initialize:function(){var a4=ae.body,a5=ae.createElement("div"),a8,ba,a9,bb,a6=parseFloat(a.css(a4,"marginTop"))||0,a7="<div style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;'><div></div></div><table style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;' cellpadding='0' cellspacing='0'><tr><td></td></tr></table>";a.extend(a5.style,{position:"absolute",top:0,left:0,margin:0,border:0,width:"1px",height:"1px",visibility:"hidden"});a5.innerHTML=a7;a4.insertBefore(a5,a4.firstChild);a8=a5.firstChild;ba=a8.firstChild;bb=a8.nextSibling.firstChild.firstChild;this.doesNotAddBorder=(ba.offsetTop!==5);this.doesAddBorderForTableAndCells=(bb.offsetTop===5);ba.style.position="fixed";ba.style.top="20px";this.supportsFixedPosition=(ba.offsetTop===20||ba.offsetTop===15);ba.style.position=ba.style.top="";a8.style.overflow="hidden";a8.style.position="relative";this.subtractsBorderForOverflowNotVisible=(ba.offsetTop===-5);this.doesNotIncludeMarginInBodyOffset=(a4.offsetTop!==a6);a4.removeChild(a5);a4=a5=a8=ba=a9=bb=null;a.offset.initialize=a.noop},bodyOffset:function(a4){var a6=a4.offsetTop,a5=a4.offsetLeft;a.offset.initialize();if(a.offset.doesNotIncludeMarginInBodyOffset){a6+=parseFloat(a.css(a4,"marginTop"))||0;a5+=parseFloat(a.css(a4,"marginLeft"))||0}return{top:a6,left:a5}},setOffset:function(a7,bg,ba){var bb=a.css(a7,"position");if(bb==="static"){a7.style.position="relative"}var a9=a(a7),a5=a9.offset(),a4=a.css(a7,"top"),be=a.css(a7,"left"),bf=(bb==="absolute"&&a.inArray("auto",[a4,be])>-1),bd={},bc={},a6,a8;if(bf){bc=a9.position()}a6=bf?bc.top:parseInt(a4,10)||0;a8=bf?bc.left:parseInt(be,10)||0;if(a.isFunction(bg)){bg=bg.call(a7,ba,a5)}if(bg.top!=null){bd.top=(bg.top-a5.top)+a6}if(bg.left!=null){bd.left=(bg.left-a5.left)+a8}if("using" in bg){bg.using.call(a7,bd)}else{a9.css(bd)}}};a.fn.extend({position:function(){if(!this[0]){return null}var a6=this[0],a5=this.offsetParent(),a7=this.offset(),a4=S.test(a5[0].nodeName)?{top:0,left:0}:a5.offset();a7.top-=parseFloat(a.css(a6,"marginTop"))||0;a7.left-=parseFloat(a.css(a6,"marginLeft"))||0;a4.top+=parseFloat(a.css(a5[0],"borderTopWidth"))||0;a4.left+=parseFloat(a.css(a5[0],"borderLeftWidth"))||0;return{top:a7.top-a4.top,left:a7.left-a4.left}},offsetParent:function(){return this.map(function(){var a4=this.offsetParent||ae.body;while(a4&&(!S.test(a4.nodeName)&&a.css(a4,"position")==="static")){a4=a4.offsetParent}return a4})}});a.each(["Left","Top"],function(a5,a4){var a6="scroll"+a4;a.fn[a6]=function(a9){var a7=this[0],a8;if(!a7){return null}if(a9!==E){return this.each(function(){a8=ap(this);if(a8){a8.scrollTo(!a5?a9:a(a8).scrollLeft(),a5?a9:a(a8).scrollTop())}else{this[a6]=a9}})}else{a8=ap(a7);return a8?("pageXOffset" in a8)?a8[a5?"pageYOffset":"pageXOffset"]:a.support.boxModel&&a8.document.documentElement[a6]||a8.document.body[a6]:a7[a6]}}});function ap(a4){return a.isWindow(a4)?a4:a4.nodeType===9?a4.defaultView||a4.parentWindow:false}a.each(["Height","Width"],function(a5,a4){var a6=a4.toLowerCase();a.fn["inner"+a4]=function(){return this[0]?parseFloat(a.css(this[0],a6,"padding")):null};a.fn["outer"+a4]=function(a7){return this[0]?parseFloat(a.css(this[0],a6,a7?"margin":"border")):null};a.fn[a6]=function(a8){var a9=this[0];if(!a9){return a8==null?null:this}if(a.isFunction(a8)){return this.each(function(bd){var bc=a(this);bc[a6](a8.call(this,bd,bc[a6]()))})}if(a.isWindow(a9)){var ba=a9.document.documentElement["client"+a4];return a9.document.compatMode==="CSS1Compat"&&ba||a9.document.body["client"+a4]||ba}else{if(a9.nodeType===9){return Math.max(a9.documentElement["client"+a4],a9.body["scroll"+a4],a9.documentElement["scroll"+a4],a9.body["offset"+a4],a9.documentElement["offset"+a4])}else{if(a8===E){var bb=a.css(a9,a6),a7=parseFloat(bb);return a.isNaN(a7)?bb:a7}else{return this.css(a6,typeof a8==="string"?a8:a8+"px")}}}}})})(window);
\ No newline at end of file
--- a/templates/workflow/editor.mako Sun Feb 06 11:29:04 2011 -0500
+++ b/templates/workflow/editor.mako Sun Feb 06 14:42:11 2011 -0500
@@ -309,7 +309,7 @@
}
- $.jStore.engineReady(function() {
+ $.jStore.ready(function() {
// On load, set the size to the pref stored in local storage if it exists
overview_size = $.jStore.store("overview-size");
if (overview_size !== undefined) {
http://bitbucket.org/galaxy/galaxy-central/changeset/c90c5ffad852/
changeset: r5013:c90c5ffad852
user: james_taylor
date: 2011-02-06 20:44:14
summary: trackster: use new jquery defereds to ensure draw happens after predraw_init in line tracks, eliminates failure to draw before scrolling
affected #: 1 file (102 bytes)
--- a/static/scripts/trackster.js Sun Feb 06 14:42:11 2011 -0500
+++ b/static/scripts/trackster.js Sun Feb 06 14:44:14 2011 -0500
@@ -1018,8 +1018,8 @@
track.content_div.text("");
track.content_div.css( "height", track.height_px + "px" );
track.enabled = true;
- track.predraw_init();
- track.draw();
+ // predraw_init may be asynchronous, wait for it and then draw
+ $.when( track.predraw_init() ).done( function() { track.draw() } );
}
}
});
@@ -1803,7 +1803,7 @@
track_id = track.view.tracks.indexOf(track);
track.vertical_range = undefined;
- $.getJSON( track.data_url, { stats: true, chrom: track.view.chrom, low: null, high: null,
+ return $.getJSON( track.data_url, { stats: true, chrom: track.view.chrom, low: null, high: null,
hda_ldda: track.hda_ldda, dataset_id: track.dataset_id }, function(result) {
track.container_div.addClass( "line-track" );
var data = result.data;
http://bitbucket.org/galaxy/galaxy-central/changeset/8b71270b7876/
changeset: r5014:8b71270b7876
user: james_taylor
date: 2011-02-07 17:38:34
summary: merge
affected #: 1 file (3.6 KB)
--- a/static/scripts/packed/trackster.js Sun Feb 06 14:44:14 2011 -0500
+++ b/static/scripts/packed/trackster.js Mon Feb 07 11:38:34 2011 -0500
@@ -1,1 +1,1 @@
-CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(d,h){if(!h.hidden){var i="param_"+d;var g=$("<div class='form-row' />").appendTo(a);g.append($("<label />").attr("for",i).text(h.label+":"));if(h.type=="bool"){g.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",b.values[h.key]))}else{if(h.type=="color"){var f=b.values[h.key];var c=$("<input />").attr("id",i).attr("name",i).val(f);var e=$("<div class='tipsy tipsy-west' style='position: absolute;' />").append($("<div class='tipsy-inner' />").farbtastic({width:100,height:100,callback:c,color:f})).hide();$("<div />").append(c).append(e).appendTo(g).hover(function(){e.css({left:$(this).position().left+$(c).width()-20,top:$(this).position().top-50}).show()},function(){e.hide()})}else{g.append($("<input />").attr("id",i).attr("name",i).val(b.values[h.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k);if(l){var m=$("<div class='track-tile'>").prepend(l);if(l.hasClass(FILTERABLE_CLASS)){m.addClass(FILTERABLE_CLASS)}l=m}}if(l){d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(G.data.length&&this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
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Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(d,h){if(!h.hidden){var i="param_"+d;var g=$("<div class='form-row' />").appendTo(a);g.append($("<label />").attr("for",i).text(h.label+":"));if(h.type=="bool"){g.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",b.values[h.key]))}else{if(h.type=="color"){var f=b.values[h.key];var c=$("<input />").attr("id",i).attr("name",i).val(f);var e=$("<div class='tipsy tipsy-north' style='position: absolute;' />").append($("<div class='tipsy-inner' />").farbtastic({width:100,height:100,callback:c,color:f})).hide();$("<div />").append(c).append(e).appendTo(g).bind("click",function(j){e.css({left:$(this).position().left+($(c).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){e.hide();$(document).unbind("click.color-picker")});j.stopPropagation()})}else{g.append($("<input />").attr("id",i).attr("name",i).val(b.values[h.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k);if(l){var m=$("<div class='track-tile'>").prepend(l);if(l.hasClass(FILTERABLE_CLASS)){m.addClass(FILTERABLE_CLASS)}l=m}}if(l){d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=5;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?SQUISH_HEIGHT:DENSE_HEIGHT))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ag,n,r,aw){var M=n*DENSITY*ag,al=(n+1)*DENSITY*ag,L=al-M;var H=this.data_cache.get_data(M,al,this.mode);if(H===undefined||H==="pending"||(this.mode!=="Auto"&&H.dataset_type==="summary_tree")){this.data_queue[[M,al]]=true;this.get_data(M,al);return}var a=Math.ceil(L*aw),ai=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ae=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(H.extra_info==="no_detail")),X=this.left_offset,av,C,ax;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(H.dataset_type==="summary_tree"){C=this.summary_draw_height}else{if(q==="Dense"){C=v;ax=10}else{ax=(ae?this.vertical_nodetail_px:this.vertical_detail_px);var w=(aw<0.0001?1/this.view.zoom_res:aw);C=this.incremental_slots(w,H.data,ae,q)*ax+v;av=this.inc_slots[w]}}p.get(0).width=a+X;p.get(0).height=C;r.parent().css("height",Math.max(this.height_px,C)+"px");var I=p.get(0).getContext("2d");I.fillStyle=h;I.font=this.default_font;I.textAlign="right";this.container_div.find(".yaxislabel").remove();if(H.dataset_type=="summary_tree"){var Z=H.data,K=H.max,b=Math.ceil(H.delta*aw);var o=$("<div />").addClass("yaxislabel");o.text(K);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var ap=0,G=Z.length;ap<G;ap++){var ab=Math.floor((Z[ap][0]-M)*aw);var aa=Z[ap][1];if(!aa){continue}var am=aa/K*this.summary_draw_height;I.fillStyle="black";I.fillRect(ab+X,this.summary_draw_height-am,b,am);if(this.prefs.show_counts&&I.measureText(aa).width<b){I.fillStyle="#bbb";I.textAlign="center";I.fillText(aa,ab+X+(b/2),this.summary_draw_height-5)}}return p}if(H.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});I.fillStyle="red";I.textAlign="left";I.fillText(H.message,100+X,ax);return p}for(var at=0;at<this.filters.length;at++){if(H.data.length&&this.filters[at].applies_to(H.data[0])){p.addClass(FILTERABLE_CLASS);break}}var au=H.data;var ao=0;for(var ap=0,G=au.length;ap<G;ap++){var T=au[ap],Q=T[0],ar=T[1],ad=T[2],N=T[3];if(this.mode!="Dense"&&av[Q]===undefined){continue}var ac=false;var V;for(var at=0;at<this.filters.length;at++){V=this.filters[at];V.update_attrs(T);if(!V.keep(T)){ac=true;break}}if(ac){continue}if(ar<=al&&ad>=M){if(H.dataset_type=="interval_index"){ad-=1}var af=Math.floor(Math.max(0,(ar-M)*aw)),J=Math.ceil(Math.min(a,Math.max(0,(ad-M)*aw))),Y=(q==="Dense"?1:(1+av[Q]))*ax;var F,aj,O=null,ay=null;if(H.dataset_type==="bai"){I.fillStyle=h;if(T[5] instanceof Array){var D=Math.floor(Math.max(0,(T[4][0]-M)*aw)),P=Math.ceil(Math.min(a,Math.max(0,(T[4][1]-M)*aw))),B=Math.floor(Math.max(0,(T[5][0]-M)*aw)),u=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-M)*aw)));if(T[4][1]>=M&&T[4][0]<=al&&T[4][2]){this.rect_or_text(I,aw,M,al,T[4][0],T[4][2],T[4][3],Y)}if(T[5][1]>=M&&T[5][0]<=al&&T[5][2]){this.rect_or_text(I,aw,M,al,T[5][0],T[5][2],T[5][3],Y)}if(B>P){I.fillStyle=CONNECTOR_COLOR;I.dashedLine(P+X,Y+5,X+B,Y+5)}}else{I.fillStyle=h;this.rect_or_text(I,aw,M,al,ar,T[4],T[5],Y)}if(q!=="Dense"&&!ae&&ar>M){I.fillStyle=this.prefs.label_color;if(n===0&&af-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+X,Y+8)}else{I.textAlign="right";I.fillText(N,af-2+X,Y+8)}I.fillStyle=h}}else{if(H.dataset_type==="interval_index"){if(q=="Auto"){if(T.length<=4){q="Squish"}else{q="Pack"}}if(q=="Dense"){I.fillStyle=h;I.fillRect(af+X,Y+5,J-af,DENSE_HEIGHT)}else{if(T.length<=4){I.fillStyle=h;I.fillRect(af+X,Y+5,J-af,1)}else{var E=T[5],W=T[6],ah=T[7],g=T[8];if(W&&ah){O=Math.floor(Math.max(0,(W-M)*aw));ay=Math.ceil(Math.min(a,Math.max(0,(ah-M)*aw)))}var aq,R;if(q=="Squish"){aq=1;R=SQUISH_HEIGHT}else{aq=5;R=PACK_HEIGHT}if(!g){if(T.strand){if(T.strand=="+"){I.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){I.fillStyle=LEFT_STRAND_INV}}}else{I.fillStyle=CONNECTOR_COLOR}I.fillRect(af+X,Y+(R-aq)/2+1,J-af,R)}else{var A,S;if(q=="Squish"){I.fillStyle=CONNECTOR_COLOR;A=Y+Math.floor(SQUISH_HEIGHT/2)+1;S=1}else{if(E){var A=Y;var S=R;if(E=="+"){I.fillStyle=RIGHT_STRAND}else{if(E=="-"){I.fillStyle=LEFT_STRAND}}}else{I.fillStyle=CONNECTOR_COLOR;A+=(SQUISH_HEIGHT/2)+1;S=1}}I.fillRect(af+X,A,J-af,S);for(var an=0,e=g.length;an<e;an++){var t=g[an],d=Math.floor(Math.max(0,(t[0]-M)*aw)),U=Math.ceil(Math.min(a,Math.max((t[1]-M)*aw)));if(d>U){continue}I.fillStyle=h;I.fillRect(d+X,Y+(R-aq)/2+1,U-d,aq);if(O!==undefined&&!(d>ay||U<O)){var ak=Math.max(d,O),z=Math.min(U,ay-1);I.fillRect(ak+X,Y+1,z-ak,R)}}}if(q=="Pack"&&ar>M){I.fillStyle=ai;if(n===0&&af-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+X,Y+8)}else{I.textAlign="right";I.fillText(N,af-2+X,Y+8)}I.fillStyle=h}}}}else{if(H.dataset_type==="vcf"){if(ae){I.fillStyle=h;I.fillRect(af+X,Y+5,J-af,1)}else{var s=T[4],m=T[5],c=T[6];F=9;aj=1;I.fillRect(af+X,Y,J-af,F);if(q!=="Dense"&&N!==undefined&&ar>M){I.fillStyle=ai;if(n===0&&af-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+X,Y+8)}else{I.textAlign="right";I.fillText(N,af-2+X,Y+8)}I.fillStyle=h}var l=s+" / "+m;if(ar>M&&I.measureText(l).width<(J-af)){I.fillStyle="white";I.textAlign="center";I.fillText(l,X+af+(J-af)/2,Y+8);I.fillStyle=h}}}}}ao++}}return p}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
--- a/static/scripts/trackster.js Sun Feb 06 14:44:14 2011 -0500
+++ b/static/scripts/trackster.js Mon Feb 07 11:38:34 2011 -0500
@@ -57,6 +57,12 @@
* Init constants & functions used throughout trackster.
*/
var
+ // Drawing constants.
+ DENSE_HEIGHT = 1,
+ SQUISH_HEIGHT = 3,
+ PACK_HEIGHT = 9,
+
+ // Other constants.
DENSITY = 200,
FEATURE_LEVELS = 10,
MAX_FEATURE_DEPTH = 100,
@@ -209,8 +215,7 @@
},
// Generate key for cache.
gen_key: function(low, high, mode) {
- // TODO: use mode to generate key?
- var key = low + "_" + high;
+ var key = low + "_" + high + "_" + mode;
/*
if (no_detail) {
key += "_" + no_detail
@@ -1980,7 +1985,7 @@
this.show_labels_scale = 0.001;
this.showing_details = false;
this.vertical_detail_px = 10;
- this.vertical_nodetail_px = 3;
+ this.vertical_nodetail_px = 5;
this.summary_draw_height = 30;
this.default_font = "9px Monaco, Lucida Console, monospace";
this.inc_slots = {};
@@ -2223,7 +2228,10 @@
} else {
ctx.fillStyle = this.prefs.block_color;
// TODO: This is a pretty hack-ish way to fill rectangle based on mode.
- ctx.fillRect(s_start + this.left_offset, y_center + (this.mode != "Dense" ? 4 : 5), s_end - s_start, (this.mode != "Dense" ? 3 : 1) );
+ ctx.fillRect(s_start + this.left_offset,
+ y_center + (this.mode != "Dense" ? 4 : 5),
+ s_end - s_start,
+ (this.mode != "Dense" ? SQUISH_HEIGHT : DENSE_HEIGHT) );
}
seq_offset += cig_len;
break;
@@ -2263,8 +2271,11 @@
break;
}
}*/
+
+ //
+ // Get tile data; if data not available, issue get_data request and return.
+ //
var result = this.data_cache.get_data(tile_low, tile_high, this.mode);
-
if (result === undefined || result === "pending" ||
(this.mode !== "Auto" && result.dataset_type === "summary_tree")) {
this.data_queue[ [tile_low, tile_high] ] = true;
@@ -2272,6 +2283,9 @@
return;
}
+ //
+ // Create/set/compute some useful vars.
+ //
var width = Math.ceil( tile_span * w_scale ),
label_color = this.prefs.label_color,
block_color = this.prefs.block_color,
@@ -2297,7 +2311,7 @@
required_height = this.incremental_slots( inc_scale, result.data, no_detail, mode ) * y_scale + min_height;
slots = this.inc_slots[inc_scale];
}
-
+
canvas.get(0).width = width + left_offset;
canvas.get(0).height = required_height;
parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px");
@@ -2398,6 +2412,11 @@
}
if (feature_start <= tile_high && feature_end >= tile_low) {
+ // -1 b/c intervals are half-open.
+ if (result.dataset_type == "interval_index") {
+ feature_end -= 1;
+ }
+
// All features need a start, end, and vertical center.
var f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
@@ -2448,12 +2467,37 @@
}
// Interval index drawing.
else if (result.dataset_type === "interval_index") {
- // console.log(feature_uid, feature_start, feature_end, f_start, f_end, y_center);
- if (no_detail) {
+ //
+ // There are really four modes for interval indices:
+ // dense, no_detail, squish, pack.
+ //
+
+ // TODO: move this code out of loop.
+ // Set mode in Auto
+ if (mode == "Auto") {
+ // Never use dense when in auto mode.
+ // TODO: decide when to use squish and when to use pack.
+ if (feature.length <= 4) {
+ mode = "Squish";
+ }
+ else {
+ mode = "Pack";
+ }
+ }
+
+ // Dense mode displays the same for all data.
+ if (mode == "Dense") {
ctx.fillStyle = block_color;
+ ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, DENSE_HEIGHT);
+ }
+ // Mode is either Squish or Pack:
+ else if (feature.length <= 4) {
+ // No details for feature, so only one way to display.
+ ctx.fillStyle = block_color;
+ // TODO: what should width be here?
ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, 1);
} else {
- // Showing labels, blocks, details.
+ // Feature has details.
var feature_strand = feature[5],
feature_ts = feature[6],
feature_te = feature[7],
@@ -2463,8 +2507,92 @@
thick_start = Math.floor( Math.max(0, (feature_ts - tile_low) * w_scale) );
thick_end = Math.ceil( Math.min(width, Math.max(0, (feature_te - tile_low) * w_scale)) );
}
- if (mode !== "Dense" && feature_name !== undefined && feature_start > tile_low) {
- // Draw label
+
+ // Set vars that depend on mode.
+ var thin_height, thick_height;
+ if (mode == "Squish") {
+ thin_height = 1;
+ thick_height = SQUISH_HEIGHT;
+ }
+ else { // mode == "Pack"
+ thin_height = 5;
+ thick_height = PACK_HEIGHT;
+ }
+
+ // Draw feature/feature blocks + connectors.
+ if (!feature_blocks) {
+ // If there are no blocks, treat the feature as one big exon.
+ if ( feature.strand ) {
+ if (feature.strand == "+") {
+ ctx.fillStyle = RIGHT_STRAND_INV;
+ } else if (feature.strand == "-") {
+ ctx.fillStyle = LEFT_STRAND_INV;
+ }
+ }
+ else { // No strand.
+ ctx.fillStyle = CONNECTOR_COLOR;
+ }
+ ctx.fillRect(f_start + left_offset, y_center + (thick_height-thin_height)/2 + 1,
+ f_end - f_start, thick_height);
+ }
+ else { // There are feature blocks and mode is either Squish or Pack.
+ //
+ // Approach: (a) draw whole feature as connector/intron and (b) draw blocks as
+ // needed. This ensures that whole feature, regardless of whether it starts with
+ // a block, is visible.
+ //
+
+ // Draw whole feature as connector/intron.
+ var cur_y_center, cur_height;
+ if (mode == "Squish") {
+ ctx.fillStyle = CONNECTOR_COLOR;
+ cur_y_center = y_center + Math.floor(SQUISH_HEIGHT/2) + 1;
+ cur_height = 1;
+ }
+ else { // mode == "Pack"
+ if (feature_strand) {
+ var cur_y_center = y_center;
+ var cur_height = thick_height;
+ if (feature_strand == "+") {
+ ctx.fillStyle = RIGHT_STRAND;
+ } else if (feature_strand == "-") {
+ ctx.fillStyle = LEFT_STRAND;
+ }
+ }
+ else {
+ ctx.fillStyle = CONNECTOR_COLOR;
+ cur_y_center += (SQUISH_HEIGHT/2) + 1;
+ cur_height = 1;
+ }
+ }
+ ctx.fillRect(f_start + left_offset, cur_y_center, f_end - f_start, cur_height);
+
+ for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
+ var block = feature_blocks[k],
+ block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ),
+ block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) );
+
+ // Skip drawing if block not on tile.
+ if (block_start > block_end) { continue; }
+
+ // Draw thin block.
+ ctx.fillStyle = block_color;
+ ctx.fillRect(block_start + left_offset, y_center + (thick_height-thin_height)/2 + 1,
+ block_end - block_start, thin_height);
+
+ // If block intersects with thick region, draw block as thick.
+ if (thick_start !== undefined && !(block_start > thick_end || block_end < thick_start) ) {
+ var block_thick_start = Math.max(block_start, thick_start),
+ // -1 b/c intervals are half-open.
+ block_thick_end = Math.min(block_end, thick_end-1);
+ ctx.fillRect(block_thick_start + left_offset, y_center + 1,
+ block_thick_end - block_thick_start, thick_height);
+ }
+ }
+ }
+
+ // Draw label for Pack mode.
+ if (mode == "Pack" && feature_start > tile_low) {
ctx.fillStyle = label_color;
if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) {
ctx.textAlign = "left";
@@ -2475,53 +2603,6 @@
}
ctx.fillStyle = block_color;
}
- if (feature_blocks) {
- // Draw introns
- if (feature_strand) {
- if (feature_strand == "+") {
- ctx.fillStyle = RIGHT_STRAND;
- } else if (feature_strand == "-") {
- ctx.fillStyle = LEFT_STRAND;
- }
- ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, 10);
- ctx.fillStyle = block_color;
- }
-
- for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
- var block = feature_blocks[k],
- block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ),
- block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) );
- if (block_start > block_end) { continue; }
- // Draw the block
- thickness = 5;
- y_start = 3;
- ctx.fillRect(block_start + left_offset, y_center + y_start, block_end - block_start, thickness);
-
- // Draw thick regions: check if block intersects with thick region
- if (thick_start !== undefined && !(block_start > thick_end || block_end < thick_start) ) {
- thickness = 9;
- y_start = 1;
- var block_thick_start = Math.max(block_start, thick_start),
- block_thick_end = Math.min(block_end, thick_end);
- ctx.fillRect(block_thick_start + left_offset, y_center + y_start, block_thick_end - block_thick_start, thickness);
-
- }
- }
- } else {
- // If there are no blocks, we treat the feature as one big exon
- thickness = 9;
- y_start = 1;
- ctx.fillRect(f_start + left_offset, y_center + y_start, f_end - f_start, thickness);
- if ( feature.strand ) {
- if (feature.strand == "+") {
- ctx.fillStyle = RIGHT_STRAND_INV;
- } else if (feature.strand == "-") {
- ctx.fillStyle = LEFT_STRAND_INV;
- }
- ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, 10);
- ctx.fillStyle = block_color;
- }
- }
}
} else if (result.dataset_type === 'vcf') {
// VCF track.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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07 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/782b7629e13a/
changeset: r5010:782b7629e13a
user: jgoecks
date: 2011-02-07 15:23:57
summary: Trackster: refactor interval index drawing. Modified interval index squish mode to display blocks and treat intervals as half-open. Also use constants to standardize the drawing height of different modes across tracks.
affected #: 2 files (4.2 KB)
--- a/static/scripts/packed/trackster.js Sun Feb 06 10:27:53 2011 -0500
+++ b/static/scripts/packed/trackster.js Mon Feb 07 09:23:57 2011 -0500
@@ -1,1 +1,1 @@
-CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(d,h){if(!h.hidden){var i="param_"+d;var g=$("<div class='form-row' />").appendTo(a);g.append($("<label />").attr("for",i).text(h.label+":"));if(h.type=="bool"){g.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",b.values[h.key]))}else{if(h.type=="color"){var f=b.values[h.key];var c=$("<input />").attr("id",i).attr("name",i).val(f);var e=$("<div class='tipsy tipsy-west' style='position: absolute;' />").append($("<div class='tipsy-inner' />").farbtastic({width:100,height:100,callback:c,color:f})).hide();$("<div />").append(c).append(e).appendTo(g).hover(function(){e.css({left:$(this).position().left+$(c).width()-20,top:$(this).position().top-50}).show()},function(){e.hide()})}else{g.append($("<input />").attr("id",i).attr("name",i).val(b.values[h.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k);if(l){var m=$("<div class='track-tile'>").prepend(l);if(l.hasClass(FILTERABLE_CLASS)){m.addClass(FILTERABLE_CLASS)}l=m}}if(l){d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(G.data.length&&this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
+CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSE_HEIGHT=1,SQUISH_HEIGHT=3,PACK_HEIGHT=9,DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(d,h){if(!h.hidden){var i="param_"+d;var g=$("<div class='form-row' />").appendTo(a);g.append($("<label />").attr("for",i).text(h.label+":"));if(h.type=="bool"){g.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",b.values[h.key]))}else{if(h.type=="color"){var f=b.values[h.key];var c=$("<input />").attr("id",i).attr("name",i).val(f);var e=$("<div class='tipsy tipsy-north' style='position: absolute;' />").append($("<div class='tipsy-inner' />").farbtastic({width:100,height:100,callback:c,color:f})).hide();$("<div />").append(c).append(e).appendTo(g).bind("click",function(j){e.css({left:$(this).position().left+($(c).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){e.hide();$(document).unbind("click.color-picker")});j.stopPropagation()})}else{g.append($("<input />").attr("id",i).attr("name",i).val(b.values[h.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k);if(l){var m=$("<div class='track-tile'>").prepend(l);if(l.hasClass(FILTERABLE_CLASS)){m.addClass(FILTERABLE_CLASS)}l=m}}if(l){d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=5;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?SQUISH_HEIGHT:DENSE_HEIGHT))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ag,n,r,aw){var M=n*DENSITY*ag,al=(n+1)*DENSITY*ag,L=al-M;var H=this.data_cache.get_data(M,al,this.mode);if(H===undefined||H==="pending"||(this.mode!=="Auto"&&H.dataset_type==="summary_tree")){this.data_queue[[M,al]]=true;this.get_data(M,al);return}var a=Math.ceil(L*aw),ai=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ae=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(H.extra_info==="no_detail")),X=this.left_offset,av,C,ax;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(H.dataset_type==="summary_tree"){C=this.summary_draw_height}else{if(q==="Dense"){C=v;ax=10}else{ax=(ae?this.vertical_nodetail_px:this.vertical_detail_px);var w=(aw<0.0001?1/this.view.zoom_res:aw);C=this.incremental_slots(w,H.data,ae,q)*ax+v;av=this.inc_slots[w]}}p.get(0).width=a+X;p.get(0).height=C;r.parent().css("height",Math.max(this.height_px,C)+"px");var I=p.get(0).getContext("2d");I.fillStyle=h;I.font=this.default_font;I.textAlign="right";this.container_div.find(".yaxislabel").remove();if(H.dataset_type=="summary_tree"){var Z=H.data,K=H.max,b=Math.ceil(H.delta*aw);var o=$("<div />").addClass("yaxislabel");o.text(K);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var ap=0,G=Z.length;ap<G;ap++){var ab=Math.floor((Z[ap][0]-M)*aw);var aa=Z[ap][1];if(!aa){continue}var am=aa/K*this.summary_draw_height;I.fillStyle="black";I.fillRect(ab+X,this.summary_draw_height-am,b,am);if(this.prefs.show_counts&&I.measureText(aa).width<b){I.fillStyle="#bbb";I.textAlign="center";I.fillText(aa,ab+X+(b/2),this.summary_draw_height-5)}}return p}if(H.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});I.fillStyle="red";I.textAlign="left";I.fillText(H.message,100+X,ax);return p}for(var at=0;at<this.filters.length;at++){if(H.data.length&&this.filters[at].applies_to(H.data[0])){p.addClass(FILTERABLE_CLASS);break}}var au=H.data;var ao=0;for(var ap=0,G=au.length;ap<G;ap++){var T=au[ap],Q=T[0],ar=T[1],ad=T[2],N=T[3];if(this.mode!="Dense"&&av[Q]===undefined){continue}var ac=false;var V;for(var at=0;at<this.filters.length;at++){V=this.filters[at];V.update_attrs(T);if(!V.keep(T)){ac=true;break}}if(ac){continue}if(ar<=al&&ad>=M){if(H.dataset_type=="interval_index"){ad-=1}var af=Math.floor(Math.max(0,(ar-M)*aw)),J=Math.ceil(Math.min(a,Math.max(0,(ad-M)*aw))),Y=(q==="Dense"?1:(1+av[Q]))*ax;var F,aj,O=null,ay=null;if(H.dataset_type==="bai"){I.fillStyle=h;if(T[5] instanceof Array){var D=Math.floor(Math.max(0,(T[4][0]-M)*aw)),P=Math.ceil(Math.min(a,Math.max(0,(T[4][1]-M)*aw))),B=Math.floor(Math.max(0,(T[5][0]-M)*aw)),u=Math.ceil(Math.min(a,Math.max(0,(T[5][1]-M)*aw)));if(T[4][1]>=M&&T[4][0]<=al&&T[4][2]){this.rect_or_text(I,aw,M,al,T[4][0],T[4][2],T[4][3],Y)}if(T[5][1]>=M&&T[5][0]<=al&&T[5][2]){this.rect_or_text(I,aw,M,al,T[5][0],T[5][2],T[5][3],Y)}if(B>P){I.fillStyle=CONNECTOR_COLOR;I.dashedLine(P+X,Y+5,X+B,Y+5)}}else{I.fillStyle=h;this.rect_or_text(I,aw,M,al,ar,T[4],T[5],Y)}if(q!=="Dense"&&!ae&&ar>M){I.fillStyle=this.prefs.label_color;if(n===0&&af-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+X,Y+8)}else{I.textAlign="right";I.fillText(N,af-2+X,Y+8)}I.fillStyle=h}}else{if(H.dataset_type==="interval_index"){if(q=="Auto"){if(T.length<=4){q="Squish"}else{q="Pack"}}if(q=="Dense"){I.fillStyle=h;I.fillRect(af+X,Y+5,J-af,DENSE_HEIGHT)}else{if(T.length<=4){I.fillStyle=h;I.fillRect(af+X,Y+5,J-af,1)}else{var E=T[5],W=T[6],ah=T[7],g=T[8];if(W&&ah){O=Math.floor(Math.max(0,(W-M)*aw));ay=Math.ceil(Math.min(a,Math.max(0,(ah-M)*aw)))}var aq,R;if(q=="Squish"){aq=1;R=SQUISH_HEIGHT}else{aq=5;R=PACK_HEIGHT}if(!g){if(T.strand){if(T.strand=="+"){I.fillStyle=RIGHT_STRAND_INV}else{if(T.strand=="-"){I.fillStyle=LEFT_STRAND_INV}}}else{I.fillStyle=CONNECTOR_COLOR}I.fillRect(af+X,Y+(R-aq)/2+1,J-af,R)}else{var A,S;if(q=="Squish"){I.fillStyle=CONNECTOR_COLOR;A=Y+Math.floor(SQUISH_HEIGHT/2)+1;S=1}else{if(E){var A=Y;var S=R;if(E=="+"){I.fillStyle=RIGHT_STRAND}else{if(E=="-"){I.fillStyle=LEFT_STRAND}}}else{I.fillStyle=CONNECTOR_COLOR;A+=(SQUISH_HEIGHT/2)+1;S=1}}I.fillRect(af+X,A,J-af,S);for(var an=0,e=g.length;an<e;an++){var t=g[an],d=Math.floor(Math.max(0,(t[0]-M)*aw)),U=Math.ceil(Math.min(a,Math.max((t[1]-M)*aw)));if(d>U){continue}I.fillStyle=h;I.fillRect(d+X,Y+(R-aq)/2+1,U-d,aq);if(O!==undefined&&!(d>ay||U<O)){var ak=Math.max(d,O),z=Math.min(U,ay-1);I.fillRect(ak+X,Y+1,z-ak,R)}}}if(q=="Pack"&&ar>M){I.fillStyle=ai;if(n===0&&af-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+X,Y+8)}else{I.textAlign="right";I.fillText(N,af-2+X,Y+8)}I.fillStyle=h}}}}else{if(H.dataset_type==="vcf"){if(ae){I.fillStyle=h;I.fillRect(af+X,Y+5,J-af,1)}else{var s=T[4],m=T[5],c=T[6];F=9;aj=1;I.fillRect(af+X,Y,J-af,F);if(q!=="Dense"&&N!==undefined&&ar>M){I.fillStyle=ai;if(n===0&&af-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+X,Y+8)}else{I.textAlign="right";I.fillText(N,af-2+X,Y+8)}I.fillStyle=h}var l=s+" / "+m;if(ar>M&&I.measureText(l).width<(J-af)){I.fillStyle="white";I.textAlign="center";I.fillText(l,X+af+(J-af)/2,Y+8);I.fillStyle=h}}}}}ao++}}return p}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
--- a/static/scripts/trackster.js Sun Feb 06 10:27:53 2011 -0500
+++ b/static/scripts/trackster.js Mon Feb 07 09:23:57 2011 -0500
@@ -57,6 +57,12 @@
* Init constants & functions used throughout trackster.
*/
var
+ // Drawing constants.
+ DENSE_HEIGHT = 1,
+ SQUISH_HEIGHT = 3,
+ PACK_HEIGHT = 9,
+
+ // Other constants.
DENSITY = 200,
FEATURE_LEVELS = 10,
MAX_FEATURE_DEPTH = 100,
@@ -209,8 +215,7 @@
},
// Generate key for cache.
gen_key: function(low, high, mode) {
- // TODO: use mode to generate key?
- var key = low + "_" + high;
+ var key = low + "_" + high + "_" + mode;
/*
if (no_detail) {
key += "_" + no_detail
@@ -1978,7 +1983,7 @@
this.show_labels_scale = 0.001;
this.showing_details = false;
this.vertical_detail_px = 10;
- this.vertical_nodetail_px = 3;
+ this.vertical_nodetail_px = 5;
this.summary_draw_height = 30;
this.default_font = "9px Monaco, Lucida Console, monospace";
this.inc_slots = {};
@@ -2221,7 +2226,10 @@
} else {
ctx.fillStyle = this.prefs.block_color;
// TODO: This is a pretty hack-ish way to fill rectangle based on mode.
- ctx.fillRect(s_start + this.left_offset, y_center + (this.mode != "Dense" ? 4 : 5), s_end - s_start, (this.mode != "Dense" ? 3 : 1) );
+ ctx.fillRect(s_start + this.left_offset,
+ y_center + (this.mode != "Dense" ? 4 : 5),
+ s_end - s_start,
+ (this.mode != "Dense" ? SQUISH_HEIGHT : DENSE_HEIGHT) );
}
seq_offset += cig_len;
break;
@@ -2261,8 +2269,11 @@
break;
}
}*/
+
+ //
+ // Get tile data; if data not available, issue get_data request and return.
+ //
var result = this.data_cache.get_data(tile_low, tile_high, this.mode);
-
if (result === undefined || result === "pending" ||
(this.mode !== "Auto" && result.dataset_type === "summary_tree")) {
this.data_queue[ [tile_low, tile_high] ] = true;
@@ -2270,6 +2281,9 @@
return;
}
+ //
+ // Create/set/compute some useful vars.
+ //
var width = Math.ceil( tile_span * w_scale ),
label_color = this.prefs.label_color,
block_color = this.prefs.block_color,
@@ -2295,7 +2309,7 @@
required_height = this.incremental_slots( inc_scale, result.data, no_detail, mode ) * y_scale + min_height;
slots = this.inc_slots[inc_scale];
}
-
+
canvas.get(0).width = width + left_offset;
canvas.get(0).height = required_height;
parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px");
@@ -2396,6 +2410,11 @@
}
if (feature_start <= tile_high && feature_end >= tile_low) {
+ // -1 b/c intervals are half-open.
+ if (result.dataset_type == "interval_index") {
+ feature_end -= 1;
+ }
+
// All features need a start, end, and vertical center.
var f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
@@ -2446,12 +2465,37 @@
}
// Interval index drawing.
else if (result.dataset_type === "interval_index") {
- // console.log(feature_uid, feature_start, feature_end, f_start, f_end, y_center);
- if (no_detail) {
+ //
+ // There are really four modes for interval indices:
+ // dense, no_detail, squish, pack.
+ //
+
+ // TODO: move this code out of loop.
+ // Set mode in Auto
+ if (mode == "Auto") {
+ // Never use dense when in auto mode.
+ // TODO: decide when to use squish and when to use pack.
+ if (feature.length <= 4) {
+ mode = "Squish";
+ }
+ else {
+ mode = "Pack";
+ }
+ }
+
+ // Dense mode displays the same for all data.
+ if (mode == "Dense") {
ctx.fillStyle = block_color;
+ ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, DENSE_HEIGHT);
+ }
+ // Mode is either Squish or Pack:
+ else if (feature.length <= 4) {
+ // No details for feature, so only one way to display.
+ ctx.fillStyle = block_color;
+ // TODO: what should width be here?
ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, 1);
} else {
- // Showing labels, blocks, details.
+ // Feature has details.
var feature_strand = feature[5],
feature_ts = feature[6],
feature_te = feature[7],
@@ -2461,8 +2505,92 @@
thick_start = Math.floor( Math.max(0, (feature_ts - tile_low) * w_scale) );
thick_end = Math.ceil( Math.min(width, Math.max(0, (feature_te - tile_low) * w_scale)) );
}
- if (mode !== "Dense" && feature_name !== undefined && feature_start > tile_low) {
- // Draw label
+
+ // Set vars that depend on mode.
+ var thin_height, thick_height;
+ if (mode == "Squish") {
+ thin_height = 1;
+ thick_height = SQUISH_HEIGHT;
+ }
+ else { // mode == "Pack"
+ thin_height = 5;
+ thick_height = PACK_HEIGHT;
+ }
+
+ // Draw feature/feature blocks + connectors.
+ if (!feature_blocks) {
+ // If there are no blocks, treat the feature as one big exon.
+ if ( feature.strand ) {
+ if (feature.strand == "+") {
+ ctx.fillStyle = RIGHT_STRAND_INV;
+ } else if (feature.strand == "-") {
+ ctx.fillStyle = LEFT_STRAND_INV;
+ }
+ }
+ else { // No strand.
+ ctx.fillStyle = CONNECTOR_COLOR;
+ }
+ ctx.fillRect(f_start + left_offset, y_center + (thick_height-thin_height)/2 + 1,
+ f_end - f_start, thick_height);
+ }
+ else { // There are feature blocks and mode is either Squish or Pack.
+ //
+ // Approach: (a) draw whole feature as connector/intron and (b) draw blocks as
+ // needed. This ensures that whole feature, regardless of whether it starts with
+ // a block, is visible.
+ //
+
+ // Draw whole feature as connector/intron.
+ var cur_y_center, cur_height;
+ if (mode == "Squish") {
+ ctx.fillStyle = CONNECTOR_COLOR;
+ cur_y_center = y_center + Math.floor(SQUISH_HEIGHT/2) + 1;
+ cur_height = 1;
+ }
+ else { // mode == "Pack"
+ if (feature_strand) {
+ var cur_y_center = y_center;
+ var cur_height = thick_height;
+ if (feature_strand == "+") {
+ ctx.fillStyle = RIGHT_STRAND;
+ } else if (feature_strand == "-") {
+ ctx.fillStyle = LEFT_STRAND;
+ }
+ }
+ else {
+ ctx.fillStyle = CONNECTOR_COLOR;
+ cur_y_center += (SQUISH_HEIGHT/2) + 1;
+ cur_height = 1;
+ }
+ }
+ ctx.fillRect(f_start + left_offset, cur_y_center, f_end - f_start, cur_height);
+
+ for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
+ var block = feature_blocks[k],
+ block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ),
+ block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) );
+
+ // Skip drawing if block not on tile.
+ if (block_start > block_end) { continue; }
+
+ // Draw thin block.
+ ctx.fillStyle = block_color;
+ ctx.fillRect(block_start + left_offset, y_center + (thick_height-thin_height)/2 + 1,
+ block_end - block_start, thin_height);
+
+ // If block intersects with thick region, draw block as thick.
+ if (thick_start !== undefined && !(block_start > thick_end || block_end < thick_start) ) {
+ var block_thick_start = Math.max(block_start, thick_start),
+ // -1 b/c intervals are half-open.
+ block_thick_end = Math.min(block_end, thick_end-1);
+ ctx.fillRect(block_thick_start + left_offset, y_center + 1,
+ block_thick_end - block_thick_start, thick_height);
+ }
+ }
+ }
+
+ // Draw label for Pack mode.
+ if (mode == "Pack" && feature_start > tile_low) {
ctx.fillStyle = label_color;
if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) {
ctx.textAlign = "left";
@@ -2473,53 +2601,6 @@
}
ctx.fillStyle = block_color;
}
- if (feature_blocks) {
- // Draw introns
- if (feature_strand) {
- if (feature_strand == "+") {
- ctx.fillStyle = RIGHT_STRAND;
- } else if (feature_strand == "-") {
- ctx.fillStyle = LEFT_STRAND;
- }
- ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, 10);
- ctx.fillStyle = block_color;
- }
-
- for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
- var block = feature_blocks[k],
- block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ),
- block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) );
- if (block_start > block_end) { continue; }
- // Draw the block
- thickness = 5;
- y_start = 3;
- ctx.fillRect(block_start + left_offset, y_center + y_start, block_end - block_start, thickness);
-
- // Draw thick regions: check if block intersects with thick region
- if (thick_start !== undefined && !(block_start > thick_end || block_end < thick_start) ) {
- thickness = 9;
- y_start = 1;
- var block_thick_start = Math.max(block_start, thick_start),
- block_thick_end = Math.min(block_end, thick_end);
- ctx.fillRect(block_thick_start + left_offset, y_center + y_start, block_thick_end - block_thick_start, thickness);
-
- }
- }
- } else {
- // If there are no blocks, we treat the feature as one big exon
- thickness = 9;
- y_start = 1;
- ctx.fillRect(f_start + left_offset, y_center + y_start, f_end - f_start, thickness);
- if ( feature.strand ) {
- if (feature.strand == "+") {
- ctx.fillStyle = RIGHT_STRAND_INV;
- } else if (feature.strand == "-") {
- ctx.fillStyle = LEFT_STRAND_INV;
- }
- ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, 10);
- ctx.fillStyle = block_color;
- }
- }
}
} else if (result.dataset_type === 'vcf') {
// VCF track.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: james_taylor: trackster: color picker shows on click, not hover, and below the input element
by Bitbucket 06 Feb '11
by Bitbucket 06 Feb '11
06 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/48d1f796acd4/
changeset: r5009:48d1f796acd4
user: james_taylor
date: 2011-02-06 16:27:53
summary: trackster: color picker shows on click, not hover, and below the input element
affected #: 1 file (215 bytes)
--- a/static/scripts/trackster.js Sun Feb 06 02:21:10 2011 -0500
+++ b/static/scripts/trackster.js Sun Feb 06 10:27:53 2011 -0500
@@ -863,18 +863,21 @@
var value = track_config.values[ param.key ];
var input = $('<input />').attr("id", id ).attr("name", id ).val( value );
// Color picker in tool tip style float
- var tip = $( "<div class='tipsy tipsy-west' style='position: absolute;' />" )
+ var tip = $( "<div class='tipsy tipsy-north' style='position: absolute;' />" )
.append( $("<div class='tipsy-inner' />")
.farbtastic( { width: 100, height: 100, callback: input, color: value } ) )
.hide();
// Outer div container input and tip for hover to work
- $("<div />").append( input ).append( tip ).appendTo( row ).hover( function () {
+ $("<div />").append( input ).append( tip ).appendTo( row ).bind( "click", function ( e ) {
tip.css( {
- left: $(this).position().left + $(input).width() - 20,
- top: $(this).position().top - 50
- } ).show();
- }, function () {
- tip.hide();
+ left: $(this).position().left + ( $(input).width() / 2 ) - 60,
+ top: $(this).position().top + $(this.height)
+ } ).show();
+ $(document).bind( "click.color-picker", function() {
+ tip.hide();
+ $(document).unbind( "click.color-picker" );
+ });
+ e.stopPropagation();
} );
} else {
row.append( $('<input />').attr("id", id ).attr("name", id ).val( track_config.values[ param.key ] ) );
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new changesets in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/f0b31bae1a64/
changeset: r5007:f0b31bae1a64
user: james_taylor
date: 2011-02-06 08:20:31
summary: trackster: color picker for color track config params
affected #: 3 files (16.7 KB)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/static/scripts/farbtastic.js Sun Feb 06 02:20:31 2011 -0500
@@ -0,0 +1,518 @@
+// Farbtastic 2.0 alpha
+(function ($) {
+
+var __debug = false;
+
+$.fn.farbtastic = function (options) {
+ $.farbtastic(this, options);
+ return this;
+};
+
+$.farbtastic = function (container, options) {
+ var container = $(container)[0];
+ return container.farbtastic || (container.farbtastic = new $._farbtastic(container, options));
+}
+
+$._farbtastic = function (container, options) {
+ var fb = this;
+
+ /////////////////////////////////////////////////////
+
+ /**
+ * Link to the given element(s) or callback.
+ */
+ fb.linkTo = function (callback) {
+ // Unbind previous nodes
+ if (typeof fb.callback == 'object') {
+ $(fb.callback).unbind('keyup', fb.updateValue);
+ }
+
+ // Reset color
+ fb.color = null;
+
+ // Bind callback or elements
+ if (typeof callback == 'function') {
+ fb.callback = callback;
+ }
+ else if (typeof callback == 'object' || typeof callback == 'string') {
+ fb.callback = $(callback);
+ fb.callback.bind('keyup', fb.updateValue);
+ if (fb.callback[0].value) {
+ fb.setColor(fb.callback[0].value);
+ }
+ }
+ return this;
+ }
+ fb.updateValue = function (event) {
+ if (this.value && this.value != fb.color) {
+ fb.setColor(this.value);
+ }
+ }
+
+ /**
+ * Change color with HTML syntax #123456
+ */
+ fb.setColor = function (color) {
+ var unpack = fb.unpack(color);
+ if (fb.color != color && unpack) {
+ fb.color = color;
+ fb.rgb = unpack;
+ fb.hsl = fb.RGBToHSL(fb.rgb);
+ fb.updateDisplay();
+ }
+ return this;
+ }
+
+ /**
+ * Change color with HSL triplet [0..1, 0..1, 0..1]
+ */
+ fb.setHSL = function (hsl) {
+ fb.hsl = hsl;
+ fb.rgb = fb.HSLToRGB(hsl);
+ fb.color = fb.pack(fb.rgb);
+ fb.updateDisplay();
+ return this;
+ }
+
+ /////////////////////////////////////////////////////
+
+ /**
+ * Initialize the color picker widget.
+ */
+ fb.initWidget = function () {
+
+ // Insert markup and size accordingly.
+ var dim = {
+ width: options.width,
+ height: options.width
+ };
+ $(container)
+ .html(
+ '<div class="farbtastic" style="position: relative">' +
+ '<div class="farbtastic-solid"></div>' +
+ '<canvas class="farbtastic-mask"></canvas>' +
+ '<canvas class="farbtastic-overlay"></canvas>' +
+ '</div>'
+ )
+ .find('*').attr(dim).css(dim).end()
+ .find('div>*').css('position', 'absolute');
+
+ // IE Fix: Recreate canvas elements with doc.createElement and excanvas.
+ $.browser.msie && $('canvas', container).each(function () {
+ // Fetch info.
+ var attr = { 'class': $(this).attr('class'), style: this.getAttribute('style') },
+ e = document.createElement('canvas');
+ // Replace element.
+ $(this).before($(e).attr(attr)).remove();
+ // Init with explorerCanvas.
+ G_vmlCanvasManager && G_vmlCanvasManager.initElement(e);
+ // Set explorerCanvas elements dimensions and absolute positioning.
+ $(e).attr(dim).css(dim).css('position', 'absolute')
+ .find('*').attr(dim).css(dim);
+ });
+
+ // Determine layout
+ fb.radius = (options.width - options.wheelWidth) / 2 - 1;
+ fb.square = Math.floor((fb.radius - options.wheelWidth / 2) * 0.7) - 1;
+ fb.mid = Math.floor(options.width / 2);
+ fb.markerSize = options.wheelWidth * 0.3;
+ fb.solidFill = $('.farbtastic-solid', container).css({
+ width: fb.square * 2 - 1,
+ height: fb.square * 2 - 1,
+ left: fb.mid - fb.square,
+ top: fb.mid - fb.square
+ });
+
+ // Set up drawing context.
+ fb.cnvMask = $('.farbtastic-mask', container);
+ fb.ctxMask = fb.cnvMask[0].getContext('2d');
+ fb.cnvOverlay = $('.farbtastic-overlay', container);
+ fb.ctxOverlay = fb.cnvOverlay[0].getContext('2d');
+ fb.ctxMask.translate(fb.mid, fb.mid);
+ fb.ctxOverlay.translate(fb.mid, fb.mid);
+
+ // Draw widget base layers.
+ fb.drawCircle();
+ fb.drawMask();
+ }
+
+ /**
+ * Draw the color wheel.
+ */
+ fb.drawCircle = function () {
+ var tm = +(new Date());
+ // Draw a hue circle with a bunch of gradient-stroked beziers.
+ // Have to use beziers, as gradient-stroked arcs don't work.
+ var n = 24,
+ r = fb.radius,
+ w = options.wheelWidth,
+ nudge = 8 / r / n * Math.PI, // Fudge factor for seams.
+ m = fb.ctxMask,
+ angle1 = 0, color1, d1;
+ m.save();
+ m.lineWidth = w / r;
+ m.scale(r, r);
+ // Each segment goes from angle1 to angle2.
+ for (var i = 0; i <= n; ++i) {
+ var d2 = i / n,
+ angle2 = d2 * Math.PI * 2,
+ // Endpoints
+ x1 = Math.sin(angle1), y1 = -Math.cos(angle1);
+ x2 = Math.sin(angle2), y2 = -Math.cos(angle2),
+ // Midpoint chosen so that the endpoints are tangent to the circle.
+ am = (angle1 + angle2) / 2,
+ tan = 1 / Math.cos((angle2 - angle1) / 2),
+ xm = Math.sin(am) * tan, ym = -Math.cos(am) * tan,
+ // New color
+ color2 = fb.pack(fb.HSLToRGB([d2, 1, 0.5]));
+ if (i > 0) {
+ if ($.browser.msie) {
+ // IE's gradient calculations mess up the colors. Correct along the diagonals.
+ var corr = (1 + Math.min(Math.abs(Math.tan(angle1)), Math.abs(Math.tan(Math.PI / 2 - angle1)))) / n;
+ color1 = fb.pack(fb.HSLToRGB([d1 - 0.15 * corr, 1, 0.5]));
+ color2 = fb.pack(fb.HSLToRGB([d2 + 0.15 * corr, 1, 0.5]));
+ // Create gradient fill between the endpoints.
+ var grad = m.createLinearGradient(x1, y1, x2, y2);
+ grad.addColorStop(0, color1);
+ grad.addColorStop(1, color2);
+ m.fillStyle = grad;
+ // Draw quadratic curve segment as a fill.
+ var r1 = (r + w / 2) / r, r2 = (r - w / 2) / r; // inner/outer radius.
+ m.beginPath();
+ m.moveTo(x1 * r1, y1 * r1);
+ m.quadraticCurveTo(xm * r1, ym * r1, x2 * r1, y2 * r1);
+ m.lineTo(x2 * r2, y2 * r2);
+ m.quadraticCurveTo(xm * r2, ym * r2, x1 * r2, y1 * r2);
+ m.fill();
+ }
+ else {
+ // Create gradient fill between the endpoints.
+ var grad = m.createLinearGradient(x1, y1, x2, y2);
+ grad.addColorStop(0, color1);
+ grad.addColorStop(1, color2);
+ m.strokeStyle = grad;
+ // Draw quadratic curve segment.
+ m.beginPath();
+ m.moveTo(x1, y1);
+ m.quadraticCurveTo(xm, ym, x2, y2);
+ m.stroke();
+ }
+ }
+ // Prevent seams where curves join.
+ angle1 = angle2 - nudge; color1 = color2; d1 = d2;
+ }
+ m.restore();
+ __debug && $('body').append('<div>drawCircle '+ (+(new Date()) - tm) +'ms');
+ };
+
+ /**
+ * Draw the saturation/luminance mask.
+ */
+ fb.drawMask = function () {
+ var tm = +(new Date());
+
+ // Iterate over sat/lum space and calculate appropriate mask pixel values.
+ var size = fb.square * 2, sq = fb.square;
+ function calculateMask(sizex, sizey, outputPixel) {
+ var isx = 1 / sizex, isy = 1 / sizey;
+ for (var y = 0; y <= sizey; ++y) {
+ var l = 1 - y * isy;
+ for (var x = 0; x <= sizex; ++x) {
+ var s = 1 - x * isx;
+ // From sat/lum to alpha and color (grayscale)
+ var a = 1 - 2 * Math.min(l * s, (1 - l) * s);
+ var c = (a > 0) ? ((2 * l - 1 + a) * .5 / a) : 0;
+ outputPixel(x, y, c, a);
+ }
+ }
+ }
+
+ // Method #1: direct pixel access (new Canvas).
+ if (fb.ctxMask.getImageData) {
+ // Create half-resolution buffer.
+ var sz = Math.floor(size / 2);
+ var buffer = document.createElement('canvas');
+ buffer.width = buffer.height = sz + 1;
+ var ctx = buffer.getContext('2d');
+ var frame = ctx.getImageData(0, 0, sz + 1, sz + 1);
+
+ var i = 0;
+ calculateMask(sz, sz, function (x, y, c, a) {
+ frame.data[i++] = frame.data[i++] = frame.data[i++] = c * 255;
+ frame.data[i++] = a * 255;
+ });
+
+ ctx.putImageData(frame, 0, 0);
+ fb.ctxMask.drawImage(buffer, 0, 0, sz + 1, sz + 1, -sq, -sq, sq * 2, sq * 2);
+ }
+ // Method #2: drawing commands (old Canvas).
+ else if (!$.browser.msie) {
+ // Render directly at half-resolution
+ var sz = Math.floor(size / 2);
+ calculateMask(sz, sz, function (x, y, c, a) {
+ c = Math.round(c * 255);
+ fb.ctxMask.fillStyle = 'rgba(' + c + ', ' + c + ', ' + c + ', ' + a +')';
+ fb.ctxMask.fillRect(x * 2 - sq - 1, y * 2 - sq - 1, 2, 2);
+ });
+ }
+ // Method #3: vertical DXImageTransform gradient strips (IE).
+ else {
+ var cache_last, cache, w = 6; // Each strip is 6 pixels wide.
+ var sizex = Math.floor(size / w);
+ // 6 vertical pieces of gradient per strip.
+ calculateMask(sizex, 6, function (x, y, c, a) {
+ if (x == 0) {
+ cache_last = cache;
+ cache = [];
+ }
+ c = Math.round(c * 255);
+ a = Math.round(a * 255);
+ // We can only start outputting gradients once we have two rows of pixels.
+ if (y > 0) {
+ var c_last = cache_last[x][0],
+ a_last = cache_last[x][1],
+ color1 = fb.packDX(c_last, a_last),
+ color2 = fb.packDX(c, a),
+ y1 = Math.round(fb.mid + ((y - 1) * .333 - 1) * sq),
+ y2 = Math.round(fb.mid + (y * .333 - 1) * sq);
+ $('<div>').css({
+ position: 'absolute',
+ filter: "progid:DXImageTransform.Microsoft.Gradient(StartColorStr="+ color1 +", EndColorStr="+ color2 +", GradientType=0)",
+ top: y1,
+ height: y2 - y1,
+ // Avoid right-edge sticking out.
+ left: fb.mid + (x * w - sq - 1),
+ width: w - (x == sizex ? Math.round(w / 2) : 0)
+ }).appendTo(fb.cnvMask);
+ }
+ cache.push([c, a]);
+ });
+ }
+ __debug && $('body').append('<div>drawMask '+ (+(new Date()) - tm) +'ms');
+ }
+
+ /**
+ * Draw the selection markers.
+ */
+ fb.drawMarkers = function () {
+ // Determine marker dimensions
+ var sz = options.width, lw = Math.ceil(fb.markerSize / 4), r = fb.markerSize - lw + 1;
+ var angle = fb.hsl[0] * 6.28,
+ x1 = Math.sin(angle) * fb.radius,
+ y1 = -Math.cos(angle) * fb.radius,
+ x2 = 2 * fb.square * (.5 - fb.hsl[1]),
+ y2 = 2 * fb.square * (.5 - fb.hsl[2]),
+ c1 = fb.invert ? '#fff' : '#000',
+ c2 = fb.invert ? '#000' : '#fff';
+ var circles = [
+ { x: x1, y: y1, r: r, c: '#000', lw: lw + 1 },
+ { x: x1, y: y1, r: fb.markerSize, c: '#fff', lw: lw },
+ { x: x2, y: y2, r: r, c: c2, lw: lw + 1 },
+ { x: x2, y: y2, r: fb.markerSize, c: c1, lw: lw },
+ ];
+
+ // Update the overlay canvas.
+ fb.ctxOverlay.clearRect(-fb.mid, -fb.mid, sz, sz);
+ for (i in circles) {
+ var c = circles[i];
+ fb.ctxOverlay.lineWidth = c.lw;
+ fb.ctxOverlay.strokeStyle = c.c;
+ fb.ctxOverlay.beginPath();
+ fb.ctxOverlay.arc(c.x, c.y, c.r, 0, Math.PI * 2, true);
+ fb.ctxOverlay.stroke();
+ }
+ }
+
+ /**
+ * Update the markers and styles
+ */
+ fb.updateDisplay = function () {
+ // Determine whether labels/markers should invert.
+ fb.invert = (fb.rgb[0] * 0.3 + fb.rgb[1] * .59 + fb.rgb[2] * .11) <= 0.6;
+
+ // Update the solid background fill.
+ fb.solidFill.css('backgroundColor', fb.pack(fb.HSLToRGB([fb.hsl[0], 1, 0.5])));
+
+ // Draw markers
+ fb.drawMarkers();
+
+ // Linked elements or callback
+ if (typeof fb.callback == 'object') {
+ // Set background/foreground color
+ $(fb.callback).css({
+ backgroundColor: fb.color,
+ color: fb.invert ? '#fff' : '#000'
+ });
+
+ // Change linked value
+ $(fb.callback).each(function() {
+ if ((typeof this.value == 'string') && this.value != fb.color) {
+ this.value = fb.color;
+ }
+ });
+ }
+ else if (typeof fb.callback == 'function') {
+ fb.callback.call(fb, fb.color);
+ }
+ }
+
+ /**
+ * Helper for returning coordinates relative to the center.
+ */
+ fb.widgetCoords = function (event) {
+ return {
+ x: event.pageX - fb.offset.left - fb.mid,
+ y: event.pageY - fb.offset.top - fb.mid
+ };
+ }
+
+ /**
+ * Mousedown handler
+ */
+ fb.mousedown = function (event) {
+ // Capture mouse
+ if (!$._farbtastic.dragging) {
+ $(document).bind('mousemove', fb.mousemove).bind('mouseup', fb.mouseup);
+ $._farbtastic.dragging = true;
+ }
+
+ // Update the stored offset for the widget.
+ fb.offset = $(container).offset();
+
+ // Check which area is being dragged
+ var pos = fb.widgetCoords(event);
+ fb.circleDrag = Math.max(Math.abs(pos.x), Math.abs(pos.y)) > (fb.square + 2);
+
+ // Process
+ fb.mousemove(event);
+ return false;
+ }
+
+ /**
+ * Mousemove handler
+ */
+ fb.mousemove = function (event) {
+ // Get coordinates relative to color picker center
+ var pos = fb.widgetCoords(event);
+
+ // Set new HSL parameters
+ if (fb.circleDrag) {
+ var hue = Math.atan2(pos.x, -pos.y) / 6.28;
+ fb.setHSL([(hue + 1) % 1, fb.hsl[1], fb.hsl[2]]);
+ }
+ else {
+ var sat = Math.max(0, Math.min(1, -(pos.x / fb.square / 2) + .5));
+ var lum = Math.max(0, Math.min(1, -(pos.y / fb.square / 2) + .5));
+ fb.setHSL([fb.hsl[0], sat, lum]);
+ }
+ return false;
+ }
+
+ /**
+ * Mouseup handler
+ */
+ fb.mouseup = function () {
+ // Uncapture mouse
+ $(document).unbind('mousemove', fb.mousemove);
+ $(document).unbind('mouseup', fb.mouseup);
+ $._farbtastic.dragging = false;
+ }
+
+ /* Various color utility functions */
+ fb.dec2hex = function (x) {
+ return (x < 16 ? '0' : '') + x.toString(16);
+ }
+
+ fb.packDX = function (c, a) {
+ return '#' + fb.dec2hex(a) + fb.dec2hex(c) + fb.dec2hex(c) + fb.dec2hex(c);
+ };
+
+ fb.pack = function (rgb) {
+ var r = Math.round(rgb[0] * 255);
+ var g = Math.round(rgb[1] * 255);
+ var b = Math.round(rgb[2] * 255);
+ return '#' + fb.dec2hex(r) + fb.dec2hex(g) + fb.dec2hex(b);
+ };
+
+ fb.unpack = function (color) {
+ if (color.length == 7) {
+ function x(i) {
+ return parseInt(color.substring(i, i + 2), 16) / 255;
+ }
+ return [ x(1), x(3), x(5) ];
+ }
+ else if (color.length == 4) {
+ function x(i) {
+ return parseInt(color.substring(i, i + 1), 16) / 15;
+ }
+ return [ x(1), x(2), x(3) ];
+ }
+ };
+
+ fb.HSLToRGB = function (hsl) {
+ var m1, m2, r, g, b;
+ var h = hsl[0], s = hsl[1], l = hsl[2];
+ m2 = (l <= 0.5) ? l * (s + 1) : l + s - l * s;
+ m1 = l * 2 - m2;
+ return [
+ this.hueToRGB(m1, m2, h + 0.33333),
+ this.hueToRGB(m1, m2, h),
+ this.hueToRGB(m1, m2, h - 0.33333)
+ ];
+ };
+
+ fb.hueToRGB = function (m1, m2, h) {
+ h = (h + 1) % 1;
+ if (h * 6 < 1) return m1 + (m2 - m1) * h * 6;
+ if (h * 2 < 1) return m2;
+ if (h * 3 < 2) return m1 + (m2 - m1) * (0.66666 - h) * 6;
+ return m1;
+ };
+
+ fb.RGBToHSL = function (rgb) {
+ var r = rgb[0], g = rgb[1], b = rgb[2],
+ min = Math.min(r, g, b),
+ max = Math.max(r, g, b),
+ delta = max - min,
+ h = 0,
+ s = 0,
+ l = (min + max) / 2;
+ if (l > 0 && l < 1) {
+ s = delta / (l < 0.5 ? (2 * l) : (2 - 2 * l));
+ }
+ if (delta > 0) {
+ if (max == r && max != g) h += (g - b) / delta;
+ if (max == g && max != b) h += (2 + (b - r) / delta);
+ if (max == b && max != r) h += (4 + (r - g) / delta);
+ h /= 6;
+ }
+ return [h, s, l];
+ };
+
+ // Parse options.
+ if (!options.callback) {
+ options = { callback: options };
+ }
+ options = $.extend({
+ width: 300,
+ wheelWidth: (options.width || 300) / 10,
+ callback: null,
+ color: "#808080"
+ }, options);
+
+ // Initialize.
+ fb.initWidget();
+
+ // Install mousedown handler (the others are set on the document on-demand)
+ $('canvas.farbtastic-overlay', container).mousedown(fb.mousedown);
+
+ // Set linked elements/callback
+ if (options.callback) {
+ fb.linkTo(options.callback);
+ }
+ // Set to gray.
+ fb.setColor( "#808080" );
+ fb.setColor( options.color );
+}
+
+})(jQuery);
--- a/static/scripts/trackster.js Sun Feb 06 00:41:03 2011 -0500
+++ b/static/scripts/trackster.js Sun Feb 06 02:20:31 2011 -0500
@@ -859,8 +859,25 @@
row.append( $('<label />').attr("for", id ).text( param.label + ":" ) );
if ( param.type == 'bool' ) {
row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', track_config.values[ param.key ] ) );
+ } else if ( param.type == 'color' ) {
+ var value = track_config.values[ param.key ];
+ var input = $('<input />').attr("id", id ).attr("name", id ).val( value );
+ // Color picker in tool tip style float
+ var tip = $( "<div class='tipsy tipsy-west' style='position: absolute;' />" )
+ .append( $("<div class='tipsy-inner' />")
+ .farbtastic( { width: 100, height: 100, callback: input, color: value } ) )
+ .hide();
+ // Outer div container input and tip for hover to work
+ $("<div />").append( input ).append( tip ).appendTo( row ).hover( function () {
+ tip.css( {
+ left: $(this).position().left + $(input).width() - 20,
+ top: $(this).position().top - 50
+ } ).show();
+ }, function () {
+ tip.hide();
+ } );
} else {
- row.append( $('<input />').attr("id", id ).attr("name", id ).val( track_config.values[ param.key ] ) );
+ row.append( $('<input />').attr("id", id ).attr("name", id ).val( track_config.values[ param.key ] ) );
}
}
});
--- a/templates/tracks/browser.mako Sun Feb 06 00:41:03 2011 -0500
+++ b/templates/tracks/browser.mako Sun Feb 06 02:20:31 2011 -0500
@@ -55,7 +55,7 @@
<script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]-->
-${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "jquery.ui.sortable.slider" )}
+${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "jquery.ui.sortable.slider", "farbtastic" )}
<script type="text/javascript">
http://bitbucket.org/galaxy/galaxy-central/changeset/7e4583eb8a11/
changeset: r5008:7e4583eb8a11
user: james_taylor
date: 2011-02-06 08:21:10
summary: trackster: packed scripts
affected #: 2 files (7.9 KB)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/static/scripts/packed/farbtastic.js Sun Feb 06 02:21:10 2011 -0500
@@ -0,0 +1,1 @@
+(function(b){var a=false;b.fn.farbtastic=function(c){b.farbtastic(this,c);return this};b.farbtastic=function(c,d){var c=b(c)[0];return c.farbtastic||(c.farbtastic=new b._farbtastic(c,d))};b._farbtastic=function(c,d){var e=this;e.linkTo=function(f){if(typeof e.callback=="object"){b(e.callback).unbind("keyup",e.updateValue)}e.color=null;if(typeof f=="function"){e.callback=f}else{if(typeof f=="object"||typeof f=="string"){e.callback=b(f);e.callback.bind("keyup",e.updateValue);if(e.callback[0].value){e.setColor(e.callback[0].value)}}}return this};e.updateValue=function(f){if(this.value&&this.value!=e.color){e.setColor(this.value)}};e.setColor=function(f){var g=e.unpack(f);if(e.color!=f&&g){e.color=f;e.rgb=g;e.hsl=e.RGBToHSL(e.rgb);e.updateDisplay()}return this};e.setHSL=function(f){e.hsl=f;e.rgb=e.HSLToRGB(f);e.color=e.pack(e.rgb);e.updateDisplay();return this};e.initWidget=function(){var f={width:d.width,height:d.width};b(c).html('<div class="farbtastic" style="position: relative"><div class="farbtastic-solid"></div><canvas class="farbtastic-mask"></canvas><canvas class="farbtastic-overlay"></canvas></div>').find("*").attr(f).css(f).end().find("div>*").css("position","absolute");b.browser.msie&&b("canvas",c).each(function(){var g={"class":b(this).attr("class"),style:this.getAttribute("style")},h=document.createElement("canvas");b(this).before(b(h).attr(g)).remove();G_vmlCanvasManager&&G_vmlCanvasManager.initElement(h);b(h).attr(f).css(f).css("position","absolute").find("*").attr(f).css(f)});e.radius=(d.width-d.wheelWidth)/2-1;e.square=Math.floor((e.radius-d.wheelWidth/2)*0.7)-1;e.mid=Math.floor(d.width/2);e.markerSize=d.wheelWidth*0.3;e.solidFill=b(".farbtastic-solid",c).css({width:e.square*2-1,height:e.square*2-1,left:e.mid-e.square,top:e.mid-e.square});e.cnvMask=b(".farbtastic-mask",c);e.ctxMask=e.cnvMask[0].getContext("2d");e.cnvOverlay=b(".farbtastic-overlay",c);e.ctxOverlay=e.cnvOverlay[0].getContext("2d");e.ctxMask.translate(e.mid,e.mid);e.ctxOverlay.translate(e.mid,e.mid);e.drawCircle();e.drawMask()};e.drawCircle=function(){var j=+(new Date());var s=24,q=e.radius,l=d.wheelWidth,p=8/q/s*Math.PI,t=e.ctxMask,g=0,z,B;t.save();t.lineWidth=l/q;t.scale(q,q);for(var v=0;v<=s;++v){var A=v/s,f=A*Math.PI*2,y=Math.sin(g),h=-Math.cos(g);x2=Math.sin(f),y2=-Math.cos(f),am=(g+f)/2,tan=1/Math.cos((f-g)/2),xm=Math.sin(am)*tan,ym=-Math.cos(am)*tan,color2=e.pack(e.HSLToRGB([A,1,0.5]));if(v>0){if(b.browser.msie){var o=(1+Math.min(Math.abs(Math.tan(g)),Math.abs(Math.tan(Math.PI/2-g))))/s;z=e.pack(e.HSLToRGB([B-0.15*o,1,0.5]));color2=e.pack(e.HSLToRGB([A+0.15*o,1,0.5]));var k=t.createLinearGradient(y,h,x2,y2);k.addColorStop(0,z);k.addColorStop(1,color2);t.fillStyle=k;var x=(q+l/2)/q,u=(q-l/2)/q;t.beginPath();t.moveTo(y*x,h*x);t.quadraticCurveTo(xm*x,ym*x,x2*x,y2*x);t.lineTo(x2*u,y2*u);t.quadraticCurveTo(xm*u,ym*u,y*u,h*u);t.fill()}else{var k=t.createLinearGradient(y,h,x2,y2);k.addColorStop(0,z);k.addColorStop(1,color2);t.strokeStyle=k;t.beginPath();t.moveTo(y,h);t.quadraticCurveTo(xm,ym,x2,y2);t.stroke()}}g=f-p;z=color2;B=A}t.restore();a&&b("body").append("<div>drawCircle "+(+(new Date())-j)+"ms")};e.drawMask=function(){var p=+(new Date());var s=e.square*2,h=e.square;function g(D,B,t){var w=1/D,v=1/B;for(var A=0;A<=B;++A){var u=1-A*v;for(var E=0;E<=D;++E){var F=1-E*w;var C=1-2*Math.min(u*F,(1-u)*F);var z=(C>0)?((2*u-1+C)*0.5/C):0;t(E,A,z,C)}}}if(e.ctxMask.getImageData){var m=Math.floor(s/2);var k=document.createElement("canvas");k.width=k.height=m+1;var q=k.getContext("2d");var j=q.getImageData(0,0,m+1,m+1);var l=0;g(m,m,function(t,w,v,u){j.data[l++]=j.data[l++]=j.data[l++]=v*255;j.data[l++]=u*255});q.putImageData(j,0,0);e.ctxMask.drawImage(k,0,0,m+1,m+1,-h,-h,h*2,h*2)}else{if(!b.browser.msie){var m=Math.floor(s/2);g(m,m,function(t,w,v,u){v=Math.round(v*255);e.ctxMask.fillStyle="rgba("+v+", "+v+", "+v+", "+u+")";e.ctxMask.fillRect(t*2-h-1,w*2-h-1,2,2)})}else{var r,f,o=6;var n=Math.floor(s/o);g(n,6,function(B,w,u,A){if(B==0){r=f;f=[]}u=Math.round(u*255);A=Math.round(A*255);if(w>0){var E=r[B][0],t=r[B][1],D=e.packDX(E,t),C=e.packDX(u,A),z=Math.round(e.mid+((w-1)*0.333-1)*h),v=Math.round(e.mid+(w*0.333-1)*h);b("<div>").css({position:"absolute",filter:"progid:DXImageTransform.Microsoft.Gradient(StartColorStr="+D+", EndColorStr="+C+", GradientType=0)",top:z,height:v-z,left:e.mid+(B*o-h-1),width:o-(B==n?Math.round(o/2):0)}).appendTo(e.cnvMask)}f.push([u,A])})}}a&&b("body").append("<div>drawMask "+(+(new Date())-p)+"ms")};e.drawMarkers=function(){var p=d.width,j=Math.ceil(e.markerSize/4),f=e.markerSize-j+1;var k=e.hsl[0]*6.28,h=Math.sin(k)*e.radius,s=-Math.cos(k)*e.radius,g=2*e.square*(0.5-e.hsl[1]),q=2*e.square*(0.5-e.hsl[2]),m=e.invert?"#fff":"#000",l=e.invert?"#000":"#fff";var n=[{x:h,y:s,r:f,c:"#000",lw:j+1},{x:h,y:s,r:e.markerSize,c:"#fff",lw:j},{x:g,y:q,r:f,c:l,lw:j+1},{x:g,y:q,r:e.markerSize,c:m,lw:j},];e.ctxOverlay.clearRect(-e.mid,-e.mid,p,p);for(i in n){var 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false};e.mousemove=function(j){var k=e.widgetCoords(j);if(e.circleDrag){var h=Math.atan2(k.x,-k.y)/6.28;e.setHSL([(h+1)%1,e.hsl[1],e.hsl[2]])}else{var g=Math.max(0,Math.min(1,-(k.x/e.square/2)+0.5));var f=Math.max(0,Math.min(1,-(k.y/e.square/2)+0.5));e.setHSL([e.hsl[0],g,f])}return false};e.mouseup=function(){b(document).unbind("mousemove",e.mousemove);b(document).unbind("mouseup",e.mouseup);b._farbtastic.dragging=false};e.dec2hex=function(f){return(f<16?"0":"")+f.toString(16)};e.packDX=function(g,f){return"#"+e.dec2hex(f)+e.dec2hex(g)+e.dec2hex(g)+e.dec2hex(g)};e.pack=function(h){var k=Math.round(h[0]*255);var j=Math.round(h[1]*255);var f=Math.round(h[2]*255);return"#"+e.dec2hex(k)+e.dec2hex(j)+e.dec2hex(f)};e.unpack=function(g){if(g.length==7){function f(h){return parseInt(g.substring(h,h+2),16)/255}return[f(1),f(3),f(5)]}else{if(g.length==4){function f(h){return parseInt(g.substring(h,h+1),16)/15}return[f(1),f(2),f(3)]}}};e.HSLToRGB=function(o){var q,p,f,m,n;var 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\ No newline at end of file
--- a/static/scripts/packed/trackster.js Sun Feb 06 02:20:31 2011 -0500
+++ b/static/scripts/packed/trackster.js Sun Feb 06 02:21:10 2011 -0500
@@ -1,1 +1,1 @@
-CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})}},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k);if(l){var m=$("<div class='track-tile'>").prepend(l);if(l.hasClass(FILTERABLE_CLASS)){m.addClass(FILTERABLE_CLASS)}l=m}}if(l){d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var 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p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
+CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(d,h){if(!h.hidden){var i="param_"+d;var g=$("<div class='form-row' />").appendTo(a);g.append($("<label />").attr("for",i).text(h.label+":"));if(h.type=="bool"){g.append($('<input type="checkbox" />').attr("id",i).attr("name",i).attr("checked",b.values[h.key]))}else{if(h.type=="color"){var f=b.values[h.key];var c=$("<input />").attr("id",i).attr("name",i).val(f);var e=$("<div class='tipsy tipsy-west' style='position: absolute;' />").append($("<div class='tipsy-inner' />").farbtastic({width:100,height:100,callback:c,color:f})).hide();$("<div />").append(c).append(e).appendTo(g).hover(function(){e.css({left:$(this).position().left+$(c).width()-20,top:$(this).position().top-50}).show()},function(){e.hide()})}else{g.append($("<input />").attr("id",i).attr("name",i).val(b.values[h.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type=="float"){e=parseFloat(e)}else{if(f.type=="int"){e=parseInt(e)}else{if(f.type=="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.track_config.build_form(),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k);if(l){var m=$("<div class='track-tile'>").prepend(l);if(l.hasClass(FILTERABLE_CLASS)){m.addClass(FILTERABLE_CLASS)}l=m}}if(l){d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;(function(g){var j=false;var i=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){j=true;h.show()},function(){j=false;if(!i){h.hide()}});h.hide().bind("dragstart",function(k,l){i=true;l.original_height=$(g.content_div).height()}).bind("drag",function(l,m){var k=Math.min(Math.max(m.original_height+m.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",k);g.height_px=k;g.draw(true)}).bind("dragend",function(k,l){g.tile_cache.clear();i=false;if(!j){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b}});var FeatureTrack=function(a,f,e,i,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=i;this.original_dataset_id=i;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true}],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(G.data.length&&this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new changesets in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/f09b01f65503/
changeset: r5005:f09b01f65503
user: james_taylor
date: 2011-02-06 06:39:09
summary: trackster: refactor track configuration to be data/configuration driven -- easier to extend
affected #: 1 file (95 bytes)
--- a/static/scripts/trackster.js Sat Feb 05 16:04:30 2011 -0500
+++ b/static/scripts/trackster.js Sun Feb 06 00:39:09 2011 -0500
@@ -829,6 +829,71 @@
return filters;
};
+var TrackConfig = function( options ) {
+ this.track = options.track;
+ this.params = options.params;
+ this.values = {}
+ if ( options.saved_values ) {
+ this.restore_values( options.saved_values );
+ }
+ this.onchange = options.onchange
+}
+$.extend( TrackConfig.prototype, {
+ restore_values: function( values ) {
+ var track_config = this;
+ $.each( this.params, function( index, param ) {
+ if ( values[ param.key ] !== undefined ) {
+ track_config.values[ param.key ] = values[ param.key ];
+ } else {
+ track_config.values[ param.key ] = param.default_value;
+ }
+ });
+ },
+ build_form: function() {
+ var track_config = this;
+ var container = $("<div />");
+ $.each( this.params, function( index, param ) {
+ if ( ! param.hidden ) {
+ var id = 'param_' + index;
+ var row = $("<div class='form-row' />").appendTo( container );
+ row.append( $('<label />').attr("for", id ).text( param.label + ":" ) );
+ if ( param.type == 'bool' ) {
+ row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', track_config.values[ param.key ] ) );
+ } else {
+ row.append( $('<input />').attr("id", id ).attr("name", id ).val( track_config.values[ param.key ] ) );
+ }
+ }
+ });
+ return container;
+ },
+ update_from_form : function( container ) {
+ var track_config = this;
+ var changed = false;
+ $.each( this.params, function( index, param ) {
+ if ( ! param.hidden ) {
+ // Parse value from form element
+ var id = 'param_' + index;
+ var value = container.find( '#' + id ).val();
+ if ( param.type == 'float' ) {
+ value = parseFloat( value );
+ } else if ( param.type == 'int' ) {
+ value = parseInt( value );
+ } else if ( param.type == 'bool' ) {
+ value = container.find( '#' + id ).is( ':checked' );
+ }
+ // Save value only if changed
+ if ( value !== track_config.values[ param.key ] ) {
+ track_config.values[ param.key ] = value;
+ changed = true;
+ }
+ }
+ });
+ if ( changed ) {
+ this.onchange();
+ }
+ }
+});
+
/**
* Tracks are objects can be added to the View.
*
@@ -943,14 +1008,6 @@
* Additional initialization required before drawing track for the first time.
*/
predraw_init: function() {},
- restore_prefs: function(prefs) {
- var that = this;
- $.each(prefs, function(pref, val) {
- if (val !== undefined) {
- that.prefs[pref] = val;
- }
- });
- },
// Provide support for updating and reverting track name. Currently, it's only possible to revert once.
update_name: function(new_name) {
this.old_name = this.name;
@@ -1186,7 +1243,11 @@
var track_dropdown = {};
track_dropdown["Edit configuration"] = function() {
var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); },
- ok_fn = function() { track.update_options(track.track_id); hide_modal(); $(window).unbind("keypress.check_enter_esc"); },
+ ok_fn = function() {
+ track.track_config.update_from_form( $(".dialog-box") );
+ hide_modal();
+ $(window).unbind("keypress.check_enter_esc");
+ },
check_enter_esc = function(e) {
if ((e.keyCode || e.which) === 27) { // Escape key
cancel_fn();
@@ -1196,7 +1257,7 @@
};
$(window).bind("keypress.check_enter_esc", check_enter_esc);
- show_modal("Configure Track", track.gen_options(track.track_id), {
+ show_modal("Configure Track", track.track_config.build_form(), {
"Cancel": cancel_fn,
"OK": ok_fn
});
@@ -1641,6 +1702,7 @@
});
var LineTrack = function ( name, view, hda_ldda, dataset_id, prefs ) {
+ var track = this;
this.track_type = "LineTrack";
this.display_modes = ["Histogram", "Line", "Filled", "Intensity"];
this.mode = "Histogram";
@@ -1655,8 +1717,30 @@
this.original_dataset_id = dataset_id;
this.data_cache = new DataCache(CACHED_DATA);
this.tile_cache = new Cache(CACHED_TILES_LINE);
- this.prefs = { 'color': 'black', 'min_value': undefined, 'max_value': undefined, 'mode': this.mode };
- this.restore_prefs(prefs);
+
+ // Define track configuration
+ this.track_config = new TrackConfig( {
+ track: this,
+ params: [
+ { key: 'color', label: 'Color', type: 'color', default_value: 'black' },
+ { key: 'min_value', label: 'Min Value', type: 'float', default_value: undefined },
+ { key: 'max_value', label: 'Max Value', type: 'float', default_value: undefined },
+ { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
+ { key: 'height', type: 'int', default_value: this.height_px, hidden: true }
+ ],
+ saved_values: prefs,
+ onchange: function() {
+ track.vertical_range = track.prefs.max_value - track.prefs.min_value;
+ // Update the y-axis
+ $('#linetrack_' + track.track_id + '_minval').text(track.prefs.min_value);
+ $('#linetrack_' + track.track_id + '_maxval').text(track.prefs.max_value);
+ track.tile_cache.clear();
+ track.draw();
+ }
+ });
+
+ this.prefs = this.track_config.values;
+ this.height_px = this.track_config.values.height;
// Add control for resizing
// Trickery here to deal with the hovering drag handle, can probably be
@@ -1687,6 +1771,7 @@
track.tile_cache.clear();
in_drag = false;
if ( ! in_handle ) { drag_control.hide(); }
+ track.track_config.values.height_px = track.height_px;
}).appendTo( track.container_div );
})(this);
};
@@ -1854,42 +1939,11 @@
ctx.stroke();
}
return canvas;
- }, gen_options: function(track_id) {
- var container = $("<div />").addClass("form-row");
-
- var color = 'track_' + track_id + '_color',
- color_label = $('<label />').attr("for", color).text("Color:"),
- color_input = $('<input />').attr("id", color).attr("name", color).val(this.prefs.color),
- minval = 'track_' + track_id + '_minval',
- min_label = $('<label></label>').attr("for", minval).text("Min value:"),
- min_val = (this.prefs.min_value === undefined ? "" : this.prefs.min_value),
- min_input = $('<input></input>').attr("id", minval).val(min_val),
- maxval = 'track_' + track_id + '_maxval',
- max_label = $('<label></label>').attr("for", maxval).text("Max value:"),
- max_val = (this.prefs.max_value === undefined ? "" : this.prefs.max_value),
- max_input = $('<input></input>').attr("id", maxval).val(max_val);
-
- return container.append(min_label).append(min_input).append(max_label)
- .append(max_input).append(color_label).append(color_input);
- }, update_options: function(track_id) {
- var min_value = $('#track_' + track_id + '_minval').val(),
- max_value = $('#track_' + track_id + '_maxval').val(),
- color = $('#track_' + track_id + '_color').val();
- if ( min_value !== this.prefs.min_value || max_value !== this.prefs.max_value || color !== this.prefs.color ) {
- this.prefs.min_value = parseFloat(min_value);
- this.prefs.max_value = parseFloat(max_value);
- this.prefs.color = color;
- this.vertical_range = this.prefs.max_value - this.prefs.min_value;
- // Update the y-axis
- $('#linetrack_' + track_id + '_minval').text(this.prefs.min_value);
- $('#linetrack_' + track_id + '_maxval').text(this.prefs.max_value);
- this.tile_cache.clear();
- this.draw();
- }
- }
+ }
});
var FeatureTrack = function (name, view, hda_ldda, dataset_id, prefs, filters, tool, parent_track) {
+ var track = this;
this.track_type = "FeatureTrack";
this.display_modes = ["Auto", "Dense", "Squish", "Pack"];
Track.call(this, name, view, view.viewport_container);
@@ -1914,8 +1968,22 @@
this.data_cache = new DataCache(20);
this.left_offset = 200;
- this.prefs = { 'block_color': '#444', 'label_color': 'black', 'show_counts': true };
- this.restore_prefs(prefs);
+ // Define track configuration
+ this.track_config = new TrackConfig( {
+ track: this,
+ params: [
+ { key: 'block_color', label: 'Block color', type: 'color', default_value: '#444' },
+ { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
+ { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true }
+ ],
+ saved_values: prefs,
+ onchange: function() {
+ track.tile_cache.clear();
+ track.draw();
+ }
+ });
+
+ this.prefs = this.track_config.values;
};
$.extend( FeatureTrack.prototype, TiledTrack.prototype, {
get_data: function( low, high ) {
@@ -2476,33 +2544,6 @@
}
}
return canvas;
- },
- gen_options: function(track_id) {
- var container = $("<div />").addClass("form-row");
-
- var block_color = 'track_' + track_id + '_block_color',
- block_color_label = $('<label />').attr("for", block_color).text("Block color:"),
- block_color_input = $('<input />').attr("id", block_color).attr("name", block_color).val(this.prefs.block_color),
- label_color = 'track_' + track_id + '_label_color',
- label_color_label = $('<label />').attr("for", label_color).text("Text color:"),
- label_color_input = $('<input />').attr("id", label_color).attr("name", label_color).val(this.prefs.label_color),
- show_count = 'track_' + track_id + '_show_count',
- show_count_label = $('<label />').attr("for", show_count).text("Show summary counts"),
- show_count_input = $('<input type="checkbox" style="float:left;"></input>').attr("id", show_count).attr("name", show_count).attr("checked", this.prefs.show_counts),
- show_count_div = $('<div />').append(show_count_input).append(show_count_label);
-
- return container.append(block_color_label).append(block_color_input).append(label_color_label).append(label_color_input).append(show_count_div);
- }, update_options: function(track_id) {
- var block_color = $('#track_' + track_id + '_block_color').val(),
- label_color = $('#track_' + track_id + '_label_color').val(),
- show_counts = $('#track_' + track_id + '_show_count').attr("checked");
- if (block_color !== this.prefs.block_color || label_color !== this.prefs.label_color || show_counts !== this.prefs.show_counts) {
- this.prefs.block_color = block_color;
- this.prefs.label_color = label_color;
- this.prefs.show_counts = show_counts;
- this.tile_cache.clear();
- this.draw();
- }
}
});
http://bitbucket.org/galaxy/galaxy-central/changeset/774738a3e49b/
changeset: r5006:774738a3e49b
user: james_taylor
date: 2011-02-06 06:41:03
summary: trackster: save line track height properly
affected #: 1 file (3 bytes)
--- a/static/scripts/trackster.js Sun Feb 06 00:39:09 2011 -0500
+++ b/static/scripts/trackster.js Sun Feb 06 00:41:03 2011 -0500
@@ -1771,7 +1771,7 @@
track.tile_cache.clear();
in_drag = false;
if ( ! in_handle ) { drag_control.hide(); }
- track.track_config.values.height_px = track.height_px;
+ track.track_config.values.height = track.height_px;
}).appendTo( track.container_div );
})(this);
};
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
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1
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3 new changesets in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/66a1c6138524/
changeset: r5002:66a1c6138524
user: james_taylor
date: 2011-02-05 21:37:56
summary: Fix problem with adding filters when no data is returned, eliminates one of the problems drawing feature track tiles
affected #: 2 files (50 bytes)
--- a/static/scripts/trackster.js Fri Feb 04 14:48:39 2011 -0500
+++ b/static/scripts/trackster.js Sat Feb 05 15:37:56 2011 -0500
@@ -1638,7 +1638,7 @@
Track.call( this, name, view, view.viewport_container );
TiledTrack.call( this );
- this.min_height_px = 12;
+ this.min_height_px = 16;
this.max_height_px = 400;
this.height_px = 80;
this.hda_ldda = hda_ldda;
@@ -2255,12 +2255,12 @@
ctx.fillText(result.message, 100 + left_offset, y_scale);
return canvas;
}
-
+
//
// If tile is filterable, add class to canvas.
//
for (var f = 0; f < this.filters.length; f++) {
- if (this.filters[f].applies_to(result.data[0])) {
+ if (result.data.length && this.filters[f].applies_to(result.data[0])) {
canvas.addClass(FILTERABLE_CLASS);
break;
}
--- a/templates/tracks/browser.mako Fri Feb 04 14:48:39 2011 -0500
+++ b/templates/tracks/browser.mako Sat Feb 05 15:37:56 2011 -0500
@@ -104,6 +104,7 @@
.track-content {
background: #eee url(${h.url_for('/static/images/tracks/diag_bg.gif')});
min-height: 16px;
+ border-top: 1px solid #eee;
}
.label-track .track-content {
http://bitbucket.org/galaxy/galaxy-central/changeset/c1a6a293c870/
changeset: r5003:c1a6a293c870
user: james_taylor
date: 2011-02-05 21:38:11
summary: Automated merge with https://bitbucket.org/galaxy/galaxy-central
affected #: 1 file (14 bytes)
--- a/static/scripts/trackster.js Fri Feb 04 21:13:36 2011 -0500
+++ b/static/scripts/trackster.js Sat Feb 05 15:38:11 2011 -0500
@@ -1647,7 +1647,7 @@
Track.call( this, name, view, view.viewport_container );
TiledTrack.call( this );
- this.min_height_px = 12;
+ this.min_height_px = 16;
this.max_height_px = 400;
this.height_px = 80;
this.hda_ldda = hda_ldda;
@@ -2264,12 +2264,12 @@
ctx.fillText(result.message, 100 + left_offset, y_scale);
return canvas;
}
-
+
//
// If tile is filterable, add class to canvas.
//
for (var f = 0; f < this.filters.length; f++) {
- if (this.filters[f].applies_to(result.data[0])) {
+ if (result.data.length && this.filters[f].applies_to(result.data[0])) {
canvas.addClass(FILTERABLE_CLASS);
break;
}
--- a/templates/tracks/browser.mako Fri Feb 04 21:13:36 2011 -0500
+++ b/templates/tracks/browser.mako Sat Feb 05 15:38:11 2011 -0500
@@ -104,6 +104,7 @@
.track-content {
background: #eee url(${h.url_for('/static/images/tracks/diag_bg.gif')});
min-height: 16px;
+ border-top: 1px solid #eee;
}
.label-track .track-content {
http://bitbucket.org/galaxy/galaxy-central/changeset/92a7af072bc6/
changeset: r5004:92a7af072bc6
user: james_taylor
date: 2011-02-05 22:04:30
summary: trackster: Move some CSS rules into trackster.css, fix CSS problem with label tracks
affected #: 3 files (4.1 KB)
--- a/static/june_2007_style/blue/trackster.css Sat Feb 05 15:38:11 2011 -0500
+++ b/static/june_2007_style/blue/trackster.css Sat Feb 05 16:04:30 2011 -0500
@@ -18,17 +18,33 @@
.overview-box{cursor:pointer;bottom:0px;z-index:100;position:absolute;margin-top:0px;height:14px;background:#C1C9E5 url(../images/visualization/draggable_horizontal.png) center center no-repeat;border:solid #666 1px;}
.viewport-canvas{width:100%;height:100px;}
.yaxislabel{color:#777;z-index:100;}
-.line-track .track-content{border-top:1px solid #ddd;border-bottom:1px solid #ddd;}
+.line-track .track-content{border-top:1px solid #eee;border-bottom:1px solid #eee;}
.track{background:white;}
.track-header{text-align:left;padding:4px 0px;color:#666;}
.track-header .menubutton{margin-left:0px;}
-.track-content{overflow:hidden;text-align:center;margin-bottom:2px;border-bottom:#eee solid 1px;}
+.track-content{overflow:hidden;text-align:center;margin-bottom:2px;border-top:1px solid #eee;border-bottom:#eee solid 1px;background:#eee url('/static/images/tracks/diag_bg.gif');min-height:16px;}
+.label-track .track-content{background:white;}
+.track-tile{background:white;}
+.track-tile canvas{position:relative;z-index:100;}
.track.error .track-content{background-color:#ECB4AF;padding:2px 0;}
.track.nodata .track-content{background-color:#ddd;padding:2px 0;}
.loading{min-height:100px;}
-.label-track{font-size:10px;border:none;padding:0;margin:0;height:1.3em;}
+.label-track{font-size:10px;border:none;padding:0;margin:0;height:1.5em;overflow:hidden;}
.label-track .label{border-left:solid #999 1px;padding:1px;padding-bottom:2px;display:inline-block;}
+.label-track .track-content{border:none;}
.reference-track{border:none;margin:0;padding:0;}
.right-float{float:right;margin-left:5px;}
.top-labeltrack{position:relative;border-bottom:solid #999 1px;}
.nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px;}
+.filter-name{float:left;}
+input{font:10px verdana;}
+table.filters{border-collapse:separate;border-spacing:7px 0px;}
+.values{padding-left:0.25em;}
+.dynamic-tool{width:400px;margin-left:0.25em;}
+.param-row{margin-top:0.4em;margin-left:1em;}
+.slider-label{float:left;font-weight:bold;}
+.slider{float:right;width:200px;position:relative;}
+.tool-name{font-size:110%;font-weight:bold;}
+.child-track-icon{background:url('../images/fugue/arrow-000-small-bw.png') no-repeat;width:30px;cursor:move;}
+.param-value{cursor:pointer;}
+.track-resize{background:white url('../images/visualization/draggable_vertical.png') no-repeat top center;position:absolute;right:3px;bottom:-4px;width:14px;height:7px;border:solid #999 1px;z-index:100;}
--- a/static/june_2007_style/trackster.css.tmpl Sat Feb 05 15:38:11 2011 -0500
+++ b/static/june_2007_style/trackster.css.tmpl Sat Feb 05 16:04:30 2011 -0500
@@ -123,8 +123,8 @@
}
/* Line track needs borders to show range */
.line-track .track-content {
- border-top: 1px solid #ddd;
- border-bottom: 1px solid #ddd;
+ border-top: 1px solid #eee;
+ border-bottom: 1px solid #eee;
}
.track {
@@ -147,7 +147,23 @@
overflow: hidden;
text-align: center;
margin-bottom: 2px;
+ border-top: 1px solid #eee;
border-bottom: #eee solid 1px;
+ background: #eee url('/static/images/tracks/diag_bg.gif');
+ min-height: 16px;
+}
+
+.label-track .track-content {
+ background: white;
+}
+
+.track-tile {
+ background: white;
+}
+
+.track-tile canvas {
+ position: relative;
+ z-index: 100;
}
.track.error .track-content {
@@ -162,14 +178,14 @@
.loading {
min-height: 100px;
}
-
.label-track {
/* font-weight: bold; */
font-size: 10px;
border: none;
padding: 0;
margin: 0;
- height: 1.3em;
+ height: 1.5em;
+ overflow: hidden;
}
.label-track .label {
border-left: solid #999 1px;
@@ -177,6 +193,9 @@
padding-bottom: 2px;
display: inline-block;
}
+.label-track .track-content {
+ border: none;
+}
.reference-track {
border: none;
margin: 0;
@@ -195,4 +214,61 @@
.nav-labeltrack {
border-top: solid #999 1px;
border-bottom: solid #333 1px;
+}
+
+## Styles for tools and filters.
+
+.filter-name {
+ float: left;
}
+input {
+ font: 10px verdana;
+}
+table.filters {
+ border-collapse: separate;
+ border-spacing: 7px 0px;
+}
+.values {
+ padding-left: 0.25em;
+}
+.dynamic-tool {
+ width: 400px;
+ margin-left: 0.25em;
+}
+.param-row {
+ margin-top: 0.4em;
+ margin-left: 1em;
+}
+.slider-label {
+ float: left;
+ font-weight: bold;
+}
+.slider {
+ float: right;
+ width: 200px;
+ position: relative;
+}
+.tool-name {
+ font-size: 110%;
+ font-weight: bold;
+}
+.child-track-icon {
+ background:url('../images/fugue/arrow-000-small-bw.png') no-repeat;
+ width: 30px;
+ cursor: move;
+}
+.param-value {
+ cursor: pointer;
+}
+
+.track-resize {
+ background: white url('../images/visualization/draggable_vertical.png') no-repeat top center;
+ position: absolute;
+ right: 3px;
+ bottom: -4px;
+ width: 14px;
+ height: 7px;
+ border: solid #999 1px;
+ z-index: 100;
+}
+
--- a/templates/tracks/browser.mako Sat Feb 05 15:38:11 2011 -0500
+++ b/templates/tracks/browser.mako Sat Feb 05 16:04:30 2011 -0500
@@ -18,16 +18,6 @@
#browser-container {
overflow: none;
}
- ul#sortable-ul {
- list-style: none;
- padding: 0;
- margin: 5px;
- }
- ul#sortable-ul li {
- display: block;
- margin: 5px 0;
- background: #eee;
- }
.nav-container {
width: 100%;
## Overriding styles from trackster.css to push nav up into title bar
@@ -42,83 +32,6 @@
background: transparent;
border: none;
}
- #
- # TODO: move these into trackster.css
- # Styles for tools and filters.
- #
- .filter-name {
- float: left;
- }
- input {
- font: 10px verdana;
- }
- table.filters {
- border-collapse: separate;
- border-spacing: 7px 0px;
- }
- .values {
- padding-left: 0.25em;
- }
- .dynamic-tool {
- width: 400px;
- margin-left: 0.25em;
- }
- .param-row {
- margin-top: 0.4em;
- margin-left: 1em;
- }
- .slider-label {
- float: left;
- font-weight: bold;
- }
- .slider {
- float: right;
- width: 200px;
- position: relative;
- }
- .tool-name {
- font-size: 110%;
- font-weight: bold;
- }
- .child-track-icon {
- background:url(${h.url_for('/static/images/fugue/arrow-000-small-bw.png')}) no-repeat;
- width: 30px;
- cursor: move;
- }
- .param-value {
- cursor: pointer;
- }
-
- .track-resize {
-
- background: white url(${h.url_for('/static/images/visualization/draggable_vertical.png')}) no-repeat top center;
- position: absolute;
- right: 3px;
- bottom: -4px;
- width: 14px;
- height: 7px;
- border: solid #999 1px;
- z-index: 100;
- }
-
- .track-content {
- background: #eee url(${h.url_for('/static/images/tracks/diag_bg.gif')});
- min-height: 16px;
- border-top: 1px solid #eee;
- }
-
- .label-track .track-content {
- background: white;
- }
-
- .track-tile {
- background: white;
- }
-
- .track-tile canvas {
- position: relative;
- z-index: 100;
- }
</style></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: kanwei: trackster: Reference track should not have the new loading background and min-height
by Bitbucket 04 Feb '11
by Bitbucket 04 Feb '11
04 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/e9c04e1dc30a/
changeset: r5001:e9c04e1dc30a
user: kanwei
date: 2011-02-05 03:13:36
summary: trackster: Reference track should not have the new loading background and min-height
affected #: 2 files (206 bytes)
--- a/static/scripts/packed/trackster.js Fri Feb 04 21:02:23 2011 -0500
+++ b/static/scripts/packed/trackster.js Fri Feb 04 21:13:36 2011 -0500
@@ -1,1 +1,1 @@
-CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})}},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k)}if(l){if(!d.initial_canvas&&!window.G_vmlCanvasManager){d.initial_canvas=$(l).clone();var o=l.get(0).getContext("2d");var m=d.initial_canvas.get(0).getContext("2d");var n=o.getImageData(0,0,o.canvas.width,o.canvas.height);m.putImageData(n,0,0);d.set_overview()}d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
+CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})}},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k);if(l){var m=$("<div class='track-tile'>").prepend(l);if(l.hasClass(FILTERABLE_CLASS)){m.addClass(FILTERABLE_CLASS)}l=m}}if(l){d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
--- a/static/scripts/trackster.js Fri Feb 04 21:02:23 2011 -0500
+++ b/static/scripts/trackster.js Fri Feb 04 21:13:36 2011 -0500
@@ -1574,6 +1574,9 @@
this.left_offset = 200;
this.height_px = 12;
this.container_div.addClass( "reference-track" );
+ this.content_div.css("background", "none");
+ this.content_div.css("min-height", "0px");
+ this.content_div.css("border", "none");
this.data_queue = {};
this.data_cache = new DataCache(CACHED_DATA);
this.tile_cache = new Cache(CACHED_TILES_LINE);
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
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1
0
commit/galaxy-central: kanwei: trackster: Fix infinite data query loop when chrom is null or 'None'
by Bitbucket 04 Feb '11
by Bitbucket 04 Feb '11
04 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/538ca7438a8a/
changeset: r5000:538ca7438a8a
user: kanwei
date: 2011-02-05 03:02:23
summary: trackster: Fix infinite data query loop when chrom is null or 'None'
affected #: 1 file (203 bytes)
--- a/static/scripts/trackster.js Fri Feb 04 16:16:00 2011 -0500
+++ b/static/scripts/trackster.js Fri Feb 04 21:02:23 2011 -0500
@@ -466,6 +466,12 @@
},
change_chrom: function(chrom, low, high) {
+
+ // Don't do anything if chrom is "None" (hackish but some browsers already have this set), or null/blank
+ if (!chrom || chrom === "None") {
+ return;
+ }
+
var view = this;
//
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
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this because you have the service enabled, addressing the recipient of
this email.
1
0
04 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/6a84a0a756b2/
changeset: r4999:6a84a0a756b2
user: greg
date: 2011-02-04 22:16:00
summary: Data library fixes and improvements:
1. Fix a bug that included the option for a regular user to upload a directory of files when the config setting existed, but the user's directory did not exist.  Instead of throwing an exception, an attempt to create the directory will now be done.  If the attempt fails, the option to "Upload a directory of files" will not be included in the select list on the upload form.
2. When browsing a data library, only display the check boxes and the actions to perform on multiple selected datasets if library datasets are displayed.
3. Clean up the behavior when performing an action on multiple library datasets.  Instead of throwing an error and not allowing the action on any of the datasets if the user is not authorized to perform the action on 1 of them, all "unauthorized" datasets are now left alone and the action is performed on all datasets for which the user is authorized to perform the action.  Appropriate messages detail what occurred.
4. Allow regular users to delete multiple datasets returned from library dataset searches based on the behavior described in 3 above.
5. Do not include the "Select datasets for import into selected histories" option in the actions pop-up menu at the data library level if the library's root folder doesn't contain any accessible datasets.  Make behavior the same for folder popup menus.
6.  Add a new LibraryFolder.active_datasets mapper and eliminate the incorrect LibraryFolder.active_library_datasets property.  Callers of the incorrect property now use the mapper.
7. Eliminate the incorrect LibraryFolder.active_datasets property.
8. Fix the queries in the library_common controller's active_folders_and_lddas() and activable_folders_and_lddas() methods to return library_datasets instead of lddas, and rename the methods to be active_folders_and_library_datasets(0 and activatable_folders_and_library_datasets() respectively.
9. Fix bug where regular user could never see deleted library items when toggling show / hide deleted items.
10. Fix functional test for uploading directories of files to a library folder.  The test generally failed because not enough time would elapse before checking if the files uploaded.  The check is now performed in a later method in the test script, hopefully allowing for enough time to pass.
11. Functional test code clarifications for the browse_library() test method.
affected #: 11 files (7.2 KB)
--- a/lib/galaxy/model/__init__.py Fri Feb 04 14:48:39 2011 -0500
+++ b/lib/galaxy/model/__init__.py Fri Feb 04 16:16:00 2011 -0500
@@ -1040,33 +1040,9 @@
return template.get_widgets( trans.user )
return []
@property
- def active_library_datasets( self ):
- def sort_by_attr( seq, attr ):
- """
- Sort the sequence of objects by object's attribute
- Arguments:
- seq - the list or any sequence (including immutable one) of objects to sort.
- attr - the name of attribute to sort by
- """
- # Use the "Schwartzian transform"
- # Create the auxiliary list of tuples where every i-th tuple has form
- # (seq[i].attr, i, seq[i]) and sort it. The second item of tuple is needed not
- # only to provide stable sorting, but mainly to eliminate comparison of objects
- # (which can be expensive or prohibited) in case of equal attribute values.
- intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq )
- intermed.sort()
- return map( operator.getitem, intermed, ( -1, ) * len( intermed ) )
- # This needs to be a list
- active_library_datasets = [ ld for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.deleted ]
- return sort_by_attr( [ ld for ld in active_library_datasets ], 'name' )
- @property
def activatable_library_datasets( self ):
# This needs to be a list
return [ ld for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.dataset.deleted ]
- @property
- def active_datasets( self ):
- # This needs to be a list
- return [ ld.library_dataset_dataset_association.dataset for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.deleted ]
def get_display_name( self ):
# Library folder name can be either a string or a unicode object. If string,
# convert to unicode object assuming 'utf-8' format.
--- a/lib/galaxy/model/mapping.py Fri Feb 04 14:48:39 2011 -0500
+++ b/lib/galaxy/model/mapping.py Fri Feb 04 16:16:00 2011 -0500
@@ -1294,6 +1294,11 @@
primaryjoin=( ( LibraryDataset.table.c.folder_id == LibraryFolder.table.c.id ) ),
order_by=asc( LibraryDataset.table.c._name ),
lazy=False,
+ viewonly=True ),
+ active_datasets=relation( LibraryDataset,
+ primaryjoin=( ( LibraryDataset.table.c.folder_id == LibraryFolder.table.c.id ) & ( not_( LibraryDataset.table.c.deleted ) ) ),
+ order_by=asc( LibraryDataset.table.c._name ),
+ lazy=False,
viewonly=True )
) )
--- a/lib/galaxy/security/__init__.py Fri Feb 04 14:48:39 2011 -0500
+++ b/lib/galaxy/security/__init__.py Fri Feb 04 16:16:00 2011 -0500
@@ -270,6 +270,26 @@
.order_by( trans.app.model.Library.name ):
accessible_libraries.append( library )
return accessible_libraries
+ def has_accessible_folders( self, trans, folder, user, roles, search_downward=True ):
+ if self.has_accessible_library_datasets( trans, folder, user, roles, search_downward=search_downward ) or \
+ self.can_add_library_item( roles, folder ) or \
+ self.can_modify_library_item( roles, folder ) or \
+ self.can_manage_library_item( roles, folder ):
+ return True
+ if search_downward:
+ for folder in folder.active_folders:
+ return self.has_accessible_folders( trans, folder, user, roles, search_downward=search_downward )
+ return False
+ def has_accessible_library_datasets( self, trans, folder, user, roles, search_downward=True ):
+ for library_dataset in trans.sa_session.query( trans.model.LibraryDataset ) \
+ .filter( and_( trans.model.LibraryDataset.table.c.deleted == False,
+ trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) ):
+ if self.can_access_library_item( roles, library_dataset, user ):
+ return True
+ if search_downward:
+ for folder in folder.active_folders:
+ return self.has_accessible_library_datasets( trans, folder, user, roles, search_downward=search_downward )
+ return False
def can_access_library_item( self, roles, item, user ):
if type( item ) == self.model.Library:
return self.can_access_library( roles, item )
@@ -504,7 +524,7 @@
permissions[ action ] = [ item_permission.role ]
return permissions
def get_accessible_request_types( self, trans, user ):
- """Return all ReqquestTypes that the received user has permission to access."""
+ """Return all RequestTypes that the received user has permission to access."""
accessible_request_types = []
current_user_role_ids = [ role.id for role in user.all_roles() ]
request_type_access_action = self.permitted_actions.REQUEST_TYPE_ACCESS.action
--- a/lib/galaxy/web/controllers/library_common.py Fri Feb 04 14:48:39 2011 -0500
+++ b/lib/galaxy/web/controllers/library_common.py Fri Feb 04 16:16:00 2011 -0500
@@ -1312,8 +1312,15 @@
if option_value == 'upload_directory':
if is_admin and not trans.app.config.library_import_dir:
continue
- elif not is_admin and not trans.app.config.user_library_import_dir:
- continue
+ elif not is_admin:
+ if not trans.app.config.user_library_import_dir:
+ continue
+ path = os.path.join( trans.app.config.user_library_import_dir, trans.user.email )
+ if not os.path.isdir( path ):
+ try:
+ os.makedirs( path )
+ except:
+ continue
elif option_value == 'upload_paths':
if not is_admin or not trans.app.config.allow_library_path_paste:
continue
@@ -1553,54 +1560,70 @@
error = True
message = 'You must select an action to perform on the selected datasets.'
else:
- # Set up the list of lddas for later, and get permission checks out of the way so we don't have to do it in multiple places later.
ldda_ids = util.listify( ldda_ids )
for ldda_id in ldda_ids:
try:
ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) )
+ lddas.append( ldda )
except:
ldda = None
- if not ldda or ( not is_admin and not trans.app.security_agent.can_access_library_item( current_user_roles, ldda, trans.user ) ):
- error = True
- message = "Invalid library dataset id ( %s ) specified." % str( ldda_id )
- break
- lddas.append( ldda )
- if not is_admin:
- if action == 'manage_permissions':
- for ldda in lddas:
- if not ( trans.app.security_agent.can_manage_library_item( current_user_roles, ldda ) and \
- trans.app.security_agent.can_manage_dataset( current_user_roles, ldda.dataset ) ):
- error = True
- message = "You are not authorized to manage permissions on library dataset '%s'." % ldda.name
- break
- elif action == 'delete':
- for ldda in lddas:
- if not trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ):
- error = True
- message = "You are not authorized to modify library dataset '%s'." % ldda.name
- break
+ message += "Invalid library dataset id (%s) specified. " % str( ldda_id )
if not error:
if action == 'manage_permissions':
- trans.response.send_redirect( web.url_for( controller='library_common',
- action='ldda_permissions',
- cntrller=cntrller,
- use_panels=use_panels,
- library_id=library_id,
- folder_id=trans.security.encode_id( lddas[0].library_dataset.folder.id ),
- id=",".join( ldda_ids ),
- show_deleted=show_deleted,
- message=util.sanitize_text( message ),
- status=status ) )
+ valid_ldda_ids = []
+ valid_lddas = []
+ invalid_lddas = []
+ for ldda in lddas:
+ if trans.app.security_agent.can_manage_library_item( current_user_roles, ldda ):
+ valid_lddas.append( ldda )
+ valid_ldda_ids.append( ldda.id )
+ else:
+ invalid_lddas.append( ldda )
+ if invalid_lddas:
+ message += "You are not authorized to manage permissions on %s: " % inflector.cond_plural( len( invalid_lddas ), "dataset" )
+ for ldda in invalid_lddas:
+ message += '(%s)' % ldda.name
+ message += '. '
+ if valid_ldda_ids:
+ folder_id = trans.security.encode_id( valid_lddas[0].library_dataset.folder.id )
+ trans.response.send_redirect( web.url_for( controller='library_common',
+ action='ldda_permissions',
+ cntrller=cntrller,
+ use_panels=use_panels,
+ library_id=library_id,
+ folder_id=folder_id,
+ id=",".join( valid_ldda_ids ),
+ show_deleted=show_deleted,
+ message=util.sanitize_text( message ),
+ status=status ) )
+ else:
+ message = "You are not authorized to manage permissions on any of the selected datasets."
elif action == 'delete':
+ valid_lddas = []
+ invalid_lddas = []
for ldda in lddas:
- # Do not delete the association, just delete the library_dataset. The
- # cleanup_datasets.py script handles everything else.
- ld = ldda.library_dataset
- ld.deleted = True
- trans.sa_session.add( ld )
- trans.sa_session.flush()
- message = "The selected datasets have been deleted."
- elif action in ['zip','tgz','tbz','ngxzip']:
+ if trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ):
+ valid_lddas.append( ldda )
+ else:
+ invalid_lddas.append( ldda )
+ if invalid_lddas:
+ message += "You are not authorized to delete %s: " % inflector.cond_plural( len( invalid_lddas ), "dataset" )
+ for ldda in invalid_lddas:
+ message += '(%s)' % ldda.name
+ message += '. '
+ if valid_lddas:
+ for ldda in valid_lddas:
+ # Do not delete the association, just delete the library_dataset. The
+ # cleanup_datasets.py script handles everything else.
+ ld = ldda.library_dataset
+ ld.deleted = True
+ trans.sa_session.add( ld )
+ trans.sa_session.flush()
+ num_valid_lddas = len( valid_lddas )
+ message += "Deleted %i %s." % ( num_valid_lddas, inflector.cond_plural( num_valid_lddas, "dataset" ) )
+ else:
+ message = "You are not authorized to delete any of the selected datasets."
+ elif action in [ 'zip','tgz','tbz','ngxzip' ]:
error = False
killme = string.punctuation + string.whitespace
trantab = string.maketrans(killme,'_'*len(killme))
@@ -1723,25 +1746,27 @@
archive.wsgi_status = trans.response.wsgi_status()
archive.wsgi_headeritems = trans.response.wsgi_headeritems()
return archive.stream
- else:
- status = 'error'
- message = 'Invalid action ( %s ) specified.' % action
+ else:
+ status = 'error'
+ message = 'Invalid action (%s) specified.' % str( action )
if library_id:
# If we have a library_id, browse the associated library
return trans.response.send_redirect( web.url_for( controller='library_common',
action='browse_library',
cntrller=cntrller,
+ current_user_roles=current_user_roles,
use_panels=use_panels,
id=library_id,
show_deleted=show_deleted,
message=util.sanitize_text( message ),
status=status ) )
else:
- # We must have arrived here from the library_dataset_search_results page, so reddirect there.
+ # We arrived here from the library_dataset_search_results page, so redirect there.
search_term = params.get( 'search_term', '' )
comptypes = get_comptypes( trans )
return trans.fill_template( '/library/common/library_dataset_search_results.mako',
cntrller=cntrller,
+ current_user_roles=current_user_roles,
search_term=search_term,
comptypes=comptypes,
lddas=lddas,
@@ -2121,27 +2146,26 @@
.options( eagerload_all( "actions" ) ) \
.order_by( trans.app.model.LibraryFolder.table.c.name ) \
.all()
-def active_folders_and_lddas( trans, folder ):
+def active_folders_and_library_datasets( trans, folder ):
folders = active_folders( trans, folder )
- # This query is much faster than the folder.active_library_datasets property
- lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \
- .filter_by( deleted=False ) \
- .join( "library_dataset" ) \
- .filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \
- .order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \
- .all()
- return folders, lddas
-def activatable_folders_and_lddas( trans, folder ):
+ library_datasets = trans.sa_session.query( trans.model.LibraryDataset ) \
+ .filter( and_( trans.model.LibraryDataset.table.c.deleted == False,
+ trans.model.LibraryDataset.table.c.folder_id == folder.id ) ) \
+ .order_by( trans.model.LibraryDataset.table.c._name ) \
+ .all()
+ return folders, library_datasets
+def activatable_folders_and_library_datasets( trans, folder ):
folders = activatable_folders( trans, folder )
- # This query is much faster than the folder.activatable_library_datasets property
- lddas = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ) \
- .join( "library_dataset" ) \
- .filter( trans.app.model.LibraryDataset.table.c.folder_id==folder.id ) \
- .join( "dataset" ) \
- .filter( trans.app.model.Dataset.table.c.deleted==False ) \
- .order_by( trans.app.model.LibraryDatasetDatasetAssociation.table.c.name ) \
- .all()
- return folders, lddas
+ library_datasets = trans.sa_session.query( trans.model.LibraryDataset ) \
+ .filter( trans.model.LibraryDataset.table.c.folder_id == folder.id ) \
+ .join( ( trans.model.LibraryDatasetDatasetAssociation.table,
+ trans.model.LibraryDataset.table.c.library_dataset_dataset_association_id == trans.model.LibraryDatasetDatasetAssociation.table.c.id ) ) \
+ .join( ( trans.model.Dataset.table,
+ trans.model.LibraryDatasetDatasetAssociation.table.c.dataset_id == trans.model.Dataset.table.c.id ) ) \
+ .filter( trans.model.Dataset.table.c.deleted == False ) \
+ .order_by( trans.model.LibraryDataset.table.c._name ) \
+ .all()
+ return folders, library_datasets
def branch_deleted( folder ):
# Return True if a folder belongs to a branch that has been deleted
if folder.deleted:
--- a/templates/library/common/browse_library.mako Fri Feb 04 14:48:39 2011 -0500
+++ b/templates/library/common/browse_library.mako Fri Feb 04 16:16:00 2011 -0500
@@ -213,7 +213,9 @@
## children, which are always lddas ). We also need to make sure we're displaying the latest version of this
## library_dataset, so we display the attributes from the ldda.
- from galaxy.web.controllers.library_common import active_folders, active_folders_and_lddas, activatable_folders_and_lddas, branch_deleted
+ from galaxy.web.controllers.library_common import branch_deleted
+
+ is_admin = trans.user_is_admin() and cntrller == 'library_admin'
if ldda.user:
uploaded_by = ldda.user.email
@@ -221,7 +223,7 @@
uploaded_by = 'anonymous'
if ldda == library_dataset.library_dataset_dataset_association:
current_version = True
- if trans.user_is_admin() and cntrller == 'library_admin':
+ if is_admin:
can_modify = can_manage = True
elif cntrller in [ 'library', 'requests' ]:
can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, library_dataset )
@@ -307,7 +309,10 @@
<%def name="render_folder( cntrller, folder, folder_pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=False, parent=None, row_counter=None, root_folder=False )"><%
- from galaxy.web.controllers.library_common import active_folders, active_folders_and_lddas, activatable_folders_and_lddas, branch_deleted
+ from galaxy.web.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, branch_deleted
+
+ is_admin = trans.user_is_admin() and cntrller == 'library_admin'
+
if root_folder:
pad = folder_pad
expander = h.url_for("/static/images/silk/resultset_bottom.png")
@@ -321,7 +326,7 @@
if str( folder.id ) in hidden_folder_ids:
return ""
my_row = None
- if trans.user_is_admin() and cntrller == 'library_admin':
+ if is_admin:
can_add = can_modify = can_manage = True
elif cntrller in [ 'library' ]:
can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, folder )
@@ -340,8 +345,11 @@
can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, folder )
else:
can_add = can_modify = can_manage = False
+
form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
info_association, inherited = folder.get_info_association( restrict=True )
+
+ has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False )
%>
%if not root_folder and ( not folder.deleted or show_deleted ):
<% encoded_id = trans.security.encode_id(folder.id) %>
@@ -371,7 +379,9 @@
<a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a>
%endif
%if not branch_deleted( folder ):
- <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select folder datasets for import into selected histories</a>
+ %if has_accessible_datasets:
+ <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a>
+ %endif
%if can_modify:
<a class="action-button" href="${h.url_for( controller='library_common', action='folder_info', cntrller=cntrller, id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit information</a>
%else:
@@ -412,12 +422,28 @@
row_counter.increment()
%>
%endif
- %if cntrller == 'library':
- <% sub_folders = active_folders( trans, folder ) %>
+ <%
+ if show_deleted:
+ sub_folders, library_datasets = activatable_folders_and_library_datasets( trans, folder )
+ else:
+ sub_folders, library_datasets = active_folders_and_library_datasets( trans, folder )
+ %>
+ %if is_admin:
+ %for sub_folder in sub_folders:
+ ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )}
+ %endfor
+ %for library_dataset in library_datasets:
+ <%
+ ldda = library_dataset.library_dataset_dataset_association
+ selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids
+ %>
+ ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )}
+ %endfor
+ %else:
%for sub_folder in sub_folders:
${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )}
%endfor
- %for library_dataset in folder.active_library_datasets:
+ %for library_dataset in library_datasets:
<%
ldda = library_dataset.library_dataset_dataset_association
can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ldda.dataset )
@@ -427,23 +453,6 @@
${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )}
%endif
%endfor
- %elif trans.user_is_admin() and cntrller == 'library_admin':
- <%
- if show_deleted:
- sub_folders, lddas = activatable_folders_and_lddas( trans, folder )
- else:
- sub_folders, lddas = active_folders_and_lddas( trans, folder )
- %>
- %for sub_folder in sub_folders:
- ${render_folder( cntrller, sub_folder, pad, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=my_row, row_counter=row_counter, root_folder=False )}
- %endfor
- %for ldda in lddas:
- <%
- library_dataset = ldda.library_dataset
- selected = created_ldda_ids and str( ldda.id ) in created_ldda_ids
- %>
- ${render_dataset( cntrller, ldda, library_dataset, selected, library, folder, pad, my_row, row_counter, tracked_datasets, show_deleted=show_deleted )}
- %endfor
%endif
</%def>
@@ -453,7 +462,9 @@
from galaxy.web.controllers.library_common import branch_deleted
from time import strftime
- if trans.user_is_admin() and cntrller == 'library_admin':
+ is_admin = trans.user_is_admin() and cntrller == 'library_admin'
+
+ if is_admin:
can_add = can_modify = can_manage = True
elif cntrller in [ 'library', 'requests' ]:
can_add = trans.app.security_agent.can_add_library_item( current_user_roles, library )
@@ -461,11 +472,15 @@
can_manage = trans.app.security_agent.can_manage_library_item( current_user_roles, library )
else:
can_add = can_modify = can_manage = False
+
info_association, inherited = library.get_info_association()
form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE
-
+
+ has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False )
+ has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles )
+
tracked_datasets = {}
-
+
class RowCounter( object ):
def __init__( self ):
self.count = 0
@@ -478,7 +493,7 @@
<h2>Data Library “${library.name}”</h2><ul class="manage-table-actions">
- %if not library.deleted and ( ( trans.user_is_admin() and cntrller == 'library_admin' ) or can_add ):
+ %if not library.deleted and ( is_admin or can_add ):
<li><a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add datasets</a></li><li><a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( library.root_folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add folder</a></li>
%endif
@@ -508,7 +523,9 @@
%endif
<a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a>
%endif
- <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a>
+ %if has_accessible_datasets:
+ <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a>
+ %endif
%elif can_modify and not library.purged:
<a class="action-button" href="${h.url_for( controller='library_common', action='undelete_library_item', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), item_id=trans.security.encode_id( library.id ), item_type='library', use_panels=use_panels )}">Undelete this data library</a>
%elif library.purged:
@@ -528,13 +545,18 @@
</div><br/>
%endif
-
- <form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}" onSubmit="javascript:return checkForm();" method="post">
+
+ %if has_accessible_datasets:
+ <form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}" onSubmit="javascript:return checkForm();" method="post">
+ %endif
+ %if has_accessible_folders:
<table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid"><thead><tr class="libraryTitle"><th>
- <input type="checkbox" id="checkAll" name=select_all_datasets_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_datasets_checkbox value="true"/>
+ %if has_accessible_datasets:
+ <input type="checkbox" id="checkAll" name=select_all_datasets_checkbox value="true" onclick='checkAllFields(1);'/><input type="hidden" name=select_all_datasets_checkbox value="true"/>
+ %endif
Name
</th><th>Message</th>
@@ -546,18 +568,21 @@
<% row_counter = RowCounter() %>
%if cntrller in [ 'library', 'requests' ]:
${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, library, hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )}
- %if not library.deleted:
+ %if not library.deleted and has_accessible_datasets:
${render_actions_on_multiple_items()}
%endif
%elif ( trans.user_is_admin() and cntrller in [ 'library_admin', 'requests_admin' ] ):
${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, library, [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )}
- %if not library.deleted and not show_deleted:
+ %if not library.deleted and not show_deleted and has_accessible_datasets:
${render_actions_on_multiple_items()}
%endif
%endif
</table>
- </form>
-
+ %endif
+ %if has_accessible_datasets:
+ </form>
+ %endif
+
%if tracked_datasets:
<script type="text/javascript">
// Updater
@@ -566,5 +591,10 @@
<!-- running: do not change this comment, used by TwillTestCase.library_wait -->
%endif
- ${render_compression_types_help( comptypes )}
+ %if has_accessible_datasets:
+ ${render_compression_types_help( comptypes )}
+ %endif
+ %if not has_accessible_folders:
+ The data library '${library.name}' does not contain any datasets that you can access.
+ %endif
</%def>
--- a/templates/library/common/common.mako Fri Feb 04 14:48:39 2011 -0500
+++ b/templates/library/common/common.mako Fri Feb 04 16:16:00 2011 -0500
@@ -395,7 +395,7 @@
<%def name="render_actions_on_multiple_items( actions_to_exclude=[] )"><%
is_admin = trans.user_is_admin() and cntrller=='library_admin'
- can_delete = 'delete' not in actions_to_exclude and is_admin
+ can_delete = 'delete' not in actions_to_exclude
can_download = 'download' not in actions_to_exclude
can_import_to_histories = 'import_to_histories' not in actions_to_exclude
can_manage_permissions = 'manage_permissions' not in actions_to_exclude
--- a/templates/library/common/library_dataset_search_results.mako Fri Feb 04 14:48:39 2011 -0500
+++ b/templates/library/common/library_dataset_search_results.mako Fri Feb 04 16:16:00 2011 -0500
@@ -95,6 +95,7 @@
<p>The string "${search_term}" was found in at least one of the following information components of the displayed library datasets.</p>
${render_searched_components()}
<form name="act_on_multiple_datasets" action="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, use_panels=use_panels, show_deleted=show_deleted )}" onSubmit="javascript:return checkForm();" method="post">
+ <input type="hidden" name=search_term value="${search_term}"/><table cellspacing="0" cellpadding="0" border="0" width="100%" class="grid" id="library-grid"><thead><tr class="libraryTitle">
--- a/test/base/twilltestcase.py Fri Feb 04 14:48:39 2011 -0500
+++ b/test/base/twilltestcase.py Fri Feb 04 16:16:00 2011 -0500
@@ -1844,10 +1844,8 @@
raise AssertionError, "String (%s) incorrectly displayed when browing library." % check_str
except:
pass
- def browse_library( self, cntrller, id, show_deleted=False, strings_displayed=[], strings_not_displayed=[] ):
- self.visit_url( '%s/library_common/browse_library?cntrller=%s&id=%s&show_deleted=%s' % ( self.url, cntrller, id, str( show_deleted ) ) )
- data=self.last_page()
- file( 'greg.html', 'wb' ).write( data )
+ def browse_library( self, cntrller, library_id, show_deleted=False, strings_displayed=[], strings_not_displayed=[] ):
+ self.visit_url( '%s/library_common/browse_library?cntrller=%s&id=%s&show_deleted=%s' % ( self.url, cntrller, library_id, str( show_deleted ) ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
for check_str in strings_not_displayed:
--- a/test/functional/test_library_features.py Fri Feb 04 14:48:39 2011 -0500
+++ b/test/functional/test_library_features.py Fri Feb 04 16:16:00 2011 -0500
@@ -78,8 +78,8 @@
global folder1
folder1 = get_folder( root_folder.id, name, description )
assert folder1 is not None, 'Problem retrieving library folder named "%s" from the database' % name
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ folder1.name, folder1.description ] )
def test_035_add_subfolder_to_folder( self ):
"""Testing adding a folder to a folder"""
@@ -94,8 +94,8 @@
global subfolder1
subfolder1 = get_folder( folder1.id, name, description )
assert subfolder1 is not None, 'Problem retrieving subfolder1 from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ subfolder1.name, subfolder1.description ] )
def test_040_add_2nd_folder_to_library1( self ):
"""Testing adding a 2nd folder to a library1"""
@@ -110,8 +110,8 @@
global folder2
folder2 = get_folder( library1.root_folder.id, name, description )
assert folder2 is not None, 'Problem retrieving library folder named "%s" from the database' % name
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ folder2.name, folder2.description ] )
def test_045_add_public_dataset_to_folder2( self ):
"""Testing adding a public dataset to folder2"""
@@ -129,8 +129,8 @@
global ldda2
ldda2 = get_latest_ldda_by_name( filename )
assert ldda2 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda2 from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ ldda2.name, ldda2.message, admin_user.email ] )
def test_050_add_2nd_public_dataset_to_folder2( self ):
"""Testing adding a 2nd public dataset folder2"""
@@ -148,8 +148,8 @@
global ldda3
ldda3 = get_latest_ldda_by_name( filename )
assert ldda3 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda3 from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ ldda3.name, ldda3.message, admin_user.email ] )
def test_055_copy_dataset_from_history_to_subfolder( self ):
"""Testing copying a dataset from the current history to a subfolder"""
@@ -168,8 +168,8 @@
global ldda4
ldda4 = get_latest_ldda_by_name( filename )
assert ldda4 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda4 from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ ldda4.name, ldda4.message, admin_user.email ] )
def test_060_editing_dataset_attribute_info( self ):
"""Testing editing a library dataset's attribute information"""
@@ -182,8 +182,8 @@
ldda4.name,
new_ldda_name=new_ldda_name )
refresh( ldda4 )
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ new_ldda_name, ldda4.message ] )
def test_065_uploading_new_dataset_version( self ):
"""Testing uploading a new version of a library dataset"""
@@ -216,8 +216,8 @@
ldda4.name,
strings_displayed=[ 'This is an expired version of this library dataset' ] )
# Make sure ldda4 is no longer displayed in the library
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_not_displayed=[ ldda4.name, ldda4.message ] )
def test_070_upload_directory_of_files_from_libraries_view( self ):
"""Testing uploading a directory of files to a root folder from the Data Libraries view"""
@@ -249,9 +249,6 @@
server_dir=regular_user1.email,
ldda_message=ldda_message,
strings_displayed = [ "Upload a directory of files" ] )
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
- strings_displayed=[ regular_user1.email, ldda_message, '1.fasta' ] )
self.logout()
self.login( regular_user3.email )
ldda_message = 'Uploaded all files in test-data/users/test3.../run1'
@@ -264,9 +261,6 @@
server_dir='run1',
ldda_message=ldda_message,
strings_displayed=[ 'Upload a directory of files', '<option>None</option>' ] )
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
- strings_displayed=[ regular_user3.email, ldda_message, '2.fasta' ] )
def test_075_download_archive_of_library_files( self ):
"""Testing downloading an archive of files from library1"""
# logged in as regular_user3
@@ -290,7 +284,21 @@
format=format )
self.check_archive_contents( archive, ( ldda1, ldda2 ) )
os.remove( archive )
- def test_080_mark_ldda2_deleted( self ):
+ def test_080_check_libraries_for_uploaded_directories_of_files( self ):
+ """Testing the results of uploading directories of files to library1"""
+ # We'll make sure the directories of files were uploaded in test_070... above.
+ # We do this here because the check would generally fail if we did it in the
+ # test_070... method since the files would not finish uploading before the check
+ # was done. Hopefully doing the check here will allow for enough time...
+ ldda_message = 'Uploaded all files in test-data/users/test1...'
+ self.browse_library( 'library',
+ self.security.encode_id( library1.id ),
+ strings_displayed=[ regular_user1.email, ldda_message, '1.fasta' ] )
+ ldda_message = 'Uploaded all files in test-data/users/test3.../run1'
+ self.browse_library( 'library',
+ self.security.encode_id( library1.id ),
+ strings_displayed=[ regular_user3.email, ldda_message, '2.fasta' ] )
+ def test_085_mark_ldda2_deleted( self ):
"""Testing marking ldda2 as deleted"""
# Logged in as admin_user
self.delete_library_item( 'library_admin',
@@ -298,20 +306,20 @@
self.security.encode_id( ldda2.library_dataset.id ),
ldda2.name,
item_type='library_dataset' )
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_not_displayed=[ ldda2.name, ldda2.message ] )
- def test_085_display_and_hide_deleted_ldda2( self ):
+ def test_090_display_and_hide_deleted_ldda2( self ):
"""Testing displaying and hiding a deleted ldda2"""
# Logged in as admin_user
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
show_deleted=True,
strings_displayed=[ ldda2.name, ldda2.message ] )
self.browse_library( 'library_admin',
self.security.encode_id( library1.id ),
strings_not_displayed=[ ldda2.name, ldda2.message ] )
- def test_090_mark_folder2_deleted( self ):
+ def test_095_mark_folder2_deleted( self ):
"""Testing marking folder2 as deleted"""
# Logged in as admin_user
self.delete_library_item( 'library_admin',
@@ -319,10 +327,10 @@
self.security.encode_id( folder2.id ),
folder2.name,
item_type='folder' )
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_not_displayed=[ folder2.name ] )
- def test_095_mark_folder_undeleted( self ):
+ def test_100_mark_folder_undeleted( self ):
"""Testing marking a library folder as undeleted"""
# Logged in as admin_user
self.undelete_library_item( 'library_admin',
@@ -332,11 +340,11 @@
item_type='folder' )
# 2.bed was deleted before the folder was deleted, so state should have been saved. In order
# for 2.bed to be displayed, it would itself have to be marked undeleted.
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ folder2.name ],
strings_not_displayed=[ ldda2.name ] )
- def test_100_mark_library_deleted( self ):
+ def test_105_mark_library_deleted( self ):
"""Testing marking a library as deleted"""
# Logged in as admin_user
# First mark folder2 as deleted to further test state saving when we undelete the library
@@ -352,7 +360,7 @@
item_type='library' )
self.browse_libraries_admin( strings_not_displayed=[ library1.name ] )
self.browse_libraries_admin( deleted=True, strings_displayed=[ library1.name ] )
- def test_105_mark_library_undeleted( self ):
+ def test_110_mark_library_undeleted( self ):
"""Testing marking a library as undeleted"""
# Logged in as admin_user
self.undelete_library_item( 'library_admin',
@@ -361,11 +369,11 @@
library1.name,
item_type='library' )
self.browse_libraries_admin( strings_displayed=[ library1.name ] )
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
- strings_displayed=[ library1.name ],
- strings_not_displayed=[ folder2.name ] )
- def test_110_purge_library( self ):
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
+ strings_displayed=[ library1.name ],
+ strings_not_displayed=[ folder2.name ] )
+ def test_115_purge_library( self ):
"""Testing purging a library"""
# Logged in as admin_user
self.delete_library_item( 'library_admin',
--- a/test/functional/test_library_security.py Fri Feb 04 14:48:39 2011 -0500
+++ b/test/functional/test_library_security.py Fri Feb 04 16:16:00 2011 -0500
@@ -155,8 +155,8 @@
global ldda1
ldda1 = get_latest_ldda_by_name( filename )
assert ldda1 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda1 from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ ldda1.name, ldda1.message, admin_user.email ] )
def test_030_access_ldda1_with_private_role_restriction( self ):
"""Testing accessing ldda1 with a private role restriction"""
@@ -174,16 +174,16 @@
# 'test3(a)bx.psu.edu' ( regular_user3's private role ) since regular_user3 has Role1
#
# admin_user should not be able to see 1.bed from the analysis view's access libraries
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
- strings_not_displayed=[ folder1.name, ldda1.name, ldda1.message ] )
+ self.browse_library( cntrller='library',
+ library_id=self.security.encode_id( library1.id ),
+ strings_not_displayed=[ folder1.name, ldda1.name, ldda1.message ] )
self.logout()
# regular_user1 should be able to see 1.bed from the Data Libraries view
# since it was associated with regular_user1's private role
self.login( email=regular_user1.email )
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
- strings_displayed=[ folder1.name, ldda1.name, ldda1.message ] )
+ self.browse_library( cntrller='library',
+ library_id=self.security.encode_id( library1.id ),
+ strings_displayed=[ folder1.name, ldda1.name, ldda1.message ] )
self.logout()
# regular_user2 should not be to see library1 since they do not have
# Role1 which is associated with the LIBRARY_ACCESS permission
@@ -192,8 +192,8 @@
self.logout()
# regular_user3 should not be able to see 1.bed from the analysis view's access librarys
self.login( email=regular_user3.email )
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library',
+ library_id=self.security.encode_id( library1.id ),
strings_not_displayed=[ folder1.name ] )
self.logout()
self.login( email=admin_user.email )
@@ -229,8 +229,8 @@
permissions_out,
ldda_name=ldda1.name )
# admin_user should now be able to see 1.bed from the analysis view's access libraries
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ ldda1.name, ldda1.message ] )
def test_040_create_ldda2_with_role2_associated_with_group_and_users( self ):
"""Testing creating ldda2 with a role that is associated with a group and users"""
@@ -261,20 +261,20 @@
ldda2 = get_latest_ldda_by_name( filename )
assert ldda2 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda2 from the database'
self.browse_library( cntrller='library',
- id=self.security.encode_id( library1.id ),
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ ldda2.name, ldda2.message, admin_user.email ] )
def test_045_accessing_ldda2_with_role_associated_with_group_and_users( self ):
"""Testing accessing ldda2 with a role that is associated with a group and users"""
# Logged in as admin_user
# admin_user should be able to see 2.bed since she is associated with role2
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ ldda2.name, ldda2.message, admin_user.email ] )
self.logout()
# regular_user1 should be able to see 2.bed since she is associated with group_two
self.login( email = regular_user1.email )
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ folder1.name, ldda2.name, ldda2.message, admin_user.email ] )
# Check the permissions on the dataset 2.bed - they are as folows:
# DATASET_MANAGE_PERMISSIONS = test(a)bx.psu.edu
@@ -304,15 +304,15 @@
self.logout()
# regular_user2 should not be able to see ldda2
self.login( email=regular_user2.email )
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library',
+ library_id=self.security.encode_id( library1.id ),
strings_not_displayed=[ folder1.name, ldda2.name, ldda2.message ] )
self.logout()
# regular_user3 should not be able to see ldda2
self.login( email=regular_user3.email )
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ folder1.name ],
strings_not_displayed=[ ldda2.name, ldda2.message ] )
self.logout()
@@ -325,8 +325,8 @@
self.logout()
# regular_user2 should now be able to see ldda2
self.login( email=regular_user2.email )
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ folder1.name, ldda2.name, ldda2.message ] )
self.logout()
self.login( email=admin_user.email )
@@ -338,8 +338,8 @@
self.logout()
# regular_user3 should now be able to see ldda1
self.login( email=regular_user3.email )
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ folder1.name, ldda1.name, ldda1.message ] )
self.logout()
self.login( email=admin_user.email )
@@ -354,8 +354,8 @@
server_dir='library',
ldda_message=ldda_message,
strings_displayed=[ "Upload a directory of files" ] )
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ admin_user.email, ldda_message ] )
def test_055_change_permissions_on_datasets_uploaded_from_library_dir( self ):
"""Testing changing the permissions on datasets uploaded from a directory from the Admin view"""
@@ -403,8 +403,8 @@
# Since regular_user2 is not associated with role1, she should not have
# access to any of the 3 datasets, so she will not see folder1 on the libraries page
self.login( email=regular_user2.email )
- self.browse_library( 'library',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library',
+ library_id=self.security.encode_id( library1.id ),
strings_not_displayed=[ folder1.name ] )
self.logout()
# regular_user3 is associated with role1, so should have all permissions on imported datasets
@@ -538,8 +538,8 @@
self.login( email=regular_user2.email )
self.visit_url( '%s/library/browse_libraries' % self.url )
self.check_page_for_string( library2.name )
- self.browse_library( 'library',
- self.security.encode_id( library2.id ),
+ self.browse_library( cntrller='library',
+ library_id=self.security.encode_id( library2.id ),
strings_displayed=[ ldda6.name, ldda6.message, ldda7.name, ldda7.message, ldda8.name, ldda8.message ] )
def test_999_reset_data_for_later_test_runs( self ):
"""Reseting data to enable later test runs to pass"""
--- a/test/functional/test_library_templates.py Fri Feb 04 14:48:39 2011 -0500
+++ b/test/functional/test_library_templates.py Fri Feb 04 16:16:00 2011 -0500
@@ -136,8 +136,8 @@
def test_025_check_library1( self ):
"""Checking library1 and its root folder"""
# Logged in as admin_user
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ folder1.name, folder1.description ] )
# Make sure the template and contents were inherited to folder1
self.folder_info( cntrller='library_admin',
@@ -179,8 +179,8 @@
global ldda1
ldda1 = get_latest_ldda_by_name( filename )
assert ldda1 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda1 from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library1.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library1.id ),
strings_displayed=[ ldda1.name, ldda1.message, admin_user.email ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
@@ -275,8 +275,8 @@
def test_060_check_library2( self ):
"""Checking library2 and its root folder"""
# Logged in as admin_user
- self.browse_library( 'library_admin',
- self.security.encode_id( library2.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library2.id ),
strings_displayed=[ folder2.name, folder2.description ] )
def test_065_save_folder2_inherited_template( self ):
"""Saving the inherited template for folder2"""
@@ -306,8 +306,8 @@
strings_displayed=[ 'CheckboxField', 'checked' ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library2.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library2.id ),
strings_displayed=[ ldda.name, ldda.message, admin_user.email ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
@@ -347,8 +347,8 @@
def test_090_check_library3( self ):
"""Checking library3 and its root folder"""
# Logged in as admin_user
- self.browse_library( 'library_admin',
- self.security.encode_id( library3.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library3.id ),
strings_displayed=[ folder3.name, folder3.description ] )
def test_095_save_folder3_inherited_template( self ):
"""Saving the inherited template for folder3"""
@@ -379,8 +379,8 @@
strings_displayed=[ 'SelectField', 'selected>Option1' ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library3.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library3.id ),
strings_displayed=[ ldda.name, ldda.message, admin_user.email ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
@@ -402,8 +402,8 @@
strings_displayed=[ '<input type="hidden" name="%s" value="Option1"/>' % select_field_name ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library3.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library3.id ),
strings_displayed=[ ldda.name, admin_user.email ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
@@ -469,8 +469,8 @@
strings_displayed=[ 'TextArea', 'This text should be inherited' ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library4.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library4.id ),
strings_displayed=[ ldda.name, ldda.message, admin_user.email ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
@@ -535,8 +535,8 @@
strings_displayed=[ 'TextField', 'This text should be inherited' ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library5.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library5.id ),
strings_displayed=[ ldda.name, ldda.message, admin_user.email ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
@@ -577,8 +577,8 @@
'TextArea' ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library5.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library5.id ),
strings_displayed=[ ldda.name, ldda.message, admin_user.email ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
@@ -642,8 +642,8 @@
strings_displayed=[ 'WorkflowField', 'none' ] )
ldda = get_latest_ldda_by_name( filename )
assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database'
- self.browse_library( 'library_admin',
- self.security.encode_id( library6.id ),
+ self.browse_library( cntrller='library_admin',
+ library_id=self.security.encode_id( library6.id ),
strings_displayed=[ ldda.name, ldda.message, admin_user.email ] )
# Make sure the library template contents were correctly saved
self.ldda_edit_info( 'library_admin',
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: james_taylor: trackster: fix for track height calculation
by Bitbucket 04 Feb '11
by Bitbucket 04 Feb '11
04 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/046e456f2c5b/
changeset: r4998:046e456f2c5b
user: james_taylor
date: 2011-02-04 20:48:39
summary: trackster: fix for track height calculation
affected #: 1 file (12 bytes)
--- a/static/scripts/trackster.js Fri Feb 04 14:49:23 2011 -0500
+++ b/static/scripts/trackster.js Fri Feb 04 14:48:39 2011 -0500
@@ -1406,7 +1406,7 @@
if (this.left_offset) {
left -= this.left_offset;
}
- tile_element.css({ position: 'absolute', top: 0, left: left });
+ tile_element.css({ position: 'absolute', top: 0, left: left, height: '' });
// Setup and show tile element.
parent_element.append( tile_element );
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Trackster history dataset selection: show history name, show and order by hid in display.
by Bitbucket 04 Feb '11
by Bitbucket 04 Feb '11
04 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/d2db43017281/
changeset: r4997:d2db43017281
user: jgoecks
date: 2011-02-04 20:49:23
summary: Trackster history dataset selection: show history name, show and order by hid in display.
affected #: 4 files (400 bytes)
--- a/lib/galaxy/web/controllers/tracks.py Fri Feb 04 14:29:23 2011 -0500
+++ b/lib/galaxy/web/controllers/tracks.py Fri Feb 04 14:49:23 2011 -0500
@@ -106,23 +106,29 @@
available_tracks = None
title = "Add Datasets"
template = "tracks/history_datasets_select_grid.mako"
- async_template = "/page/select_items_grid_async.mako"
model_class = model.HistoryDatasetAssociation
default_filter = { "deleted" : "False" , "shared" : "All" }
- default_sort_key = "name"
+ default_sort_key = "-hid"
use_async = True
use_paging = False
columns = [
+ grids.GridColumn( "Id", key="hid" ),
grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ),
grids.TextColumn( "Filetype", key="extension", model_class=model.HistoryDatasetAssociation ),
HistoryColumn( "History", key="history", visible=False ),
DbKeyColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=True, sortable=False )
]
columns.append(
- grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ],
+ grids.MulticolFilterColumn( "Search name and filetype", cols_to_filter=[ columns[1], columns[2] ],
key="free-text-search", visible=False, filterable="standard" )
)
-
+
+ def get_current_item( self, trans, **kwargs ):
+ """
+ Current item for grid is the history being queried. This is a bit
+ of hack since current_item typically means the current item in the grid.
+ """
+ return model.History.get( trans.security.decode_id( kwargs[ 'f-history' ] ) )
def build_initial_query( self, trans, **kwargs ):
return trans.sa_session.query( self.model_class ).join( model.History.table ).join( model.Dataset.table )
def apply_query_filter( self, trans, query, **kwargs ):
@@ -144,13 +150,9 @@
use_async = True
use_paging = False
columns = [
- grids.TextColumn( "Title", key="title", model_class=model.Visualization ),
+ grids.TextColumn( "Title", key="title", model_class=model.Visualization, filterable="standard" ),
grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization )
]
- columns.append(
- grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0] ],
- key="free-text-search", visible=False, filterable="standard" )
- )
def build_initial_query( self, trans, **kwargs ):
return trans.sa_session.query( self.model_class )
--- a/lib/galaxy/web/framework/helpers/grids.py Fri Feb 04 14:29:23 2011 -0500
+++ b/lib/galaxy/web/framework/helpers/grids.py Fri Feb 04 14:49:23 2011 -0500
@@ -271,7 +271,7 @@
message = message,
use_panels=self.use_panels,
webapp=webapp,
- show_item_checkboxes = kwargs.get( "show_item_checkboxes", False ),
+ show_item_checkboxes = ( kwargs.get( 'show_item_checkboxes', '' ) in ['True', 'true'] ),
# Pass back kwargs so that grid template can set and use args without
# grid explicitly having to pass them.
kwargs=kwargs )
--- a/templates/grid_base.mako Fri Feb 04 14:29:23 2011 -0500
+++ b/templates/grid_base.mako Fri Feb 04 14:49:23 2011 -0500
@@ -262,6 +262,9 @@
// Add sort argument to URL args.
url_args['sort'] = "${sort_key}";
+ // Add show_item_checkboxes argument to URL args.
+ url_args['show_item_checkboxes'] = ("${context.get('show_item_checkboxes', False)}" === "True");
+
// Add async keyword to URL args.
url_args['async'] = true;
--- a/templates/tracks/history_datasets_select_grid.mako Fri Feb 04 14:29:23 2011 -0500
+++ b/templates/tracks/history_datasets_select_grid.mako Fri Feb 04 14:49:23 2011 -0500
@@ -11,6 +11,5 @@
%>
## Use class 'label' to piggyback on URL functionality in parent template.
<a class="label" href="${h.url_for( **url_dict )}">Back to histories</a>
- <br /><br />
- ${parent.title()}
+ <h2>History '${grid.get_current_item( trans, **kwargs ).name}'</h2></%def>
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: james_taylor: Disable overview canvas saving for now, need to do this right
by Bitbucket 04 Feb '11
by Bitbucket 04 Feb '11
04 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/4aa68bbab83f/
changeset: r4996:4aa68bbab83f
user: james_taylor
date: 2011-02-04 20:29:23
summary: Disable overview canvas saving for now, need to do this right
affected #: 1 file (173 bytes)
--- a/static/scripts/trackster.js Fri Feb 04 14:17:07 2011 -0500
+++ b/static/scripts/trackster.js Fri Feb 04 14:29:23 2011 -0500
@@ -1374,6 +1374,8 @@
}
if (tile_element) {
// Store initial canvas in case we need to use it for overview
+ /* This is completely broken, just saves the first tile it sees
+ regardless of if it should be the overview
if (!track.initial_canvas && !window.G_vmlCanvasManager) {
track.initial_canvas = $(tile_element).clone();
var src_ctx = tile_element.get(0).getContext("2d");
@@ -1382,6 +1384,7 @@
tgt_ctx.putImageData(data, 0, 0);
track.set_overview();
}
+ */
// Add tile to cache and show tile.
track.tile_cache.set(key, tile_element);
track.show_tile(tile_element, parent_element, tile_low);
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: james_taylor: trackster: give tile tracks a background that shows when loading tiles
by Bitbucket 04 Feb '11
by Bitbucket 04 Feb '11
04 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/570bbff943b1/
changeset: r4995:570bbff943b1
user: james_taylor
date: 2011-02-04 20:17:07
summary: trackster: give tile tracks a background that shows when loading tiles
affected #: 3 files (766 bytes)
--- a/static/scripts/trackster.js Fri Feb 04 11:33:30 2011 -0500
+++ b/static/scripts/trackster.js Fri Feb 04 14:17:07 2011 -0500
@@ -51,6 +51,8 @@
});
}
+
+
/**
* Init constants & functions used throughout trackster.
*/
@@ -1360,6 +1362,15 @@
}
if (!tile_element) {
tile_element = track.draw_tile(resolution, tile_index, parent_element, w_scale);
+ if ( tile_element ) {
+ // Wrap element in div for background
+ var wrapper_element = $("<div class='track-tile'>").prepend( tile_element );
+ // HACK: filtering
+ if ( tile_element.hasClass( FILTERABLE_CLASS ) ) {
+ wrapper_element.addClass( FILTERABLE_CLASS );
+ }
+ tile_element = wrapper_element;
+ }
}
if (tile_element) {
// Store initial canvas in case we need to use it for overview
@@ -1398,6 +1409,7 @@
parent_element.append( tile_element );
track.max_height = Math.max( track.max_height, tile_element.height() );
track.content_div.css("height", track.max_height + "px");
+ parent_element.children().css("height", track.max_height + "px");
if (track.hidden) { return; }
--- a/templates/tracks/browser.mako Fri Feb 04 11:33:30 2011 -0500
+++ b/templates/tracks/browser.mako Fri Feb 04 14:17:07 2011 -0500
@@ -102,13 +102,22 @@
}
.track-content {
- background: #eee;
+ background: #eee url(${h.url_for('/static/images/tracks/diag_bg.gif')});
min-height: 16px;
}
.label-track .track-content {
background: white;
}
+
+ .track-tile {
+ background: white;
+ }
+
+ .track-tile canvas {
+ position: relative;
+ z-index: 100;
+ }
</style></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/93f1baaa89ec/
changeset: r4994:93f1baaa89ec
user: jgoecks
date: 2011-02-04 17:33:30
summary: Trackster: support large (10,000+) sets of chromosomes/contigs, as is often the case for lower coverage genomes. Subsets of chromosomes are loaded into in the chrom select and there are options to move to the previous/next set of chromosomes. If user enters chrom not loaded into navigation box, chrom is loaded and then navigation is performed.
affected #: 3 files (4.3 KB)
--- a/lib/galaxy/web/controllers/tracks.py Thu Feb 03 17:13:49 2011 -0500
+++ b/lib/galaxy/web/controllers/tracks.py Fri Feb 04 11:33:30 2011 -0500
@@ -241,9 +241,10 @@
return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset )
@web.json
- def chroms(self, trans, vis_id=None, dbkey=None ):
+ def chroms( self, trans, vis_id=None, dbkey=None, num=None, chrom=None, low=None ):
"""
Returns a naturally sorted list of chroms/contigs for either a given visualization or a given dbkey.
+ Use either chrom or low to specify the starting chrom in the return list.
"""
def check_int(s):
if s.isdigit():
@@ -254,6 +255,25 @@
def split_by_number(s):
return [ check_int(c) for c in re.split('([0-9]+)', s) ]
+ #
+ # Parameter check, setting.
+ #
+ if num:
+ num = int( num )
+ else:
+ num = sys.maxint
+
+ if low:
+ low = int( low )
+ if low < 0:
+ low = 0
+ else:
+ low = 0
+
+ #
+ # Get viz, dbkey.
+ #
+
# Must specify either vis_id or dbkey.
if not vis_id and not dbkey:
return trans.show_error_message("No visualization id or dbkey specified.")
@@ -269,46 +289,96 @@
# No vis_id, so visualization is new. User is current user, dbkey must be given.
vis_user = trans.user
vis_dbkey = dbkey
+
+ #
+ # Get len file.
+ #
+ len_file = None
+ len_ds = None
+ # If there is any dataset in the history of extension `len`, this will use it
+ if 'dbkeys' in vis_user.preferences:
+ user_keys = from_json_string( vis_user.preferences['dbkeys'] )
+ if vis_dbkey in user_keys:
+ len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ vis_dbkey ][ 'len' ] ).file_name
+
+ if not len_file:
+ len_ds = trans.db_dataset_for( dbkey )
+ if not len_ds:
+ len_file = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % vis_dbkey )
+ else:
+ len_file = len_ds.file_name
- # Get chroms data.
- chroms = self._chroms( trans, vis_user, vis_dbkey )
+ #
+ # Get chroms data:
+ # (a) chrom name, len;
+ # (b) whether there are previous, next chroms;
+ # (c) index of start chrom.
+ #
+ len_file_enumerate = enumerate( open( len_file ) )
+ chroms = {}
+ prev_chroms = False
+ start_index = 0
+ if chrom:
+ # Use starting chrom to start list.
+ found = False
+ count = 0
+ for line_num, line in len_file_enumerate:
+ if line.startswith("#"):
+ continue
+ name, len = line.split("\t")
+ if found:
+ chroms[ name ] = int( len )
+ count += 1
+ elif name == chrom:
+ # Found starting chrom.
+ chroms[ name ] = int ( len )
+ count += 1
+ found = True
+ start_index = line_num
+ if line_num != 0:
+ prev_chroms = True
+ if count >= num:
+ break
+ else:
+ # Use low to start list.
+ high = low + int( num )
+ prev_chroms = ( low != 0 )
+ start_index = low
+
+ # Read chrom data from len file.
+ # TODO: this may be too slow for very large numbers of chroms/contigs,
+ # but try it out for now.
+ if not os.path.exists( len_file ):
+ return None
+
+ for line_num, line in len_file_enumerate:
+ if line_num < low:
+ continue
+ if line_num >= high:
+ break
+ if line.startswith("#"):
+ continue
+ # LEN files have format:
+ # <chrom_name><tab><chrom_length>
+ fields = line.split("\t")
+ chroms[ fields[0] ] = int( fields[1] )
+
+ # Set flag to indicate whether there are more chroms after list.
+ next_chroms = False
+ try:
+ len_file_enumerate.next()
+ next_chroms = True
+ except:
+ # No more chroms to read.
+ pass
# Check for reference chrom
if self.available_genomes is None: self._init_references(trans)
to_sort = [{ 'chrom': chrom, 'len': length } for chrom, length in chroms.iteritems()]
to_sort.sort(lambda a,b: cmp( split_by_number(a['chrom']), split_by_number(b['chrom']) ))
- return { 'reference': vis_dbkey in self.available_genomes, 'chrom_info': to_sort }
-
- def _chroms( self, trans, user, dbkey ):
- """
- Helper method that returns chrom lengths for a given user and dbkey.
- """
- len_file = None
- len_ds = None
- # If there is any dataset in the history of extension `len`, this will use it
- if 'dbkeys' in user.preferences:
- user_keys = from_json_string( user.preferences['dbkeys'] )
- if dbkey in user_keys:
- len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[dbkey]['len'] ).file_name
-
- if not len_file:
- len_ds = trans.db_dataset_for( dbkey )
- if not len_ds:
- len_file = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey )
- else:
- len_file = len_ds.file_name
- manifest = {}
- if not os.path.exists( len_file ):
- return None
- for line in open( len_file ):
- if line.startswith("#"):
- continue
- # LEN files have format:
- # <chrom_name><tab><chrom_length>
- fields = line.split("\t")
- manifest[fields[0]] = int(fields[1])
- return manifest
+ return { 'reference': vis_dbkey in self.available_genomes, 'chrom_info': to_sort,
+ 'prev_chroms' : prev_chroms, 'next_chroms' : next_chroms, 'start_index' : start_index }
@web.json
def reference( self, trans, dbkey, chrom, low, high, **kwargs ):
--- a/static/scripts/packed/trackster.js Thu Feb 03 17:13:49 2011 -0500
+++ b/static/scripts/packed/trackster.js Fri Feb 04 11:33:30 2011 -0500
@@ -1,1 +1,1 @@
-CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})}},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k)}if(l){if(!d.initial_canvas&&!window.G_vmlCanvasManager){d.initial_canvas=$(l).clone();var o=l.get(0).getContext("2d");var m=d.initial_canvas.get(0).getContext("2d");var n=o.getImageData(0,0,o.canvas.width,o.canvas.height);m.putImageData(n,0,0);d.set_overview()}d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
+CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){var d=this;if(e=="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e=="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})}},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k)}if(l){if(!d.initial_canvas&&!window.G_vmlCanvasManager){d.initial_canvas=$(l).clone();var o=l.get(0).getContext("2d");var m=d.initial_canvas.get(0).getContext("2d");var n=o.getImageData(0,0,o.canvas.width,o.canvas.height);m.putImageData(n,0,0);d.set_overview()}d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
--- a/static/scripts/trackster.js Thu Feb 03 17:13:49 2011 -0500
+++ b/static/scripts/trackster.js Fri Feb 04 11:33:30 2011 -0500
@@ -59,6 +59,8 @@
FEATURE_LEVELS = 10,
MAX_FEATURE_DEPTH = 100,
DEFAULT_DATA_QUERY_WAIT = 5000,
+ // Maximum number of chromosomes that are selectable at any one time.
+ MAX_CHROMS_SELECTABLE = 100,
CONNECTOR_COLOR = "#ccc",
DATA_ERROR = "There was an error in indexing this dataset. ",
DATA_NOCONVERTER = "A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",
@@ -301,34 +303,13 @@
this.zo_link = $("<a id='zoom-out' />").click(function() { view.zoom_out(); view.redraw(); }).appendTo(this.chrom_form);
this.zi_link = $("<a id='zoom-in' />").click(function() { view.zoom_in(); view.redraw(); }).appendTo(this.chrom_form);
- $.ajax({
- url: chrom_url,
- data: (this.vis_id !== undefined ? { vis_id: this.vis_id } : { dbkey: this.dbkey }),
- dataType: "json",
- success: function ( result ) {
- if (result.reference) {
- view.add_label_track( new ReferenceTrack(view) );
- }
- view.chrom_data = result.chrom_info;
- var chrom_options = '<option value="">Select Chrom/Contig</option>';
- for (var i = 0, len = view.chrom_data.length; i < len; i++) {
- var chrom = view.chrom_data[i].chrom;
- chrom_options += '<option value="' + chrom + '">' + chrom + '</option>';
- }
- view.chrom_select.html(chrom_options);
- view.intro_div.show();
- view.chrom_select.bind("change", function() {
- view.change_chrom(view.chrom_select.val());
- });
- if ( callback ) {
- callback();
- }
- },
- error: function() {
- alert( "Could not load chroms for this dbkey:", view.dbkey );
- }
+ // Get initial set of chroms.
+ this.load_chroms({low: 0}, callback);
+ this.chrom_select.bind("change", function() {
+ view.change_chrom(view.chrom_select.val());
});
-
+ this.intro_div.show();
+
/*
this.content_div.bind("mousewheel", function( e, delta ) {
if (Math.abs(delta) < 0.5) {
@@ -446,42 +427,98 @@
this.location_span.text( commatize(low) + ' - ' + commatize(high) );
this.nav_input.val( this.chrom + ':' + commatize(low) + '-' + commatize(high) );
},
+ load_chroms: function(url_parms, callback) {
+ url_parms['num'] = MAX_CHROMS_SELECTABLE;
+ $.extend( url_parms, (this.vis_id !== undefined ? { vis_id: this.vis_id } : { dbkey: this.dbkey } ) );
+ var view = this;
+ $.ajax({
+ url: chrom_url,
+ data: url_parms,
+ dataType: "json",
+ success: function ( result ) {
+ if (result.reference) {
+ view.add_label_track( new ReferenceTrack(view) );
+ }
+ view.chrom_data = result.chrom_info;
+ var chrom_options = '<option value="">Select Chrom/Contig</option>';
+ for (var i = 0, len = view.chrom_data.length; i < len; i++) {
+ var chrom = view.chrom_data[i].chrom;
+ chrom_options += '<option value="' + chrom + '">' + chrom + '</option>';
+ }
+ if (result.prev_chroms) {
+ chrom_options += '<option value="previous">Previous ' + MAX_CHROMS_SELECTABLE + '</option>';
+ }
+ if (result.next_chroms) {
+ chrom_options += '<option value="next">Next ' + MAX_CHROMS_SELECTABLE + '</option>';
+ }
+ view.chrom_select.html(chrom_options);
+ if ( callback ) {
+ callback();
+ }
+ view.chrom_start_index = result.start_index;
+ },
+ error: function() {
+ alert( "Could not load chroms for this dbkey:", view.dbkey );
+ }
+ });
+
+ },
change_chrom: function(chrom, low, high) {
var view = this;
+
+ //
+ // If user is navigating to previous/next set of chroms, load new chrom set and return.
+ //
+ if (chrom == "previous") {
+ view.load_chroms({low: this.chrom_start_index - MAX_CHROMS_SELECTABLE});
+ return;
+ }
+ if (chrom == "next") {
+ view.load_chroms({low: this.chrom_start_index + MAX_CHROMS_SELECTABLE});
+ return;
+ }
+
+ //
+ // User is loading a particular chrom. Look first in current set; if not in current set, load new
+ // chrom set.
+ //
var found = $.grep(view.chrom_data, function(v, i) {
return v.chrom === chrom;
})[0];
if (found === undefined) {
- // Invalid chrom
+ // Try to load chrom and then change to chrom.
+ view.load_chroms({'chrom': chrom}, function() { view.change_chrom(chrom, low, high); });
return;
}
- if (chrom !== view.chrom) {
- view.chrom = chrom;
- if (!view.chrom) {
- // No chrom selected
- view.intro_div.show();
- } else {
- view.intro_div.hide();
- }
- view.chrom_select.val(view.chrom);
- view.max_high = found.len;
- view.reset();
- view.redraw(true);
-
- for (var track_id = 0, len = view.tracks.length; track_id < len; track_id++) {
- var track = view.tracks[track_id];
- if (track.init) {
- track.init();
+ else {
+ // Switching to local chrom.
+ if (chrom !== view.chrom) {
+ view.chrom = chrom;
+ if (!view.chrom) {
+ // No chrom selected
+ view.intro_div.show();
+ } else {
+ view.intro_div.hide();
+ }
+ view.chrom_select.val(view.chrom);
+ view.max_high = found.len;
+ view.reset();
+ view.redraw(true);
+
+ for (var track_id = 0, len = view.tracks.length; track_id < len; track_id++) {
+ var track = view.tracks[track_id];
+ if (track.init) {
+ track.init();
+ }
}
}
+ if (low !== undefined && high !== undefined) {
+ view.low = Math.max(low, 0);
+ view.high = Math.min(high, view.max_high);
+ }
+ view.reset_overview();
+ view.redraw();
}
- if (low !== undefined && high !== undefined) {
- view.low = Math.max(low, 0);
- view.high = Math.min(high, view.max_high);
- }
- view.reset_overview();
- view.redraw();
-
},
go_to: function(str) {
var view = this,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Trackseter: fix bug that prevented draw(force) from working.
by Bitbucket 03 Feb '11
by Bitbucket 03 Feb '11
03 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/2ddaa3ca7478/
changeset: r4993:2ddaa3ca7478
user: jgoecks
date: 2011-02-03 23:13:49
summary: Trackseter: fix bug that prevented draw(force) from working.
affected #: 2 files (109 bytes)
--- a/static/scripts/packed/trackster.js Thu Feb 03 17:01:17 2011 -0500
+++ b/static/scripts/packed/trackster.js Thu Feb 03 17:13:49 2011 -0500
@@ -1,1 +1,1 @@
-CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var k=this.view.low,f=this.view.high,h=f-k,e=this.view.resolution;var n=$("<div style='position: relative;'></div>"),o=this.content_div.width()/h;this.content_div.append(n);this.max_height=0;var b=Math.floor(k/e/DENSITY);var j=0;while((b*DENSITY*e)<f){var l=this.content_div.width()+"_"+o+"_"+b;var d=this.tile_cache.get(l);if(!a&&d){this.show_tile(d,n,b)}else{this.delayed_draw(l,k,f,b,e,n,o,j)}b+=1}var c=this;var m=setInterval(function(){if(j===0){var r=c.content_div.children();var q=false;for(var s=r.length-1,p=0;s>=p;s--){var u=$(r[s]);if(q){u.remove()}else{if(u.children().length!==0){q=true}}}for(var t=0;t<c.filters.length;t++){c.filters[t].update_ui_elt()}clearInterval(m)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(h,g,e,b,d,i,j,f){var c=this;var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.tile_cache.get(h);if(!k){k=c.draw_tile(d,b,i,j)}if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i,b)}}delete f--},50);f++},show_tile:function(g,h,a){var b=this;var e=this.view.high-this.view.low,d=this.view.resolution,i=this.content_div.width()/e;var f=a*DENSITY*this.view.resolution;var c=(f-this.view.low)*i;if(this.left_offset){c-=this.left_offset}g.css({position:"absolute",top:0,left:c});h.append(g);b.max_height=Math.max(b.max_height,g.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(g.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
+CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!=null){$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})}},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var l=this.view.low,f=this.view.high,h=f-l,e=this.view.resolution;var o=$("<div style='position: relative;'></div>"),q=this.content_div.width()/h;this.content_div.append(o);this.max_height=0;var b=Math.floor(l/e/DENSITY);var k=0;while((b*DENSITY*e)<f){var m=this.content_div.width()+"_"+q+"_"+b;var d=this.tile_cache.get(m);var j=b*DENSITY*this.view.resolution;var p=j+DENSITY*this.view.resolution;if(!a&&d){this.show_tile(d,o,j)}else{this.delayed_draw(a,m,j,p,b,e,o,q,k)}b+=1}var c=this;var n=setInterval(function(){if(k===0){var t=c.content_div.children();var s=false;for(var u=t.length-1,r=0;u>=r;u--){var w=$(t[u]);if(s){w.remove()}else{if(w.children().length!==0){s=true}}}for(var v=0;v<c.filters.length;v++){c.filters[v].update_ui_elt()}clearInterval(n)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(b,h,g,j,c,e,i,k,f){var d=this;var a=setTimeout(function(){if(g<=d.view.high&&j>=d.view.low){var l;if(!b){l=d.tile_cache.get(h)}if(!l){l=d.draw_tile(e,c,i,k)}if(l){if(!d.initial_canvas&&!window.G_vmlCanvasManager){d.initial_canvas=$(l).clone();var o=l.get(0).getContext("2d");var m=d.initial_canvas.get(0).getContext("2d");var n=o.getImageData(0,0,o.canvas.width,o.canvas.height);m.putImageData(n,0,0);d.set_overview()}d.tile_cache.set(h,l);d.show_tile(l,i,g)}}delete f--},50);f++},show_tile:function(a,f,d){var b=this;var c=this.view.high-this.view.low,g=this.content_div.width()/c,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
--- a/static/scripts/trackster.js Thu Feb 03 17:01:17 2011 -0500
+++ b/static/scripts/trackster.js Thu Feb 03 17:13:49 2011 -0500
@@ -1264,7 +1264,7 @@
if ( !force && cached ) {
this.show_tile( cached, parent_element, tile_low );
} else {
- this.delayed_draw(key, tile_low, tile_high, tile_index, resolution, parent_element, w_scale, draw_tile_count);
+ this.delayed_draw(force, key, tile_low, tile_high, tile_index, resolution, parent_element, w_scale, draw_tile_count);
}
tile_index += 1;
}
@@ -1311,13 +1311,16 @@
this.child_tracks[i].draw(force);
}
},
- delayed_draw: function(key, tile_low, tile_high, tile_index, resolution, parent_element, w_scale, draw_tile_count) {
+ delayed_draw: function(force, key, tile_low, tile_high, tile_index, resolution, parent_element, w_scale, draw_tile_count) {
var track = this;
// Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data
var id = setTimeout(function() {
if (tile_low <= track.view.high && tile_high >= track.view.low) {
// Show/draw tile: check cache for tile; if tile not in cache, draw it.
- var tile_element = track.tile_cache.get(key);
+ var tile_element;
+ if (!force) {
+ tile_element = track.tile_cache.get(key);
+ }
if (!tile_element) {
tile_element = track.draw_tile(resolution, tile_index, parent_element, w_scale);
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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03 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/ecc887998e72/
changeset: r4992:ecc887998e72
user: james_taylor
date: 2011-02-03 23:01:17
summary: trackster: do not init tracks with null chromosome, use correct low and high when testing tiles in delayed draw, calculate position in show_tile without tile_index (which cna change)
affected #: 2 files (357 bytes)
--- a/static/scripts/trackster.js Thu Feb 03 16:06:20 2011 -0500
+++ b/static/scripts/trackster.js Thu Feb 03 17:01:17 2011 -0500
@@ -838,9 +838,11 @@
track.data_cache.clear();
track.initial_canvas = undefined;
track.content_div.css("height", "auto");
+ /*
if (!track.content_div.text()) {
track.content_div.text(DATA_LOADING);
}
+ */
track.container_div.removeClass("nodata error pending");
//
@@ -849,46 +851,48 @@
if (!track.dataset_id) {
return;
}
-
- // Get dataset state; if state is fine, enable and draw track. Otherwise, show message
- // about track status.
- $.getJSON(this.dataset_check_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id,
- chrom: track.view.chrom, low: track.view.max_low, high: track.view.max_high},
- function (result) {
- if (!result || result === "error" || result.kind === "error") {
- track.container_div.addClass("error");
- track.content_div.text(DATA_ERROR);
- if (result.message) {
- var track_id = track.view.tracks.indexOf(track);
- var error_link = $(" <a href='javascript:void(0);'></a>").attr("id", track_id + "_error");
- error_link.text("View error");
- $("#" + track_id + "_error").live("click", function() {
- show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } );
- });
- track.content_div.append(error_link);
+
+ if ( track.view.chrom != null ) {
+ // Get dataset state; if state is fine, enable and draw track. Otherwise, show message
+ // about track status.
+ $.getJSON(this.dataset_check_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id,
+ chrom: track.view.chrom, low: track.view.max_low, high: track.view.max_high},
+ function (result) {
+ if (!result || result === "error" || result.kind === "error") {
+ track.container_div.addClass("error");
+ track.content_div.text(DATA_ERROR);
+ if (result.message) {
+ var track_id = track.view.tracks.indexOf(track);
+ var error_link = $(" <a href='javascript:void(0);'></a>").attr("id", track_id + "_error");
+ error_link.text("View error");
+ $("#" + track_id + "_error").live("click", function() {
+ show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } );
+ });
+ track.content_div.append(error_link);
+ }
+ } else if (result === "no converter") {
+ track.container_div.addClass("error");
+ track.content_div.text(DATA_NOCONVERTER);
+ } else if (result === "no data" || (result.data !== undefined && (result.data === null || result.data.length === 0))) {
+ track.container_div.addClass("nodata");
+ track.content_div.text(DATA_NONE);
+ } else if (result === "pending") {
+ track.container_div.addClass("pending");
+ track.content_div.text(DATA_PENDING);
+ setTimeout(function() { track.init(); }, track.data_query_wait);
+ } else if (result === "data") {
+ // Only draw in user has selected a chromosome.
+ track.content_div.text(DATA_OK);
+ if (track.view.chrom) {
+ track.content_div.text("");
+ track.content_div.css( "height", track.height_px + "px" );
+ track.enabled = true;
+ track.predraw_init();
+ track.draw();
+ }
}
- } else if (result === "no converter") {
- track.container_div.addClass("error");
- track.content_div.text(DATA_NOCONVERTER);
- } else if (result === "no data" || (result.data !== undefined && (result.data === null || result.data.length === 0))) {
- track.container_div.addClass("nodata");
- track.content_div.text(DATA_NONE);
- } else if (result === "pending") {
- track.container_div.addClass("pending");
- track.content_div.text(DATA_PENDING);
- setTimeout(function() { track.init(); }, track.data_query_wait);
- } else if (result === "data") {
- // Only draw in user has selected a chromosome.
- track.content_div.text(DATA_OK);
- if (track.view.chrom) {
- track.content_div.text("");
- track.content_div.css( "height", track.height_px + "px" );
- track.enabled = true;
- track.predraw_init();
- track.draw();
- }
- }
- });
+ });
+ }
},
/**
* Additional initialization required before drawing track for the first time.
@@ -1254,11 +1258,13 @@
// Check in cache
var key = this.content_div.width() + '_' + w_scale + '_' + tile_index;
var cached = this.tile_cache.get(key);
+ var tile_low = tile_index * DENSITY * this.view.resolution;
+ var tile_high = tile_low + DENSITY * this.view.resolution;
// console.log(cached, this.tile_cache);
if ( !force && cached ) {
- this.show_tile( cached, parent_element, tile_index );
+ this.show_tile( cached, parent_element, tile_low );
} else {
- this.delayed_draw(key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_count);
+ this.delayed_draw(key, tile_low, tile_high, tile_index, resolution, parent_element, w_scale, draw_tile_count);
}
tile_index += 1;
}
@@ -1304,11 +1310,12 @@
for (var i = 0; i < this.child_tracks.length; i++) {
this.child_tracks[i].draw(force);
}
- }, delayed_draw: function(key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_count) {
+ },
+ delayed_draw: function(key, tile_low, tile_high, tile_index, resolution, parent_element, w_scale, draw_tile_count) {
var track = this;
// Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data
var id = setTimeout(function() {
- if (low <= track.view.high && high >= track.view.low) {
+ if (tile_low <= track.view.high && tile_high >= track.view.low) {
// Show/draw tile: check cache for tile; if tile not in cache, draw it.
var tile_element = track.tile_cache.get(key);
if (!tile_element) {
@@ -1326,7 +1333,7 @@
}
// Add tile to cache and show tile.
track.tile_cache.set(key, tile_element);
- track.show_tile(tile_element, parent_element, tile_index);
+ track.show_tile(tile_element, parent_element, tile_low);
}
}
delete draw_tile_count--;
@@ -1334,19 +1341,14 @@
draw_tile_count++
},
// Show track tile and perform associated actions.
- show_tile: function( tile_element, parent_element, tile_index ) {
+ show_tile: function( tile_element, parent_element, tile_low ) {
// Readability.
var track = this;
- // Position tile element
-
- // Recalculate left position at display time
- // FIXME: Should calculate this without tile_index
+ // Position tile element, recalculate left position at display time
var range = this.view.high - this.view.low,
- resolution = this.view.resolution,
- w_scale = this.content_div.width() / range;
- var tile_low = tile_index * DENSITY * this.view.resolution;
- var left = ( tile_low - this.view.low ) * w_scale;
+ w_scale = this.content_div.width() / range,
+ left = ( tile_low - this.view.low ) * w_scale;
if (this.left_offset) {
left -= this.left_offset;
}
--- a/templates/tracks/browser.mako Thu Feb 03 16:06:20 2011 -0500
+++ b/templates/tracks/browser.mako Thu Feb 03 17:01:17 2011 -0500
@@ -100,6 +100,15 @@
border: solid #999 1px;
z-index: 100;
}
+
+ .track-content {
+ background: #eee;
+ min-height: 16px;
+ }
+
+ .label-track .track-content {
+ background: white;
+ }
</style></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Uncomment BLAST+ tools in the sample config.
by Bitbucket 03 Feb '11
by Bitbucket 03 Feb '11
03 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/8d388719e25c/
changeset: r4991:8d388719e25c
user: natefoo
date: 2011-02-03 22:06:20
summary: Uncomment BLAST+ tools in the sample config.
affected #: 1 file (108 bytes)
--- a/tool_conf.xml.sample Thu Feb 03 15:52:44 2011 -0500
+++ b/tool_conf.xml.sample Thu Feb 03 16:06:20 2011 -0500
@@ -219,8 +219,6 @@
<tool file="fastx_toolkit/fasta_nucleotide_changer.xml" /><tool file="fastx_toolkit/fastx_collapser.xml" /></section>
- <!-- The BLAST+ tools are not hosted on Galaxy Test but are provided for
- local installations
<section name="NCBI BLAST+" id="ncbi_blast_plus_tools"><tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" /><tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
@@ -229,7 +227,6 @@
<tool file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml" /><tool file="ncbi_blast_plus/blastxml_to_tabular.xml" /></section>
- --><section name="NGS: QC and manipulation" id="cshl_library_information"><label text="Illumina data" id="illumina" /><tool file="fastq/fastq_groomer.xml" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: natefoo: Fix for the histogram tool for the "'x' must be numeric" error experienced by some local installations. Thanks, Jim Johnson.
by Bitbucket 03 Feb '11
by Bitbucket 03 Feb '11
03 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/1c997fdae745/
changeset: r4990:1c997fdae745
user: natefoo
date: 2011-02-03 21:52:44
summary: Fix for the histogram tool for the "'x' must be numeric" error experienced by some local installations. Thanks, Jim Johnson.
affected #: 1 file (7 bytes)
--- a/tools/plotting/histogram.py Thu Feb 03 15:33:45 2011 -0500
+++ b/tools/plotting/histogram.py Thu Feb 03 15:52:44 2011 -0500
@@ -69,7 +69,7 @@
first_invalid_line = i+1
if valid:
- matrix.append( row )
+ matrix += row
if skipped_lines < i:
try:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Trackster bug fixes: (a) fix read packing bug caused by bad guide and (b) better clean up of old tiles/canvases.
by Bitbucket 03 Feb '11
by Bitbucket 03 Feb '11
03 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/49d87af2dcab/
changeset: r4989:49d87af2dcab
user: jgoecks
date: 2011-02-03 21:33:45
summary: Trackster bug fixes: (a) fix read packing bug caused by bad guide and (b) better clean up of old tiles/canvases.
affected #: 4 files (882 bytes)
--- a/lib/galaxy/visualization/tracks/data_providers.py Thu Feb 03 14:57:49 2011 -0500
+++ b/lib/galaxy/visualization/tracks/data_providers.py Thu Feb 03 15:33:45 2011 -0500
@@ -288,7 +288,7 @@
if read.is_proper_pair:
if qname in paired_pending: # one in dict is always first
pair = paired_pending[qname]
- results.append( [ "%i_%s" % ( read.pos-start, qname ),
+ results.append( [ "%i_%s" % ( read.pos, qname ),
pair['start'],
read.pos + read_len,
qname,
@@ -299,7 +299,7 @@
else:
paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos, 'rlen': read_len, 'cigar': read.cigar }
else:
- results.append( [ "%i_%s" % ( read.pos-start, qname ), read.pos, read.pos + read_len, qname, read.cigar, read.seq] )
+ results.append( [ "%i_%s" % ( read.pos, qname ), read.pos, read.pos + read_len, qname, read.cigar, read.seq] )
# Take care of reads whose mates are out of range.
for qname, read in paired_pending.iteritems():
if read['mate_start'] < read['start']:
@@ -319,7 +319,7 @@
r1 = [ read['start'], read['end'], read['cigar'], read['seq'] ]
r2 = [ read['mate_start'], read['mate_start'] ]
- results.append( [ "%i_%s" % ( read_start-start, qname ), read_start, read_end, qname, r1, r2 ] )
+ results.append( [ "%i_%s" % ( read_start, qname ), read_start, read_end, qname, r1, r2 ] )
bamfile.close()
return { 'data': results, 'message': message }
--- a/static/scripts/packed/jquery.mousewheel.js Thu Feb 03 14:57:49 2011 -0500
+++ b/static/scripts/packed/jquery.mousewheel.js Thu Feb 03 15:33:45 2011 -0500
@@ -1,11 +1,1 @@
-/* Copyright (c) 2009 Brandon Aaron (http://brandonaaron.net)
- * Dual licensed under the MIT (http://www.opensource.org/licenses/mit-license.php)
- * and GPL (http://www.opensource.org/licenses/gpl-license.php) licenses.
- * Thanks to: http://adomas.org/javascript-mouse-wheel/ for some pointers.
- * Thanks to: Mathias Bank(http://www.mathias-bank.de) for a scope bug fix.
- *
- * Version: 3.0.2
- *
- * Requires: 1.2.2+
- */
-(function(c){var a=["DOMMouseScroll","mousewheel"];c.event.special.mousewheel={setup:function(){if(this.addEventListener){for(var d=a.length;d;){this.addEventListener(a[--d],b,false)}}else{this.onmousewheel=b}},teardown:function(){if(this.removeEventListener){for(var d=a.length;d;){this.removeEventListener(a[--d],b,false)}}else{this.onmousewheel=null}}};c.fn.extend({mousewheel:function(d){return d?this.bind("mousewheel",d):this.trigger("mousewheel")},unmousewheel:function(d){return this.unbind("mousewheel",d)}});function b(f){var d=[].slice.call(arguments,1),g=0,e=true;f=c.event.fix(f||window.event);f.type="mousewheel";if(f.wheelDelta){g=f.wheelDelta/120}if(f.detail){g=-f.detail/3}d.unshift(f,g);return c.event.handle.apply(this,d)}})(jQuery);
\ No newline at end of file
+(function(c){var a=["DOMMouseScroll","mousewheel"];c.event.special.mousewheel={setup:function(){if(this.addEventListener){for(var d=a.length;d;){this.addEventListener(a[--d],b,false)}}else{this.onmousewheel=b}},teardown:function(){if(this.removeEventListener){for(var d=a.length;d;){this.removeEventListener(a[--d],b,false)}}else{this.onmousewheel=null}}};c.fn.extend({mousewheel:function(d){return d?this.bind("mousewheel",d):this.trigger("mousewheel")},unmousewheel:function(d){return this.unbind("mousewheel",d)}});function b(i){var g=i||window.event,f=[].slice.call(arguments,1),j=0,h=true,e=0,d=0;i=c.event.fix(g);i.type="mousewheel";if(i.wheelDelta){j=i.wheelDelta/120}if(i.detail){j=-i.detail/3}d=j;if(g.axis!==undefined&&g.axis===g.HORIZONTAL_AXIS){d=0;e=-1*j}if(g.wheelDeltaY!==undefined){d=g.wheelDeltaY/120}if(g.wheelDeltaX!==undefined){e=-1*g.wheelDeltaX/120}f.unshift(i,j,e,d);return c.event.handle.apply(this,f)}})(jQuery);
\ No newline at end of file
--- a/static/scripts/packed/trackster.js Thu Feb 03 14:57:49 2011 -0500
+++ b/static/scripts/packed/trackster.js Thu Feb 03 15:33:45 2011 -0500
@@ -1,1 +1,1 @@
-CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX;g.enable_pan=(f.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(h,j){if(!j.enable_pan){return}var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var m=this.view.low,g=this.view.high,j=g-m,f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/j;this.content_div.append(p);this.max_height=0;var b=Math.floor(m/f/DENSITY);var l={};while((b*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+b;var e=this.tile_cache.get(n);if(!a&&e){var k=b*DENSITY*f;var d=(k-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(n,m,g,b,f,p,q,l)}b+=1}var c=this;var o=setInterval(function(){if(obj_length(l)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var i=0;i<c.filters.length;i++){c.filters[i].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(a)}},delayed_draw:function(h,g,e,b,d,i,j,f){var c=this;var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.tile_cache.get(h);if(!k){k=c.draw_tile(d,b,i,j)}if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.css({position:"absolute",top:0,left:(L-this.view.low)*ar-U});p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}r.append(p);return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
+CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,j){var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}).bind("mousewheel",function(h,j,g,f){if(g){var i=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var k=this.view.low,f=this.view.high,h=f-k,e=this.view.resolution;var n=$("<div style='position: relative;'></div>"),o=this.content_div.width()/h;this.content_div.append(n);this.max_height=0;var b=Math.floor(k/e/DENSITY);var j=0;while((b*DENSITY*e)<f){var l=this.content_div.width()+"_"+o+"_"+b;var d=this.tile_cache.get(l);if(!a&&d){this.show_tile(d,n,b)}else{this.delayed_draw(l,k,f,b,e,n,o,j)}b+=1}var c=this;var m=setInterval(function(){if(j===0){var r=c.content_div.children();var q=false;for(var s=r.length-1,p=0;s>=p;s--){var u=$(r[s]);if(q){u.remove()}else{if(u.children().length!==0){q=true}}}for(var t=0;t<c.filters.length;t++){c.filters[t].update_ui_elt()}clearInterval(m)}},50);for(var g=0;g<this.child_tracks.length;g++){this.child_tracks[g].draw(a)}},delayed_draw:function(h,g,e,b,d,i,j,f){var c=this;var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.tile_cache.get(h);if(!k){k=c.draw_tile(d,b,i,j)}if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i,b)}}delete f--},50);f++},show_tile:function(g,h,a){var b=this;var e=this.view.high-this.view.low,d=this.view.resolution,i=this.content_div.width()/e;var f=a*DENSITY*this.view.resolution;var c=(f-this.view.low)*i;if(this.left_offset){c-=this.left_offset}g.css({position:"absolute",top:0,left:c});h.append(g);b.max_height=Math.max(b.max_height,g.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(g.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
--- a/static/scripts/trackster.js Thu Feb 03 14:57:49 2011 -0500
+++ b/static/scripts/trackster.js Thu Feb 03 15:33:45 2011 -0500
@@ -1249,7 +1249,7 @@
var tile_index = Math.floor( low / resolution / DENSITY );
// A list of setTimeout() ids used when drawing tiles. Each ID indicates
// a tile has been requested to be drawn or is being drawn.
- var draw_tile_ids = {};
+ var draw_tile_count = 0;
while ( ( tile_index * DENSITY * resolution ) < high ) {
// Check in cache
var key = this.content_div.width() + '_' + w_scale + '_' + tile_index;
@@ -1258,7 +1258,7 @@
if ( !force && cached ) {
this.show_tile( cached, parent_element, tile_index );
} else {
- this.delayed_draw(key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids);
+ this.delayed_draw(key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_count);
}
tile_index += 1;
}
@@ -1270,18 +1270,29 @@
//
var track = this;
var intervalId = setInterval(function() {
- // Only do stuff if all tile drawing is complete:
- if (obj_length(draw_tile_ids) === 0) {
- // All drawing has finished; if there is more than one child in the content div,
- // remove the first one, which is the oldest.
- if ( track.content_div.children().length > 1 ) {
- track.content_div.children( ":first" ).remove();
+ if (draw_tile_count === 0) {
+ // All tiles have been drawn; clear out track content in order to show the most recent content.
+ // Most recent content is the div with children (tiles) most recently appended to track.
+ // However, do not delete recently-appended empty content as calls to draw() may still be active
+ // and using these divs.
+ var track_content = track.content_div.children();
+ var remove = false;
+ for (var i = track_content.length-1, len = 0; i >= len; i--) {
+ var child = $(track_content[i]);
+ if (remove) {
+ child.remove();
+ }
+ else if (child.children().length !== 0) {
+ // Found most recent content with tiles: set remove to start removing old elements.
+ remove = true;
+ }
}
// Update filtering UI.
for (var f = 0; f < track.filters.length; f++) {
track.filters[f].update_ui_elt();
}
+
// Method complete; do not call it again.
clearInterval(intervalId);
}
@@ -1293,7 +1304,7 @@
for (var i = 0; i < this.child_tracks.length; i++) {
this.child_tracks[i].draw(force);
}
- }, delayed_draw: function(key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids) {
+ }, delayed_draw: function(key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_count) {
var track = this;
// Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data
var id = setTimeout(function() {
@@ -1318,10 +1329,9 @@
track.show_tile(tile_element, parent_element, tile_index);
}
}
- // Remove setTimeout id.
- delete draw_tile_ids[id];
+ delete draw_tile_count--;
}, 50);
- draw_tile_ids[id] = true;
+ draw_tile_count++
},
// Show track tile and perform associated actions.
show_tile: function( tile_element, parent_element, tile_index ) {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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4 new changesets in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/36f1b8193cb0/
changeset: r4985:36f1b8193cb0
user: james_taylor
date: 2011-02-03 17:46:14
summary: trackster: capture horizontal mouse wheel events for scrolling (left right drags on mac touch pads)
affected #: 3 files (1.2 KB)
--- a/static/scripts/jquery.mousewheel.js Wed Feb 02 16:21:23 2011 -0500
+++ b/static/scripts/jquery.mousewheel.js Thu Feb 03 11:46:14 2011 -0500
@@ -1,10 +1,11 @@
-/*! Copyright (c) 2009 Brandon Aaron (http://brandonaaron.net)
- * Dual licensed under the MIT (http://www.opensource.org/licenses/mit-license.php)
- * and GPL (http://www.opensource.org/licenses/gpl-license.php) licenses.
+/* Copyright (c) 2010 Brandon Aaron (http://brandonaaron.net)
+ * Licensed under the MIT License (LICENSE.txt).
+ *
* Thanks to: http://adomas.org/javascript-mouse-wheel/ for some pointers.
* Thanks to: Mathias Bank(http://www.mathias-bank.de) for a scope bug fix.
+ * Thanks to: Seamus Leahy for adding deltaX and deltaY
*
- * Version: 3.0.2
+ * Version: 3.0.4
*
* Requires: 1.2.2+
*/
@@ -14,47 +15,64 @@
var types = ['DOMMouseScroll', 'mousewheel'];
$.event.special.mousewheel = {
- setup: function() {
- if ( this.addEventListener )
- for ( var i=types.length; i; )
- this.addEventListener( types[--i], handler, false );
- else
- this.onmousewheel = handler;
- },
-
- teardown: function() {
- if ( this.removeEventListener )
- for ( var i=types.length; i; )
- this.removeEventListener( types[--i], handler, false );
- else
- this.onmousewheel = null;
- }
+ setup: function() {
+ if ( this.addEventListener ) {
+ for ( var i=types.length; i; ) {
+ this.addEventListener( types[--i], handler, false );
+ }
+ } else {
+ this.onmousewheel = handler;
+ }
+ },
+
+ teardown: function() {
+ if ( this.removeEventListener ) {
+ for ( var i=types.length; i; ) {
+ this.removeEventListener( types[--i], handler, false );
+ }
+ } else {
+ this.onmousewheel = null;
+ }
+ }
};
$.fn.extend({
- mousewheel: function(fn) {
- return fn ? this.bind("mousewheel", fn) : this.trigger("mousewheel");
- },
-
- unmousewheel: function(fn) {
- return this.unbind("mousewheel", fn);
- }
+ mousewheel: function(fn) {
+ return fn ? this.bind("mousewheel", fn) : this.trigger("mousewheel");
+ },
+
+ unmousewheel: function(fn) {
+ return this.unbind("mousewheel", fn);
+ }
});
function handler(event) {
- var args = [].slice.call( arguments, 1 ), delta = 0, returnValue = true;
-
- event = $.event.fix(event || window.event);
- event.type = "mousewheel";
-
- if ( event.wheelDelta ) delta = event.wheelDelta/120;
- if ( event.detail ) delta = -event.detail/3;
-
- // Add events and delta to the front of the arguments
- args.unshift(event, delta);
+ var orgEvent = event || window.event, args = [].slice.call( arguments, 1 ), delta = 0, returnValue = true, deltaX = 0, deltaY = 0;
+ event = $.event.fix(orgEvent);
+ event.type = "mousewheel";
- return $.event.handle.apply(this, args);
+ // Old school scrollwheel delta
+ if ( event.wheelDelta ) { delta = event.wheelDelta/120; }
+ if ( event.detail ) { delta = -event.detail/3; }
+
+ // New school multidimensional scroll (touchpads) deltas
+ deltaY = delta;
+
+ // Gecko
+ if ( orgEvent.axis !== undefined && orgEvent.axis === orgEvent.HORIZONTAL_AXIS ) {
+ deltaY = 0;
+ deltaX = -1*delta;
+ }
+
+ // Webkit
+ if ( orgEvent.wheelDeltaY !== undefined ) { deltaY = orgEvent.wheelDeltaY/120; }
+ if ( orgEvent.wheelDeltaX !== undefined ) { deltaX = -1*orgEvent.wheelDeltaX/120; }
+
+ // Add event and delta to the front of the arguments
+ args.unshift(event, delta, deltaX, deltaY);
+
+ return $.event.handle.apply(this, args);
}
-})(jQuery);
\ No newline at end of file
+})(jQuery);
--- a/static/scripts/trackster.js Wed Feb 02 16:21:23 2011 -0500
+++ b/static/scripts/trackster.js Thu Feb 03 11:46:14 2011 -0500
@@ -390,6 +390,14 @@
d.current_x = d.offsetX;
var delta_chrom = Math.round(delta / view.viewport_container.width() * (view.high - view.low));
view.move_delta(delta_chrom);
+ // Also capture mouse wheel for left/right scrolling
+ }).bind( 'mousewheel', function( e, d, dx, dy ) {
+ // Only act on x axis scrolling if we see if, y will be i
+ // handled by the browser when the event bubbles up
+ if ( dx ) {
+ var delta_chrom = Math.round( - dx / view.viewport_container.width() * (view.high - view.low) );
+ view.move_delta( delta_chrom );
+ }
});
// Dragging in the top label track allows selecting a region
--- a/templates/tracks/browser.mako Wed Feb 02 16:21:23 2011 -0500
+++ b/templates/tracks/browser.mako Thu Feb 03 11:46:14 2011 -0500
@@ -123,7 +123,7 @@
<script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]-->
-${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag", "jquery.autocomplete", "trackster", "jquery.ui.sortable.slider" )}
+${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "jquery.ui.sortable.slider" )}
<script type="text/javascript">
http://bitbucket.org/galaxy/galaxy-central/changeset/cb9f790675f3/
changeset: r4986:cb9f790675f3
user: james_taylor
date: 2011-02-03 19:15:34
summary: trackster: better supression of drags starting in scrollbar using the draginit event
affected #: 1 file (60 bytes)
--- a/static/scripts/trackster.js Thu Feb 03 11:46:14 2011 -0500
+++ b/static/scripts/trackster.js Thu Feb 03 13:15:34 2011 -0500
@@ -374,14 +374,16 @@
});
// Dragging in the viewport scrolls
- this.viewport_container.bind( "dragstart", function( e, d ) {
+ this.viewport_container.bind( "draginit", function( e, d ) {
+ // Disable interaction if started in scrollbar (for webkit)
+ if ( e.clientX > view.viewport_container.width() - 16 ) {
+ return false;
+ }
+ }).bind( "dragstart", function( e, d ) {
d.original_low = view.low;
d.current_height = e.clientY;
d.current_x = d.offsetX;
- // Fix webkit scrollbar
- d.enable_pan = (e.clientX < view.viewport_container.width() - 16) ? true : false;
}).bind( "drag", function( e, d ) {
- if (!d.enable_pan) { return; }
var container = $(this);
var delta = d.offsetX - d.current_x;
var new_scroll = container.scrollTop() - (e.clientY - d.current_height);
http://bitbucket.org/galaxy/galaxy-central/changeset/cef67cb89049/
changeset: r4987:cef67cb89049
user: james_taylor
date: 2011-02-03 20:54:40
summary: trackster: clean up positioning of tiles somewhat
affected #: 1 file (177 bytes)
--- a/static/scripts/trackster.js Thu Feb 03 13:15:34 2011 -0500
+++ b/static/scripts/trackster.js Thu Feb 03 14:54:40 2011 -0500
@@ -1256,13 +1256,7 @@
var cached = this.tile_cache.get(key);
// console.log(cached, this.tile_cache);
if ( !force && cached ) {
- var tile_low = tile_index * DENSITY * resolution;
- var left = ( tile_low - low ) * w_scale;
- if (this.left_offset) {
- left -= this.left_offset;
- }
- cached.css({ left: left });
- this.show_tile( cached, parent_element );
+ this.show_tile( cached, parent_element, tile_index );
} else {
this.delayed_draw(this, key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids);
}
@@ -1299,7 +1293,8 @@
for (var i = 0; i < this.child_tracks.length; i++) {
this.child_tracks[i].draw(force);
}
- }, delayed_draw: function(track, key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids) {
+ },
+ delayed_draw: function(track, key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids) {
// Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data
var id = setTimeout(function() {
if (low <= track.view.high && high >= track.view.low) {
@@ -1316,7 +1311,7 @@
}
// Add tile to cache and show tile.
track.tile_cache.set(key, tile_element);
- track.show_tile(tile_element, parent_element);
+ track.show_tile(tile_element, parent_element, tile_index);
}
}
// Remove setTimeout id.
@@ -1325,10 +1320,24 @@
draw_tile_ids[id] = true;
},
// Show track tile and perform associated actions.
- show_tile: function( tile_element, parent_element ) {
+ show_tile: function( tile_element, parent_element, tile_index ) {
// Readability.
var track = this;
+
+ // Position tile element
+ // Recalculate left position at display time
+ // FIXME: Should calculate this without tile_index
+ var range = this.view.high - this.view.low,
+ resolution = this.view.resolution,
+ w_scale = this.content_div.width() / range;
+ var tile_low = tile_index * DENSITY * this.view.resolution;
+ var left = ( tile_low - this.view.low ) * w_scale;
+ if (this.left_offset) {
+ left -= this.left_offset;
+ }
+ tile_element.css({ position: 'absolute', top: 0, left: left });
+
// Setup and show tile element.
parent_element.append( tile_element );
track.max_height = Math.max( track.max_height, tile_element.height() );
@@ -1538,13 +1547,7 @@
canvas.get(0).width = Math.ceil( tile_length * w_scale + this.left_offset);
canvas.get(0).height = this.height_px;
-
- canvas.css( {
- position: "absolute",
- top: 0,
- left: ( tile_low - this.view.low ) * w_scale - this.left_offset
- });
-
+
for (var c = 0, str_len = seq.length; c < str_len; c++) {
var c_start = Math.round(c * w_scale),
gap = Math.round(w_scale / 2);
@@ -1690,12 +1693,6 @@
var data = this.data_cache.get(key);
if (!data) { return; }
- canvas.css( {
- position: "absolute",
- top: 0,
- left: ( tile_low - this.view.low ) * w_scale
- });
-
canvas.get(0).width = Math.ceil( tile_length * w_scale );
canvas.get(0).height = this.height_px;
var ctx = canvas.get(0).getContext("2d"),
@@ -1776,7 +1773,6 @@
} else {
ctx.stroke();
}
- parent_element.append(canvas);
return canvas;
}, gen_options: function(track_id) {
var container = $("<div />").addClass("form-row");
@@ -2131,12 +2127,7 @@
required_height = this.incremental_slots( inc_scale, result.data, no_detail, mode ) * y_scale + min_height;
slots = this.inc_slots[inc_scale];
}
-
- canvas.css({
- position: "absolute",
- top: 0,
- left: ( tile_low - this.view.low ) * w_scale - left_offset
- });
+
canvas.get(0).width = width + left_offset;
canvas.get(0).height = required_height;
parent_element.parent().css("height", Math.max(this.height_px, required_height) + "px");
@@ -2177,13 +2168,12 @@
ctx.fillText(y, x + left_offset + (delta_x_px/2), this.summary_draw_height - 5);
}
}
- parent_element.append( canvas );
return canvas;
}
//
// Show message. If there is a message, return canvas.
- //
+ // FIXME: Why is this drawn on a canvas instead of a div?
if (result.message) {
canvas.css({
border: "solid red",
@@ -2406,7 +2396,8 @@
}
}
return canvas;
- }, gen_options: function(track_id) {
+ },
+ gen_options: function(track_id) {
var container = $("<div />").addClass("form-row");
var block_color = 'track_' + track_id + '_block_color',
http://bitbucket.org/galaxy/galaxy-central/changeset/7b85e1b25a21/
changeset: r4988:7b85e1b25a21
user: james_taylor
date: 2011-02-03 20:57:49
summary: trackster: merge
affected #: 1 file (213 bytes)
--- a/lib/galaxy/datatypes/data.py Thu Feb 03 14:54:40 2011 -0500
+++ b/lib/galaxy/datatypes/data.py Thu Feb 03 14:57:49 2011 -0500
@@ -397,6 +397,15 @@
if line and not line.startswith( '#' ):
data_lines += 1
dataset.metadata.data_lines = data_lines
+ def estimate_file_lines( self, dataset ):
+ # Perform a rough estimate by extrapolating number of lines from a small read.
+ sample_size = 1048576
+ dataset_fh = open( dataset.file_name )
+ dataset_read = dataset_fh.read(sample_size)
+ dataset_fh.close()
+ sample_lines = dataset_read.count('\n')
+ est_lines = int(sample_lines * (float(dataset.get_size()) / float(sample_size)))
+ return est_lines
def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
if not dataset.dataset.purged:
# The file must exist on disk for the get_file_peek() method
@@ -409,13 +418,7 @@
# Number of lines is not known ( this should not happen ), and auto-detect is
# needed to set metadata
# This can happen when the file is larger than max_optional_metadata_filesize.
- # Perform a rough estimate by extrapolating number of lines from a small read.
- sample_size = 1048576
- dataset_fh = open( dataset.file_name )
- dataset_read = dataset_fh.read(sample_size)
- dataset_fh.close()
- sample_lines = dataset_read.count('\n')
- est_lines = int(sample_lines * (float(dataset.get_size()) / float(sample_size)))
+ est_lines = self.estimate_file_lines(dataset)
dataset.blurb = "~%s %s" % ( util.commaify(str(est_lines)), inflector.cond_plural(est_lines, "line") )
else:
dataset.blurb = "%s %s" % util.commaify( str(line_count) ), inflector.cond_plural(line_count, "line")
--- a/lib/galaxy/datatypes/interval.py Thu Feb 03 14:54:40 2011 -0500
+++ b/lib/galaxy/datatypes/interval.py Thu Feb 03 14:57:49 2011 -0500
@@ -71,7 +71,7 @@
else:
# Number of lines is not known ( this should not happen ), and auto-detect is
# needed to set metadata
- dataset.blurb = "? regions"
+ dataset.blurb = "~%s regions" % util.commaify( str( self.estimate_file_lines(dataset) ) )
else:
dataset.blurb = "%s regions" % util.commaify( str( line_count ) )
else:
--- a/static/scripts/packed/trackster.js Thu Feb 03 14:54:40 2011 -0500
+++ b/static/scripts/packed/trackster.js Thu Feb 03 14:57:49 2011 -0500
@@ -1,1 +1,1 @@
-CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX;g.enable_pan=(f.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(h,j){if(!j.enable_pan){return}var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var m=this.view.low,g=this.view.high,j=g-m,f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/j;this.content_div.append(p);this.max_height=0;var b=Math.floor(m/f/DENSITY);var l={};while((b*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+b;var e=this.tile_cache.get(n);if(!a&&e){var k=b*DENSITY*f;var d=(k-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(this,n,m,g,b,f,p,q,l)}b+=1}var c=this;var o=setInterval(function(){if(obj_length(l)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var i=0;i<c.filters.length;i++){c.filters[i].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(a)}},delayed_draw:function(c,h,g,e,b,d,i,j,f){var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.css({position:"absolute",top:0,left:(L-this.view.low)*ar-U});p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}r.append(p);return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
+CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX;g.enable_pan=(f.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(h,j){if(!j.enable_pan){return}var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var m=this.view.low,g=this.view.high,j=g-m,f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/j;this.content_div.append(p);this.max_height=0;var b=Math.floor(m/f/DENSITY);var l={};while((b*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+b;var e=this.tile_cache.get(n);if(!a&&e){var k=b*DENSITY*f;var d=(k-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(n,m,g,b,f,p,q,l)}b+=1}var c=this;var o=setInterval(function(){if(obj_length(l)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var i=0;i<c.filters.length;i++){c.filters[i].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(a)}},delayed_draw:function(h,g,e,b,d,i,j,f){var c=this;var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.tile_cache.get(h);if(!k){k=c.draw_tile(d,b,i,j)}if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.css({position:"absolute",top:0,left:(L-this.view.low)*ar-U});p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}r.append(p);return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
--- a/static/scripts/trackster.js Thu Feb 03 14:54:40 2011 -0500
+++ b/static/scripts/trackster.js Thu Feb 03 14:57:49 2011 -0500
@@ -1258,7 +1258,7 @@
if ( !force && cached ) {
this.show_tile( cached, parent_element, tile_index );
} else {
- this.delayed_draw(this, key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids);
+ this.delayed_draw(key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids);
}
tile_index += 1;
}
@@ -1293,12 +1293,16 @@
for (var i = 0; i < this.child_tracks.length; i++) {
this.child_tracks[i].draw(force);
}
- },
- delayed_draw: function(track, key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids) {
+ }, delayed_draw: function(key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids) {
+ var track = this;
// Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data
var id = setTimeout(function() {
if (low <= track.view.high && high >= track.view.low) {
- var tile_element = track.draw_tile(resolution, tile_index, parent_element, w_scale);
+ // Show/draw tile: check cache for tile; if tile not in cache, draw it.
+ var tile_element = track.tile_cache.get(key);
+ if (!tile_element) {
+ tile_element = track.draw_tile(resolution, tile_index, parent_element, w_scale);
+ }
if (tile_element) {
// Store initial canvas in case we need to use it for overview
if (!track.initial_canvas && !window.G_vmlCanvasManager) {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dannon: Interval now uses line estimates instead of '? regions' for the peek.
by Bitbucket 03 Feb '11
by Bitbucket 03 Feb '11
03 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/2a8cb9436c2b/
changeset: r4984:2a8cb9436c2b
user: dannon
date: 2011-02-03 19:12:46
summary: Interval now uses line estimates instead of '? regions' for the peek.
affected #: 2 files (116 bytes)
--- a/lib/galaxy/datatypes/data.py Thu Feb 03 09:34:39 2011 -0500
+++ b/lib/galaxy/datatypes/data.py Thu Feb 03 13:12:46 2011 -0500
@@ -397,6 +397,15 @@
if line and not line.startswith( '#' ):
data_lines += 1
dataset.metadata.data_lines = data_lines
+ def estimate_file_lines( self, dataset ):
+ # Perform a rough estimate by extrapolating number of lines from a small read.
+ sample_size = 1048576
+ dataset_fh = open( dataset.file_name )
+ dataset_read = dataset_fh.read(sample_size)
+ dataset_fh.close()
+ sample_lines = dataset_read.count('\n')
+ est_lines = int(sample_lines * (float(dataset.get_size()) / float(sample_size)))
+ return est_lines
def set_peek( self, dataset, line_count=None, is_multi_byte=False ):
if not dataset.dataset.purged:
# The file must exist on disk for the get_file_peek() method
@@ -409,13 +418,7 @@
# Number of lines is not known ( this should not happen ), and auto-detect is
# needed to set metadata
# This can happen when the file is larger than max_optional_metadata_filesize.
- # Perform a rough estimate by extrapolating number of lines from a small read.
- sample_size = 1048576
- dataset_fh = open( dataset.file_name )
- dataset_read = dataset_fh.read(sample_size)
- dataset_fh.close()
- sample_lines = dataset_read.count('\n')
- est_lines = int(sample_lines * (float(dataset.get_size()) / float(sample_size)))
+ est_lines = self.estimate_file_lines(dataset)
dataset.blurb = "~%s %s" % ( util.commaify(str(est_lines)), inflector.cond_plural(est_lines, "line") )
else:
dataset.blurb = "%s %s" % util.commaify( str(line_count) ), inflector.cond_plural(line_count, "line")
--- a/lib/galaxy/datatypes/interval.py Thu Feb 03 09:34:39 2011 -0500
+++ b/lib/galaxy/datatypes/interval.py Thu Feb 03 13:12:46 2011 -0500
@@ -71,7 +71,7 @@
else:
# Number of lines is not known ( this should not happen ), and auto-detect is
# needed to set metadata
- dataset.blurb = "? regions"
+ dataset.blurb = "~%s regions" % util.commaify( str( self.estimate_file_lines(dataset) ) )
else:
dataset.blurb = "%s regions" % util.commaify( str( line_count ) )
else:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Trackster: avoid drawing tiles multiple times by checking cache in delayed_draw.
by Bitbucket 03 Feb '11
by Bitbucket 03 Feb '11
03 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/b23f64804904/
changeset: r4983:b23f64804904
user: jgoecks
date: 2011-02-03 15:34:39
summary: Trackster: avoid drawing tiles multiple times by checking cache in delayed_draw.
affected #: 2 files (251 bytes)
--- a/static/scripts/packed/trackster.js Wed Feb 02 16:21:23 2011 -0500
+++ b/static/scripts/packed/trackster.js Thu Feb 03 09:34:39 2011 -0500
@@ -1,1 +1,1 @@
-CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX;g.enable_pan=(f.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(h,j){if(!j.enable_pan){return}var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var m=this.view.low,g=this.view.high,j=g-m,f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/j;this.content_div.append(p);this.max_height=0;var b=Math.floor(m/f/DENSITY);var l={};while((b*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+b;var e=this.tile_cache.get(n);if(!a&&e){var k=b*DENSITY*f;var d=(k-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(this,n,m,g,b,f,p,q,l)}b+=1}var c=this;var o=setInterval(function(){if(obj_length(l)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var i=0;i<c.filters.length;i++){c.filters[i].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(a)}},delayed_draw:function(c,h,g,e,b,d,i,j,f){var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.css({position:"absolute",top:0,left:(L-this.view.low)*ar-U});p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}r.append(p);return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
+CanvasRenderingContext2D.prototype.dashedLine=function(c,i,b,h,f){if(f==undefined){f=4}var e=b-c;var d=h-i;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var k=e/g;var j=d/g;for(var a=0;a<g;a++,c+=k,i+=j){if(a%2!=0){continue}this.fillRect(c,i,f,1)}};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();for(var c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c==f.length){if(this!=f.get(c-1)){g.append(this)}}else{if(this!=f.get(c)){$(this).insertBefore(f.get(c))}}})}var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",FILTERABLE_CLASS="filterable",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var i=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(i/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX;g.enable_pan=(f.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(h,j){if(!j.enable_pan){return}var f=$(this);var k=j.offsetX-j.current_x;var g=f.scrollTop()-(h.clientY-j.current_height);f.scrollTop(g);j.current_height=h.clientY;j.current_x=j.offsetX;var i=Math.round(k/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j,k){$(k.proxy).css({left:Math.min(j.pageX,k.startX),width:Math.abs(j.pageX-k.startX)});var g=Math.min(j.pageX,k.startX)-a.container.offset().left,f=Math.max(j.pageX,k.startX)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low)}).bind("dragend",function(k,l){var g=Math.min(k.pageX,l.startX),f=Math.max(k.pageX,l.startX),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;$(l.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)==0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(this.dataset_check_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom,low:a.view.max_low,high:a.view.max_high},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").attr("id",d+"_error");c.text("View error");$("#"+d+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b==="data"){a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;a.predraw_init();a.draw()}}}}}}})},predraw_init:function(){},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(g,d,s){var o=this,j=o.view;this.filters=(g!==undefined?get_filters_from_dict(g):[]);this.tool=(d!==undefined?get_tool_from_dict(d):undefined);this.parent_track=s;this.child_tracks=[];if(o.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var t=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(w,z){var v=$("<tr>").appendTo(t);var y=$("<th class='filter-info'>").appendTo(v);var u=$("<span class='name'>").appendTo(y);u.text(z.name+" ");var i=$("<span class='values'>").appendTo(y);var x=$("<td>").appendTo(v);z.control_element=$("<div id='"+z.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(x);z.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(B,C){var A=C.values;i.text("["+A[0]+"-"+A[1]+"]");z.low=A[0];z.high=A[1];o.draw(true)},change:function(A,B){z.control_element.slider("option","slide").call(z.control_element,A,B)}});z.slider=z.control_element;z.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var l=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var e=this.tool.params;var o=this;$.each(this.tool.params,function(A,v){var y=$("<div>").addClass("param-row").appendTo(o.dynamic_tool_div);var x=$("<div>").addClass("slider-label").appendTo(y);var C=$("<span class='param-name'>").text(v.label+" ").appendTo(x);var w=$("<span/>").text(v.value);var z=$("<span class='param-value'>").appendTo(x).append("[").append(w).append("]");var B=$("<div/>").addClass("slider").appendTo(y);var i=$("<div id='"+v.name+"-param-control'>").appendTo(B);var u=(v.max<=1?0.01:(v.max<=1000?1:5));i.slider({min:v.min,max:v.max,step:u,value:v.value,slide:function(D,F){var E=F.value;v.value=E;if(0<E&&E<1){E=parseFloat(E).toFixed(2)}w.text(E)},change:function(D,E){v.value=E.value}});z.click(function(){var F=w,E=F.text(),D=(v.max<=1?4:v.max.length);F.text("");$("<input type='text'/>").attr("size",D).attr("maxlength",D).attr("value",E).appendTo(F).focus().select().click(function(G){G.stopPropagation()}).blur(function(){$(this).remove();F.text(E)}).keyup(function(I){if(I.keyCode===27){$(this).trigger("blur")}else{if(I.keyCode===13){var G=$(this),H=parseFloat(G.val());if(isNaN(H)||H>v.max||H<v.min){alert("Parameter value must be in the range ["+v.min+"-"+v.max+"]");return $(this)}F.text(H);i.slider("value",H);v.value=H}}})});$("<div style='clear: both;'/>").appendTo(y)});var b=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var n=$("<input type='submit'>").attr("value","Run").appendTo(b);var o=this;n.click(function(){o.run_tool()})}o.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();o.container_div.append(o.child_tracks_container);if(o.display_modes!==undefined){if(o.mode_div===undefined){o.mode_div=$("<div class='right-float menubutton popup' />").appendTo(o.header_div);var m=o.display_modes[0];o.mode=m;o.mode_div.text(m);var a=function(i){o.mode_div.text(i);o.mode=i;o.tile_cache.clear();o.draw()};var f={};for(var q=0,r=o.display_modes.length;q<r;q++){var k=o.display_modes[q];f[k]=function(i){return function(){a(i)}}(k)}make_popupmenu(o.mode_div,f)}else{o.mode_div.hide()}}var h={};h["Edit configuration"]=function(){var v=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){o.update_options(o.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},u=function(w){if((w.keyCode||w.which)===27){v()}else{if((w.keyCode||w.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",u);show_modal("Configure Track",o.gen_options(o.track_id),{Cancel:v,OK:i})};h["Set as overview"]=function(){j.overview_viewport.find("canvas").remove();o.is_overview=true;o.set_overview();for(var i in j.tracks){if(j.tracks[i]!==o){j.tracks[i].is_overview=false}}};if(o.filters.length>0){h["Show filters"]=function(){var i;if(!o.filtering_div.is(":visible")){i="Hide filters";o.filters_visible=true}else{i="Show filters";o.filters_visible=false}o.filtering_div.toggle()}}if(o.tool){h["Toggle Tool"]=function(){var i;if(!o.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";o.update_name(o.name+o.tool_region_and_parameters_str())}else{i="Show dynamic tool";o.revert_name()}o.dynamic_tool_div.toggle()}}var c=j;var p=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;p=function(){}}h.Remove=function(){c.remove_track(o);if(c.num_tracks===0){p()}};o.popup_menu=make_popupmenu(o.name_div,h)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var m=this.view.low,g=this.view.high,j=g-m,f=this.view.resolution;var p=$("<div style='position: relative;'></div>"),q=this.content_div.width()/j;this.content_div.append(p);this.max_height=0;var b=Math.floor(m/f/DENSITY);var l={};while((b*DENSITY*f)<g){var n=this.content_div.width()+"_"+q+"_"+b;var e=this.tile_cache.get(n);if(!a&&e){var k=b*DENSITY*f;var d=(k-m)*q;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,p)}else{this.delayed_draw(n,m,g,b,f,p,q,l)}b+=1}var c=this;var o=setInterval(function(){if(obj_length(l)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var i=0;i<c.filters.length;i++){c.filters[i].update_ui_elt()}clearInterval(o)}},50);for(var h=0;h<this.child_tracks.length;h++){this.child_tracks[h].draw(a)}},delayed_draw:function(h,g,e,b,d,i,j,f){var c=this;var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.tile_cache.get(h);if(!k){k=c.draw_tile(d,b,i,j)}if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type=="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,e,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.min_height_px=12;this.max_height_px=400;this.height_px=80;this.hda_ldda=e;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c);(function(f){var i=false;var h=false;var g=$("<div class='track-resize'>");$(f.container_div).hover(function(){i=true;g.show()},function(){i=false;if(!h){g.hide()}});g.hide().bind("dragstart",function(j,k){h=true;k.original_height=$(f.content_div).height()}).bind("drag",function(k,l){var j=Math.min(Math.max(l.original_height+l.deltaY,f.min_height_px),f.max_height_px);$(f.content_div).css("height",j);f.height_px=j;f.draw(true)}).bind("dragend",function(j,k){f.tile_cache.clear();h=false;if(!i){g.hide()}}).appendTo(f.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;$.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,x=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(x)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(x);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;var w=Math.round(d+k/m*d);n.beginPath();n.moveTo(0,w);n.lineTo(a*e,w);n.fillStyle="#aaa";n.stroke();n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(h/m*d);n.fillRect(u,w,f,-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,w);n.lineTo(0,w)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,h,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=h;this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,hda_ldda:b.hda_ldda,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set_data(a,d,b.mode,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{}}return j},rect_or_text:function(r,l,u,b,q,j,g,f){r.textAlign="center";var d=0,s=0,p=Math.round(l/2);for(var m=0,t=j.length;m<t;m++){var k=j[m],e="MIDNSHP=X"[k[0]],n=k[1];if(e==="H"||e==="S"){d-=n}var h=q+d,x=Math.floor(Math.max(0,(h-u)*l)),i=Math.floor(Math.max(0,(h+n-u)*l));switch(e){case"H":break;case"S":case"M":case"=":var o=g.slice(s,s+n);if((this.mode==="Pack"||this.mode==="Auto")&&g!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+1,i-x,9);r.fillStyle=CONNECTOR_COLOR;for(var v=0,a=o.length;v<a;v++){if(h+v>=u&&h+v<=b){var w=Math.floor(Math.max(0,(h+v-u)*l));r.fillText(o[v],w+this.left_offset+p,f+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(x+this.left_offset,f+(this.mode!="Dense"?4:5),i-x,(this.mode!="Dense"?3:1))}s+=n;break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(x+this.left_offset,f+5,i-x,1);break;case"D":r.fillStyle="red";r.fillRect(x+this.left_offset,f+4,i-x,3);break;case"P":break;case"I":s+=n;break;case"X":s+=n;break}d+=n}},draw_tile:function(ad,n,r,ar){var L=n*DENSITY*ad,ai=(n+1)*DENSITY*ad,K=ai-L;var G=this.data_cache.get_data(L,ai,this.mode);if(G===undefined||G==="pending"||(this.mode!=="Auto"&&G.dataset_type==="summary_tree")){this.data_queue[[L,ai]]=true;this.get_data(L,ai);return}var a=Math.ceil(K*ar),af=this.prefs.label_color,h=this.prefs.block_color,q=this.mode,v=25,ab=(q==="Squish")||(q==="Dense")&&(q!=="Pack")||(q==="Auto"&&(G.extra_info==="no_detail")),U=this.left_offset,aq,B,at;var p=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(p)}p=$(p);if(G.dataset_type==="summary_tree"){B=this.summary_draw_height}else{if(q==="Dense"){B=v;at=10}else{at=(ab?this.vertical_nodetail_px:this.vertical_detail_px);var w=(ar<0.0001?1/this.view.zoom_res:ar);B=this.incremental_slots(w,G.data,ab,q)*at+v;aq=this.inc_slots[w]}}p.css({position:"absolute",top:0,left:(L-this.view.low)*ar-U});p.get(0).width=a+U;p.get(0).height=B;r.parent().css("height",Math.max(this.height_px,B)+"px");var H=p.get(0).getContext("2d");H.fillStyle=h;H.font=this.default_font;H.textAlign="right";this.container_div.find(".yaxislabel").remove();if(G.dataset_type=="summary_tree"){var W=G.data,J=G.max,b=Math.ceil(G.delta*ar);var o=$("<div />").addClass("yaxislabel");o.text(J);o.css({position:"absolute",top:"22px",left:"10px"});o.prependTo(this.container_div);for(var am=0,F=W.length;am<F;am++){var Y=Math.floor((W[am][0]-L)*ar);var X=W[am][1];if(!X){continue}var aj=X/J*this.summary_draw_height;H.fillStyle="black";H.fillRect(Y+U,this.summary_draw_height-aj,b,aj);if(this.prefs.show_counts&&H.measureText(X).width<b){H.fillStyle="#bbb";H.textAlign="center";H.fillText(X,Y+U+(b/2),this.summary_draw_height-5)}}r.append(p);return p}if(G.message){p.css({border:"solid red","border-width":"2px 2px 2px 0px"});H.fillStyle="red";H.textAlign="left";H.fillText(G.message,100+U,at);return p}for(var ao=0;ao<this.filters.length;ao++){if(this.filters[ao].applies_to(G.data[0])){p.addClass(FILTERABLE_CLASS);break}}var ap=G.data;var al=0;for(var am=0,F=ap.length;am<F;am++){var Q=ap[am],P=Q[0],an=Q[1],aa=Q[2],M=Q[3];if(this.mode!="Dense"&&aq[P]===undefined){continue}var Z=false;var S;for(var ao=0;ao<this.filters.length;ao++){S=this.filters[ao];S.update_attrs(Q);if(!S.keep(Q)){Z=true;break}}if(Z){continue}if(an<=ai&&aa>=L){var ac=Math.floor(Math.max(0,(an-L)*ar)),I=Math.ceil(Math.min(a,Math.max(0,(aa-L)*ar))),V=(q==="Dense"?1:(1+aq[P]))*at;var E,ag,N=null,au=null;if(G.dataset_type==="bai"){H.fillStyle=h;if(Q[5] instanceof Array){var C=Math.floor(Math.max(0,(Q[4][0]-L)*ar)),O=Math.ceil(Math.min(a,Math.max(0,(Q[4][1]-L)*ar))),A=Math.floor(Math.max(0,(Q[5][0]-L)*ar)),u=Math.ceil(Math.min(a,Math.max(0,(Q[5][1]-L)*ar)));if(Q[4][1]>=L&&Q[4][0]<=ai&&Q[4][2]){this.rect_or_text(H,ar,L,ai,Q[4][0],Q[4][2],Q[4][3],V)}if(Q[5][1]>=L&&Q[5][0]<=ai&&Q[5][2]){this.rect_or_text(H,ar,L,ai,Q[5][0],Q[5][2],Q[5][3],V)}if(A>O){H.fillStyle=CONNECTOR_COLOR;H.dashedLine(O+U,V+5,U+A,V+5)}}else{H.fillStyle=h;this.rect_or_text(H,ar,L,ai,an,Q[4],Q[5],V)}if(q!=="Dense"&&!ab&&an>L){H.fillStyle=this.prefs.label_color;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}}else{if(G.dataset_type==="interval_index"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var D=Q[5],T=Q[6],ae=Q[7],g=Q[8];if(T&&ae){N=Math.floor(Math.max(0,(T-L)*ar));au=Math.ceil(Math.min(a,Math.max(0,(ae-L)*ar)))}if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}if(g){if(D){if(D=="+"){H.fillStyle=RIGHT_STRAND}else{if(D=="-"){H.fillStyle=LEFT_STRAND}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}for(var ak=0,e=g.length;ak<e;ak++){var t=g[ak],d=Math.floor(Math.max(0,(t[0]-L)*ar)),R=Math.ceil(Math.min(a,Math.max((t[1]-L)*ar)));if(d>R){continue}E=5;ag=3;H.fillRect(d+U,V+ag,R-d,E);if(N!==undefined&&!(d>au||R<N)){E=9;ag=1;var ah=Math.max(d,N),z=Math.min(R,au);H.fillRect(ah+U,V+ag,z-ah,E)}}}else{E=9;ag=1;H.fillRect(ac+U,V+ag,I-ac,E);if(Q.strand){if(Q.strand=="+"){H.fillStyle=RIGHT_STRAND_INV}else{if(Q.strand=="-"){H.fillStyle=LEFT_STRAND_INV}}H.fillRect(ac+U,V,I-ac,10);H.fillStyle=h}}}}else{if(G.dataset_type==="vcf"){if(ab){H.fillStyle=h;H.fillRect(ac+U,V+5,I-ac,1)}else{var s=Q[4],m=Q[5],c=Q[6];E=9;ag=1;H.fillRect(ac+U,V,I-ac,E);if(q!=="Dense"&&M!==undefined&&an>L){H.fillStyle=af;if(n===0&&ac-H.measureText(M).width<0){H.textAlign="left";H.fillText(M,I+2+U,V+8)}else{H.textAlign="right";H.fillText(M,ac-2+U,V+8)}H.fillStyle=h}var l=s+" / "+m;if(an>L&&H.measureText(l).width<(I-ac)){H.fillStyle="white";H.textAlign="center";H.fillText(l,U+ac+(I-ac)/2,V+8);H.fillStyle=h}}}}}al++}}return p},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()==0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id},function(c){})}};a()}});
\ No newline at end of file
--- a/static/scripts/trackster.js Wed Feb 02 16:21:23 2011 -0500
+++ b/static/scripts/trackster.js Thu Feb 03 09:34:39 2011 -0500
@@ -1254,7 +1254,7 @@
cached.css({ left: left });
this.show_tile( cached, parent_element );
} else {
- this.delayed_draw(this, key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids);
+ this.delayed_draw(key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids);
}
tile_index += 1;
}
@@ -1289,11 +1289,16 @@
for (var i = 0; i < this.child_tracks.length; i++) {
this.child_tracks[i].draw(force);
}
- }, delayed_draw: function(track, key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids) {
+ }, delayed_draw: function(key, low, high, tile_index, resolution, parent_element, w_scale, draw_tile_ids) {
+ var track = this;
// Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data
var id = setTimeout(function() {
if (low <= track.view.high && high >= track.view.low) {
- var tile_element = track.draw_tile(resolution, tile_index, parent_element, w_scale);
+ // Show/draw tile: check cache for tile; if tile not in cache, draw it.
+ var tile_element = track.tile_cache.get(key);
+ if (!tile_element) {
+ tile_element = track.draw_tile(resolution, tile_index, parent_element, w_scale);
+ }
if (tile_element) {
// Store initial canvas in case we need to use it for overview
if (!track.initial_canvas && !window.G_vmlCanvasManager) {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: rc: Fix to support older postgres versions (<8.3) which does not support 'alter sequence'.
by Bitbucket 02 Feb '11
by Bitbucket 02 Feb '11
02 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/b2b7be6597c6/
changeset: r4982:b2b7be6597c6
user: rc
date: 2011-02-02 22:21:23
summary: Fix to support older postgres versions (<8.3) which does not support 'alter sequence'.
affected #: 1 file (3 bytes)
--- a/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py Wed Feb 02 15:07:14 2011 -0500
+++ b/lib/galaxy/model/migrate/versions/0068_rename_sequencer_to_external_services.py Wed Feb 02 16:21:23 2011 -0500
@@ -102,7 +102,7 @@
return
# if running postgres then rename the primary key sequence too
if migrate_engine.name == 'postgres':
- cmd = "ALTER SEQUENCE sequencer_id_seq RENAME TO external_service_id_seq"
+ cmd = "ALTER TABLE sequencer_id_seq RENAME TO external_service_id_seq"
db_session.execute( cmd )
# rename 'sequencer_type_id' column to 'external_service_type_id' in the table 'external_service'
# create the column as 'external_service_type_id'
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: kanwei: Fix adding datasets to trackster from history pane
by Bitbucket 02 Feb '11
by Bitbucket 02 Feb '11
02 Feb '11
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/0bfb73dea188/
changeset: r4981:0bfb73dea188
user: kanwei
date: 2011-02-02 21:07:14
summary: Fix adding datasets to trackster from history pane
affected #: 1 file (4 bytes)
--- a/templates/tracks/browser.mako Wed Feb 02 15:06:10 2011 -0500
+++ b/templates/tracks/browser.mako Wed Feb 02 15:07:14 2011 -0500
@@ -224,7 +224,7 @@
%if add_dataset is not None:
$.ajax( {
url: "${h.url_for( action='add_track_async' )}",
- data: { id: "${add_dataset}" },
+ data: { hda_id: "${add_dataset}" },
dataType: "json",
success: add_async_success
});
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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