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commit/galaxy-central: jgoecks: Trackster: use hammer for tool icon instead of toolbox.
by Bitbucket 18 Mar '12

18 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f89751a01107/ changeset: f89751a01107 user: jgoecks date: 2012-03-18 19:42:04 summary: Trackster: use hammer for tool icon instead of toolbox. affected #: 3 files diff -r 4d446332535159d19dd8afde49324fbbac981bc5 -r f89751a0110713afb868caf72c80fc75890509bb static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -72,6 +72,8 @@ .settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;} .overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;} .overview-icon:hover{background:transparent url(../images/fugue/application-dock-270.png) no-repeat;} +.hammer{background:transparent url(../images/fugue/hammer-bw.png) no-repeat;} +.hammer:hover{background:transparent url(../images/fugue/hammer.png) no-repeat;} .toolbox{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;} .toolbox:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;} .filters-icon{background:transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat;} diff -r 4d446332535159d19dd8afde49324fbbac981bc5 -r f89751a0110713afb868caf72c80fc75890509bb static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -369,7 +369,12 @@ .overview-icon:hover { background:transparent url(../images/fugue/application-dock-270.png) no-repeat; } - +.hammer { + background: transparent url(../images/fugue/hammer-bw.png) no-repeat; +} +.hammer:hover { + background: transparent url(../images/fugue/hammer.png) no-repeat; +} .toolbox { background: transparent url(../images/fugue/toolbox-bw.png) no-repeat; } diff -r 4d446332535159d19dd8afde49324fbbac981bc5 -r f89751a0110713afb868caf72c80fc75890509bb static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -3209,8 +3209,8 @@ // Toggle track tool. { name: "tools_icon", - title: "Tools", - css_class: "toolbox", + title: "Tool", + css_class: "hammer", on_click_fn: function(track) { // TODO: update tipsy text. 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 this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 16 Mar '12

16 Mar '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/58a40d05be54/ changeset: 58a40d05be54 user: jgoecks date: 2012-03-16 19:25:13 summary: Match CSS class name with icon name. affected #: 4 files diff -r 7bb305f17ba795bc5a8b414e6ecfcc4b115d9193 -r 58a40d05be544fb1a625b5513a9523f50f51bcdb static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -72,8 +72,8 @@ .settings-icon:hover{background:transparent url(../images/fugue/gear.png) no-repeat;} .overview-icon{background:transparent url(../images/fugue/application-dock-270-bw.png) no-repeat;} .overview-icon:hover{background:transparent url(../images/fugue/application-dock-270.png) no-repeat;} -.tools-icon{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;} -.tools-icon:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;} +.toolbox{background:transparent url(../images/fugue/toolbox-bw.png) no-repeat;} +.toolbox:hover{background:transparent url(../images/fugue/toolbox.png) no-repeat;} .filters-icon{background:transparent url(../images/fugue/ui-slider-050-bw.png) no-repeat;} .filters-icon:hover{background:transparent url(../images/fugue/ui-slider-050.png) no-repeat;} .remove-icon,.overview-close{background:transparent url(../images/fugue/cross-small-bw.png) no-repeat;} diff -r 7bb305f17ba795bc5a8b414e6ecfcc4b115d9193 -r 58a40d05be544fb1a625b5513a9523f50f51bcdb static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -370,10 +370,10 @@ background:transparent url(../images/fugue/application-dock-270.png) no-repeat; } -.tools-icon { +.toolbox { background: transparent url(../images/fugue/toolbox-bw.png) no-repeat; } -.tools-icon:hover { +.toolbox:hover { background: transparent url(../images/fugue/toolbox.png) no-repeat; } .filters-icon { diff -r 7bb305f17ba795bc5a8b414e6ecfcc4b115d9193 -r 58a40d05be544fb1a625b5513a9523f50f51bcdb static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});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/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").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_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").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();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.content_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.content_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;ac<ag.length;ac++){if(!this._keep_val(ag[ac])){ae=false;break}}return ae}else{return this._keep_val(ad[this.index])}},update_attrs:function(af){var ac=false;if(!this.applies_to(af)){return ac}var ad=af[this.index];if(!(ad instanceof Array)){ad=[ad]}for(var ae=0;ae<ad.length;ae++){var ag=ad[ae];if(ag<this.min){this.min=Math.floor(ag);ac=true}if(ag>this.max){this.max=Math.ceil(ag);ac=true}}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);this.add_resize_handle()}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.tiles_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.tiles_div.text(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.tiles_div.text(V);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.after_show_tile(ae)},after_show_tile:function(ac){},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={todo:"label",todo:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,"reference",ac,{content_div:ac.top_labeltrack},{});ac.reference_track=this;this.left_offset=200;this.visible_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_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false)};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){af.content_div.css("height","0px");return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}return new b(af,ad,ag,ae,ak)}this.content_div.css("height","0px")}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{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:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};p(j.prototype,q.prototype,K.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},after_show_tile:function(ac){this.max_height_px=Math.max(this.max_height_px,ac.html_elt.height());ac.html_elt.parent().children().css("height",this.max_height_px+"px");var ad=this.max_height_px;if(this.visible_height_px!==0){ad=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ad+"px")},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".tipsy").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});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/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").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_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").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();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.content_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.content_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;ac<ag.length;ac++){if(!this._keep_val(ag[ac])){ae=false;break}}return ae}else{return this._keep_val(ad[this.index])}},update_attrs:function(af){var ac=false;if(!this.applies_to(af)){return ac}var ad=af[this.index];if(!(ad instanceof Array)){ad=[ad]}for(var ae=0;ae<ad.length;ae++){var ag=ad[ae];if(ag<this.min){this.min=Math.floor(ag);ac=true}if(ag>this.max){this.max=Math.ceil(ag);ac=true}}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);this.add_resize_handle()}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tools",css_class:"toolbox",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.tiles_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.tiles_div.text(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.tiles_div.text(V);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.after_show_tile(ae)},after_show_tile:function(ac){},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={todo:"label",todo:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,"reference",ac,{content_div:ac.top_labeltrack},{});ac.reference_track=this;this.left_offset=200;this.visible_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_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false)};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){af.content_div.css("height","0px");return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}return new b(af,ad,ag,ae,ak)}this.content_div.css("height","0px")}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{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:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};p(j.prototype,q.prototype,K.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},after_show_tile:function(ac){this.max_height_px=Math.max(this.max_height_px,ac.html_elt.height());ac.html_elt.parent().children().css("height",this.max_height_px+"px");var ad=this.max_height_px;if(this.visible_height_px!==0){ad=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ad+"px")},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".tipsy").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r 7bb305f17ba795bc5a8b414e6ecfcc4b115d9193 -r 58a40d05be544fb1a625b5513a9523f50f51bcdb static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -3209,7 +3209,7 @@ { name: "tools_icon", title: "Tools", - css_class: "tools-icon", + css_class: "toolbox", on_click_fn: function(track) { // TODO: update tipsy text. https://bitbucket.org/galaxy/galaxy-central/changeset/4b82812e5d2f/ changeset: 4b82812e5d2f user: jgoecks date: 2012-03-16 19:31:04 summary: Make running tools compatible with 4a7374937251 affected #: 1 file diff -r 58a40d05be544fb1a625b5513a9523f50f51bcdb -r 4b82812e5d2f9d9b628f18638e3e115b7953e65c static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2092,7 +2092,7 @@ new_track.set_filters_manager(current_track.filters_manager.copy(new_track)); new_track.update_icons(); container.add_drawable(new_track); - new_track.content_div.text("Starting job."); + new_track.tiles_div.text("Starting job."); // Run tool. this.update_params(); @@ -2100,7 +2100,7 @@ // Success callback. function(track_data) { new_track.dataset_id = track_data.dataset_id; - new_track.content_div.text("Running job."); + new_track.tiles_div.text("Running job."); new_track.init(); } ); https://bitbucket.org/galaxy/galaxy-central/changeset/4d4463325351/ changeset: 4d4463325351 user: jgoecks date: 2012-03-16 20:10:07 summary: Trackster: better message when indexing data. affected #: 1 file diff -r 4b82812e5d2f9d9b628f18638e3e115b7953e65c -r 4d446332535159d19dd8afde49324fbbac981bc5 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -393,7 +393,8 @@ 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_PENDING = "Preparing data. This takes seconds for a small dataset but longer for a large dataset.<br/>\ + You can save and close the visualization and preparation will continue.<br/>", DATA_CANNOT_RUN_TOOL = "Tool cannot be rerun: ", DATA_LOADING = "Loading data...", DATA_OK = "Ready for display", @@ -3420,7 +3421,8 @@ track.tiles_div.text(DATA_NONE); } else if (result === "pending") { track.container_div.addClass("pending"); - track.tiles_div.text(DATA_PENDING); + track.tiles_div.html(DATA_PENDING); + //$("<img/>").attr("src", image_path + "/yui/rel_interstitial_loading.gif").appendTo(track.tiles_div); setTimeout(function() { track.init(); }, track.data_query_wait); } else if (result['status'] === "data") { if (result['valid_chroms']) { 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 this email.

1 0

commit/galaxy-central: dan: Add GATK tools to tool_conf.xml.main.
by Bitbucket 16 Mar '12

16 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7bb305f17ba7/ changeset: 7bb305f17ba7 user: dan date: 2012-03-16 16:30:21 summary: Add GATK tools to tool_conf.xml.main. affected #: 1 file diff -r 7d021b926344dc5b2766c6c634c5d7c54f2098e7 -r 7bb305f17ba795bc5a8b414e6ecfcc4b115d9193 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -390,6 +390,39 @@ <tool file="samtools/samtools_flagstat.xml" /><tool file="samtools/samtools_rmdup.xml" /></section> + <section name="NGS: GATK Tools (beta)" id="gatk"> + <label text="Alignment Utilities" id="gatk_bam_utilities"/> + <tool file="gatk/depth_of_coverage.xml" /> + <tool file="gatk/print_reads.xml" /> + + <label text="Realignment" id="gatk_realignment" /> + <tool file="gatk/realigner_target_creator.xml" /> + <tool file="gatk/indel_realigner.xml" /> + + <label text="Base Recalibration" id="gatk_recalibration" /> + <tool file="gatk/count_covariates.xml" /> + <tool file="gatk/table_recalibration.xml" /> + <tool file="gatk/analyze_covariates.xml" /> + + <label text="Genotyping" id="gatk_genotyping" /> + <tool file="gatk/unified_genotyper.xml" /> + + <label text="Annotation" id="gatk_annotation" /> + <tool file="gatk/variant_annotator.xml" /> + + <label text="Filtration" id="gatk_filtration" /> + <tool file="gatk/variant_filtration.xml" /> + <tool file="gatk/variant_select.xml" /> + + <label text="Variant Quality Score Recalibration" id="gatk_variant_quality_score_recalibration" /> + <tool file="gatk/variant_recalibrator.xml" /> + <tool file="gatk/variant_apply_recalibration.xml" /> + + <label text="Variant Utilities" id="gatk_variant_utilities"/> + <tool file="gatk/variants_validate.xml" /> + <tool file="gatk/variant_eval.xml" /> + <tool file="gatk/variant_combine.xml" /> + </section><section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" /><tool file="indels/indel_sam2interval.xml" /> 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 this email.

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commit/galaxy-central: natefoo: Change the hardcoding of UCSC servers to a config file option, and remove the dependence on ucsc_display_sites, so any display server can be allowed. If you've modified your remoteuser.py, beware the merge.
by Bitbucket 16 Mar '12

16 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7d021b926344/ changeset: 7d021b926344 user: natefoo date: 2012-03-16 16:16:49 summary: Change the hardcoding of UCSC servers to a config file option, and remove the dependence on ucsc_display_sites, so any display server can be allowed. If you've modified your remoteuser.py, beware the merge. affected #: 3 files diff -r 143abc931cdb507bd1948b80c4078ce51e9e6386 -r 7d021b926344dc5b2766c6c634c5d7c54f2098e7 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -183,9 +183,9 @@ # upstream server if asbool(conf.get( 'use_remote_user', False )): from galaxy.web.framework.middleware.remoteuser import RemoteUser - app = RemoteUser( app, maildomain=conf.get( 'remote_user_maildomain', None ), - ucsc_display_sites=conf.get( 'ucsc_display_sites', [] ), - admin_users=conf.get( 'admin_users', '' ).split( ',' ) ) + app = RemoteUser( app, maildomain = conf.get( 'remote_user_maildomain', None ), + display_servers = util.listify( conf.get( 'display_servers', '' ) ), + admin_users = conf.get( 'admin_users', '' ).split( ',' ) ) log.debug( "Enabling 'remote user' middleware" ) # The recursive middleware allows for including requests in other # requests or forwarding of requests, all on the server side. diff -r 143abc931cdb507bd1948b80c4078ce51e9e6386 -r 7d021b926344dc5b2766c6c634c5d7c54f2098e7 lib/galaxy/web/framework/middleware/remoteuser.py --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -35,42 +35,22 @@ </html> """ -UCSC_MAIN_SERVERS = ( - 'hgw1.cse.ucsc.edu', - 'hgw2.cse.ucsc.edu', - 'hgw3.cse.ucsc.edu', - 'hgw4.cse.ucsc.edu', - 'hgw5.cse.ucsc.edu', - 'hgw6.cse.ucsc.edu', - 'hgw7.cse.ucsc.edu', - 'hgw8.cse.ucsc.edu', -) -UCSC_ARCHAEA_SERVERS = ( - 'lowepub.cse.ucsc.edu', -) - class RemoteUser( object ): - def __init__( self, app, maildomain=None, ucsc_display_sites=[], admin_users=[] ): + def __init__( self, app, maildomain=None, display_servers=None, admin_users=None ): self.app = app self.maildomain = maildomain - self.allow_ucsc_main = False - self.allow_ucsc_archaea = False - self.admin_users = admin_users - if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites: - self.allow_ucsc_main = True - if 'archaea' in ucsc_display_sites: - self.allow_ucsc_archaea = True + self.display_servers = display_servers or [] + self.admin_users = admin_users or [] def __call__( self, environ, start_response ): - # Allow through UCSC if the UCSC display links are enabled - if ( self.allow_ucsc_main or self.allow_ucsc_archaea ) and environ.has_key( 'REMOTE_ADDR' ): + # Allow display servers + if self.display_servers and environ.has_key( 'REMOTE_ADDR' ): try: host = socket.gethostbyaddr( environ[ 'REMOTE_ADDR' ] )[0] except( socket.error, socket.herror, socket.gaierror, socket.timeout ): # in the event of a lookup failure, deny access host = None - if ( self.allow_ucsc_main and host in UCSC_MAIN_SERVERS ) or \ - ( self.allow_ucsc_archaea and host in UCSC_ARCHAEA_SERVERS ): - environ[ 'HTTP_REMOTE_USER' ] = 'ucsc_browser_display(a)example.org' + if host in self.display_servers: + environ[ 'HTTP_REMOTE_USER' ] = 'remote_display_server@%s' % ( self.maildomain or 'example.org' ) return self.app( environ, start_response ) # Apache sets REMOTE_USER to the string '(null)' when using the # Rewrite* method for passing REMOTE_USER and a user is diff -r 143abc931cdb507bd1948b80c4078ce51e9e6386 -r 7d021b926344dc5b2766c6c634c5d7c54f2098e7 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -210,6 +210,20 @@ # GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt #genetrack_display_sites = main,test +# If use_remote_user = True, display application servers will be denied access +# to Galaxy and so displaying datasets in these sites will fail. +# display_servers contains a list of hostnames which should be allowed to +# bypass security to display datasets. Please be aware that there are security +# implications if this is allowed. More details (including required changes to +# the proxy server config) are available in the Apache proxy documentation on +# the wiki. +# +# The list of servers in this sample config are for the UCSC Main, Test and +# Archaea browsers, but the default if left commented is to not allow any +# display sites to bypass security (you must uncomment the line below to allow +# them). +#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw… + # -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. use_nglims = False 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 this email.

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commit/galaxy-central: greg: More fixes for handling mor ethan one non-shed tool anel config when installing tools migrated from the distrobution to the tool shed.
by Bitbucket 15 Mar '12

15 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/143abc931cdb/ changeset: 143abc931cdb user: greg date: 2012-03-15 19:12:59 summary: More fixes for handling mor ethan one non-shed tool anel config when installing tools migrated from the distrobution to the tool shed. affected #: 4 files diff -r d332e63b5367ed035dcaf6ee3aafed566200b617 -r 143abc931cdb507bd1948b80c4078ce51e9e6386 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -18,8 +18,7 @@ self.app = app self.toolbox = self.app.toolbox self.migrated_tools_config = migrated_tools_config - # Get the local non-shed related tool panel config (the default name is tool_conf.xml). If the user has more than 1 - # non-shed tool panel config it could cause problems. + # Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml). self.proprietary_tool_confs = self.non_shed_tool_panel_configs self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number ) # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config. diff -r d332e63b5367ed035dcaf6ee3aafed566200b617 -r 143abc931cdb507bd1948b80c4078ce51e9e6386 lib/galaxy/tool_shed/migrate/check.py --- a/lib/galaxy/tool_shed/migrate/check.py +++ b/lib/galaxy/tool_shed/migrate/check.py @@ -46,11 +46,11 @@ # New installations will not be missing tools, so we don't need to worry about them. missing_tool_configs = [] else: - tool_panel_config = get_non_shed_tool_panel_config( app ) - if tool_panel_config is None: + tool_panel_configs = get_non_shed_tool_panel_configs( app ) + if tool_panel_configs: + missing_tool_configs = check_for_missing_tools( tool_panel_configs, latest_tool_migration_script_number ) + else: missing_tool_configs = [] - else: - missing_tool_configs = check_for_missing_tools( tool_panel_config, latest_tool_migration_script_number ) config_arg = '' if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file: config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' ) @@ -62,13 +62,19 @@ if return_code != 0: raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output ) elif missing_tool_configs: + if len( tool_panel_configs ) == 1: + plural = '' + tool_panel_config_file_names = tool_panel_configs[ 0 ] + else: + plural = 's' + tool_panel_config_file_names = ', '.join( tool_panel_configs ) msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools can be automatically installed\n" msg += "from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n" msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n" - msg += "be removed from your file named %s.\n\n" % tool_panel_config + msg += "be removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names ) msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n" msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n" msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">). The default location\n' @@ -84,7 +90,7 @@ msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n" msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n" msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n" - msg += "removed from your file named %s, but only after the installation process finishes.\n\n" % tool_panel_config + msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names ) for i, missing_tool_config in enumerate( missing_tool_configs ): msg += "%s\n" % missing_tool_config # Should we do the following? diff -r d332e63b5367ed035dcaf6ee3aafed566200b617 -r 143abc931cdb507bd1948b80c4078ce51e9e6386 lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -39,8 +39,9 @@ if name in migrated_tool_configs: missing_tool_configs.append( name ) return missing_tool_configs -def get_non_shed_tool_panel_config( app ): - # Get the non-shed related tool panel config value from the Galaxy config - the default is tool_conf.xml. +def get_non_shed_tool_panel_configs( app ): + # Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml. + config_filenames = [] for config_filename in app.config.tool_configs: # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related. # <toolbox tool_path="../shed_tools"> @@ -48,9 +49,8 @@ root = tree.getroot() tool_path = root.get( 'tool_path', None ) if tool_path is None: - # There will be a problem here if the user has defined 2 non-shed related configs. - return config_filename - return None + config_filenames.append( config_filename ) + return config_filenames class MigrateToolsApplication( object ): """Encapsulates the state of a basic Galaxy Universe application in order to initiate the Install Manager""" def __init__( self, tools_migration_config ): diff -r d332e63b5367ed035dcaf6ee3aafed566200b617 -r 143abc931cdb507bd1948b80c4078ce51e9e6386 scripts/migrate_tools/migrate_tools.py --- a/scripts/migrate_tools/migrate_tools.py +++ b/scripts/migrate_tools/migrate_tools.py @@ -20,12 +20,14 @@ app = MigrateToolsApplication( sys.argv[ 1 ] ) non_shed_tool_confs = app.install_manager.proprietary_tool_confs -msg = "\nThe installation process is finished. You should now remove entries for the installed tools from " if len( non_shed_tool_confs ) == 1: - msg += "your file named %s and start your Galaxy server." % non_shed_tool_conf + plural = '' + file_names = non_shed_tool_confs[ 0 ] else: + plural = 's' file_names = ', '.join( non_shed_tool_confs ) - msg += "your files named %s, and start your Galaxy server." % file_names +msg = "\nThe installation process is finished. You should now remove entries for the installed tools from your file%s named\n" % plural +msg += "%s and start your Galaxy server.\n" % file_names print msg app.shutdown() sys.exit( 0 ) 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 this email.

1 0

commit/galaxy-central: jgoecks: Ensure reference track does not scroll.
by Bitbucket 15 Mar '12

15 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d332e63b5367/ changeset: d332e63b5367 user: jgoecks date: 2012-03-15 18:28:47 summary: Ensure reference track does not scroll. affected #: 1 file diff -r 3b9be709d138197d8076f1d5790187c124e98955 -r d332e63b5367ed035dcaf6ee3aafed566200b617 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -4238,7 +4238,7 @@ }); var ReferenceTrack = function (view) { - TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack, resize: false }, {}); + TiledTrack.call(this, view, { content_div: view.top_labeltrack, resize: false }, {}); view.reference_track = this; this.left_offset = 200; 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 this email.

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commit/galaxy-central: greg: Use an odict instead of a dict when acquuiring elements for generating entries for the migrated_tools_conf.xml from the InstallManager, and handle multiple proprietary non-shed tool panel configs with the InstallManger.
by Bitbucket 15 Mar '12

15 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3b9be709d138/ changeset: 3b9be709d138 user: greg date: 2012-03-15 16:47:46 summary: Use an odict instead of a dict when acquuiring elements for generating entries for the migrated_tools_conf.xml from the InstallManager, and handle multiple proprietary non-shed tool panel configs with the InstallManger. affected #: 3 files diff -r aafbc71077ec50054c0617bac3bf20443750885b -r 3b9be709d138197d8076f1d5790187c124e98955 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -6,6 +6,7 @@ from galaxy.tools import ToolSection from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * +from galaxy.util.odict import odict log = logging.getLogger( __name__ ) class InstallManager( object ): @@ -19,7 +20,7 @@ self.migrated_tools_config = migrated_tools_config # Get the local non-shed related tool panel config (the default name is tool_conf.xml). If the user has more than 1 # non-shed tool panel config it could cause problems. - self.proprietary_tool_conf = self.non_shed_tool_panel_config + self.proprietary_tool_confs = self.non_shed_tool_panel_configs self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number ) # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config. tree = util.parse_xml( migrated_tools_config ) @@ -50,10 +51,11 @@ tool = self.toolbox.load_tool( full_path ) return generate_tool_guid( repository_clone_url, tool ) def get_proprietary_tool_panel_elems( self, latest_tool_migration_script_number ): - # Parse self.proprietary_tool_conf (the default is tool_conf.xml) and generate a list of Elements that are either ToolSection elements - # or Tool elements. These will be used to generate new entries in the migrated_tools_conf.xml file for the installed tools. + # Parse each config in self.proprietary_tool_confs (the default is tool_conf.xml) and generate a list of Elements that are + # either ToolSection elements or Tool elements. These will be used to generate new entries in the migrated_tools_conf.xml + # file for the installed tools. tools_xml_file_path = os.path.abspath( os.path.join( 'scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number ) ) - # Parse the XML and load the file attributes for later checking against self.proprietary_tool_conf. + # Parse the XML and load the file attributes for later checking against the integrated elements from self.proprietary_tool_confs. migrated_tool_configs = [] tree = util.parse_xml( tools_xml_file_path ) root = tree.getroot() @@ -61,30 +63,31 @@ if elem.tag == 'repository': for tool_elem in elem: migrated_tool_configs.append( tool_elem.get( 'file' ) ) - # Parse self.proprietary_tool_conf and generate the list of tool panel Elements that contain them. + # Parse each file in self.proprietary_tool_confs and generate the integrated list of tool panel Elements that contain them. tool_panel_elems = [] - tree = util.parse_xml( self.proprietary_tool_conf ) - root = tree.getroot() - for elem in root: - if elem.tag == 'tool': - # Tools outside of sections. - file_path = elem.get( 'file', None ) - if file_path: - path, name = os.path.split( file_path ) - if name in migrated_tool_configs: - if elem not in tool_panel_elems: - tool_panel_elems.append( elem ) - elif elem.tag == 'section': - # Tools contained in a section. - for section_elem in elem: - if section_elem.tag == 'tool': - file_path = section_elem.get( 'file', None ) - if file_path: - path, name = os.path.split( file_path ) - if name in migrated_tool_configs: - # Append the section, not the tool. - if elem not in tool_panel_elems: - tool_panel_elems.append( elem ) + for proprietary_tool_conf in self.proprietary_tool_confs: + tree = util.parse_xml( proprietary_tool_conf ) + root = tree.getroot() + for elem in root: + if elem.tag == 'tool': + # Tools outside of sections. + file_path = elem.get( 'file', None ) + if file_path: + path, name = os.path.split( file_path ) + if name in migrated_tool_configs: + if elem not in tool_panel_elems: + tool_panel_elems.append( elem ) + elif elem.tag == 'section': + # Tools contained in a section. + for section_elem in elem: + if section_elem.tag == 'tool': + file_path = section_elem.get( 'file', None ) + if file_path: + path, name = os.path.split( file_path ) + if name in migrated_tool_configs: + # Append the section, not the tool. + if elem not in tool_panel_elems: + tool_panel_elems.append( elem ) return tool_panel_elems def get_containing_tool_sections( self, tool_config ): """ @@ -122,7 +125,7 @@ # updated to the desired changeset_revision before metadata is set because the process for setting metadata uses the repository files on disk. # The values for the keys in each of the following dictionaries will be a list to allow for the same tool to be displayed in multiple places # in the tool panel. - tool_panel_dict_for_display = {} + tool_panel_dict_for_display = odict() for tool_elem in repository_elem: # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> tool_config = tool_elem.get( 'file' ) @@ -264,8 +267,9 @@ print "Error cloning repository '", name, "': ", str( tmp_stderr.read() ) tmp_stderr.close() @property - def non_shed_tool_panel_config( self ): - # Get the non-shed related tool panel config value from the Galaxy config - the default is tool_conf.xml. + def non_shed_tool_panel_configs( self ): + # Get the non-shed related tool panel config file names from the Galaxy config - the default is tool_conf.xml. + config_filenames = [] for config_filename in self.app.config.tool_configs: # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related. # <toolbox tool_path="../shed_tools"> @@ -274,8 +278,8 @@ tool_path = root.get( 'tool_path', None ) if tool_path is None: # There will be a problem here if the user has defined 2 non-shed related configs. - return config_filename - return None + config_filenames.append( config_filename ) + return config_filenames def __get_url_from_tool_shed( self, tool_shed ): # The value of tool_shed is something like: toolshed.g2.bx.psu.edu # We need the URL to this tool shed, which is something like: diff -r aafbc71077ec50054c0617bac3bf20443750885b -r 3b9be709d138197d8076f1d5790187c124e98955 lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -70,6 +70,7 @@ self.config = galaxy.config.Configuration( **galaxy_config_dict ) if self.config.database_connection is None: self.config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database + self.config.update_integrated_tool_panel = True self.object_store = build_object_store_from_config( self.config ) # Setup the database engine and ORM self.model = galaxy.model.mapping.init( self.config.file_path, diff -r aafbc71077ec50054c0617bac3bf20443750885b -r 3b9be709d138197d8076f1d5790187c124e98955 scripts/migrate_tools/migrate_tools.py --- a/scripts/migrate_tools/migrate_tools.py +++ b/scripts/migrate_tools/migrate_tools.py @@ -19,8 +19,13 @@ from galaxy.tool_shed.migrate.common import * app = MigrateToolsApplication( sys.argv[ 1 ] ) -non_shed_tool_conf = app.install_manager.proprietary_tool_conf -print "\nThe installation process is finished. You should now remove entries for the installed tools from" -print "your file named %s and start your Galaxy server." % non_shed_tool_conf +non_shed_tool_confs = app.install_manager.proprietary_tool_confs +msg = "\nThe installation process is finished. You should now remove entries for the installed tools from " +if len( non_shed_tool_confs ) == 1: + msg += "your file named %s and start your Galaxy server." % non_shed_tool_conf +else: + file_names = ', '.join( non_shed_tool_confs ) + msg += "your files named %s, and start your Galaxy server." % file_names +print msg app.shutdown() sys.exit( 0 ) 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 this email.

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commit/galaxy-central: greg: Update the integrated_toon_conf.xml file only if a new config setting is True. This keeps things that start up the app (like functional tests) from updating the file.
by Bitbucket 14 Mar '12

14 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/aafbc71077ec/ changeset: aafbc71077ec user: greg date: 2012-03-14 22:21:03 summary: Update the integrated_toon_conf.xml file only if a new config setting is True. This keeps things that start up the app (like functional tests) from updating the file. affected #: 4 files diff -r 3b1f0bb99b43924b869cfc0df626738f18d968fc -r aafbc71077ec50054c0617bac3bf20443750885b lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -70,6 +70,7 @@ self.hours_between_check = 12 except: self.hours_between_check = 12 + self.update_integrated_tool_panel = kwargs.get( "update_integrated_tool_panel", True ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) ) diff -r 3b1f0bb99b43924b869cfc0df626738f18d968fc -r aafbc71077ec50054c0617bac3bf20443750885b lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -75,10 +75,12 @@ if self.integrated_tool_panel_config_has_contents: # Load self.tool_panel based on the order in self.integrated_tool_panel. self.load_tool_panel() - # Always write the current in-memory integrated_tool_panel to the integrated_tool_panel.xml file. - # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel - # config files, adding or removing locally developed tools or workflows. - self.write_integrated_tool_panel_config_file() + if app.config.update_integrated_tool_panel: + # Write the current in-memory integrated_tool_panel to the integrated_tool_panel.xml file. + # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel + # config files, adding or removing locally developed tools or workflows. The value of integrated_tool_panel + # will be False when things like functional tests are the caller. + self.write_integrated_tool_panel_config_file() def init_tools( self, config_filename ): """ Read the configuration file and load each tool. The following tags are currently supported: diff -r 3b1f0bb99b43924b869cfc0df626738f18d968fc -r aafbc71077ec50054c0617bac3bf20443750885b lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -430,7 +430,6 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repositories', **kwd ) ) - # Render the list view return self.repository_metadata_list_grid( trans, **kwd ) @web.expose @web.require_admin @@ -504,7 +503,7 @@ else: del kwd[ 'operation' ] elif operation == 'delete': - return self.mark_repository_deleted( trans, **kwd ) + return self.delete_repository( trans, **kwd ) elif operation == "undelete": return self.undelete_repository( trans, **kwd ) # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change @@ -528,12 +527,13 @@ return self.repository_list_grid( trans, **kwd ) @web.expose @web.require_admin - def mark_repository_deleted( self, trans, **kwd ): + def delete_repository( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) id = kwd.get( 'id', None ) if id: + # Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. ids = util.listify( id ) count = 0 deleted_repositories = "" @@ -564,6 +564,7 @@ status = params.get( 'status', 'done' ) id = kwd.get( 'id', None ) if id: + # Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id. ids = util.listify( id ) count = 0 undeleted_repositories = "" diff -r 3b1f0bb99b43924b869cfc0df626738f18d968fc -r aafbc71077ec50054c0617bac3bf20443750885b scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -167,6 +167,7 @@ file_path = file_path, new_file_path = new_file_path, tool_path = tool_path, + update_integrated_tool_panel = False, tool_config_file = tool_config_file, datatype_converters_config_file = "datatype_converters_conf.xml.sample", tool_parse_help = False, 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 this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 13 Mar '12

13 Mar '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/287d56ffaf6e/ changeset: 287d56ffaf6e user: jgoecks date: 2012-03-13 22:15:46 summary: Trackster: prevent resizing of label and reference tracks. affected #: 1 file diff -r 7fe7059a78a37323dc3e8efb832f5831be625dd8 -r 287d56ffaf6e7d8f5130469d427e65a9a68c6fb1 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -3161,7 +3161,9 @@ this.content_div = $("<div class='track-content'>").appendTo(this.container_div); if (this.container) { this.container.content_div.append(this.container_div); - this.add_resize_handle(); + if ( !("resize" in obj_dict) || obj_dict.resize ) { + this.add_resize_handle(); + } } }; @@ -3920,8 +3922,7 @@ var LabelTrack = function (view, container) { var obj_dict = { - todo: "label", - todo: false + resize: false }; Track.call(this, view, container, obj_dict); this.container_div.addClass( "label-track" ); @@ -4237,7 +4238,7 @@ }); var ReferenceTrack = function (view) { - TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, {}); + TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack, resize: false }, {}); view.reference_track = this; this.left_offset = 200; https://bitbucket.org/galaxy/galaxy-central/changeset/3b1f0bb99b43/ changeset: 3b1f0bb99b43 user: jgoecks date: 2012-03-13 22:22:56 summary: Trackster: make reference track compatible with changeset 8e9d2b492c4c. affected #: 1 file diff -r 287d56ffaf6e7d8f5130469d427e65a9a68c6fb1 -r 3b1f0bb99b43924b869cfc0df626738f18d968fc static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -4281,6 +4281,14 @@ return new Tile(track, tile_index, resolution, canvas, seq); } this.content_div.css("height", "0px"); + }, + /** + * If there is a tile with sequence data, set content div so that data is visible. + */ + after_show_tile: function(tile) { + if (tile) { + this.content_div.css("height", "12px"); + } } }); 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 this email.

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commit/galaxy-central: greg: When uploading a tarball to a tool shed repository, eliminate as many undesired directories (.svn, .git, .hg, .cvs) and files (hgrc, .hg_archival.txt, .DS_Store) as possible from the archive before committing the contents to the repository.
by Bitbucket 13 Mar '12

13 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7fe7059a78a3/ changeset: 7fe7059a78a3 user: greg date: 2012-03-13 21:25:15 summary: When uploading a tarball to a tool shed repository, eliminate as many undesired directories (.svn, .git, .hg, .cvs) and files (hgrc, .hg_archival.txt, .DS_Store) as possible from the archive before committing the contents to the repository. affected #: 1 file diff -r 48b64ce958b4ed9ec28639c1057adc67f70ae016 -r 7fe7059a78a37323dc3e8efb832f5831be625dd8 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -8,6 +8,8 @@ log = logging.getLogger( __name__ ) +undesirable_dirs = [ '.hg', '.svn', '.git', '.cvs' ] +undesirable_files = [ '.hg_archival.txt', 'hgrc', '.DS_Store' ] # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" CHUNK_SIZE = 2**20 # 1Mb @@ -92,14 +94,14 @@ tar = None istar = False if istar: - ok, message, files_to_remove, content_alert_str = self.upload_tar( trans, - repository, - tar, - uploaded_file, - upload_point, - remove_repo_files_not_in_tar, - commit_message, - new_repo_alert ) + ok, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed = self.upload_tar( trans, + repository, + tar, + uploaded_file, + upload_point, + remove_repo_files_not_in_tar, + commit_message, + new_repo_alert ) else: if ( isgzip or isbz2 ) and uncompress_file: uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ) @@ -150,6 +152,9 @@ else: uncompress_str = ' ' message = "The file '%s' has been successfully%suploaded to the repository." % ( uploaded_file_filename, uncompress_str ) + if istar and ( undesirable_dirs_removed or undesirable_files_removed ): + items_removed = undesirable_dirs_removed + undesirable_files_removed + message += " %d undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) were removed from the archive." % items_removed if istar and remove_repo_files_not_in_tar and files_to_remove: if upload_point is not None: message += " %d files were removed from the repository relative to the selected upload point '%s'." % ( len( files_to_remove ), upload_point ) @@ -206,7 +211,21 @@ full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) ) else: full_path = os.path.abspath( repo_dir ) - filenames_in_archive = [ tarinfo_obj.name for tarinfo_obj in tar.getmembers() ] + undesirable_dirs_removed = 0 + undesirable_files_removed = 0 + filenames_in_archive = [] + for tarinfo_obj in tar.getmembers(): + ok = os.path.basename( tarinfo_obj.name ) not in undesirable_files + if ok: + for file_path_item in tarinfo_obj.name.split( '/' ): + if file_path_item in undesirable_dirs: + undesirable_dirs_removed += 1 + ok = False + break + else: + undesirable_files_removed += 1 + if ok: + filenames_in_archive.append( tarinfo_obj.name ) filenames_in_archive = [ os.path.join( full_path, name ) for name in filenames_in_archive ] # Extract the uploaded tar to the load_point within the repository hierarchy. tar.extractall( path=full_path ) @@ -216,14 +235,15 @@ # We have a repository that is not new (it contains files), so discover # those files that are in the repository, but not in the uploaded archive. for root, dirs, files in os.walk( full_path ): - if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: - if '.hg' in dirs: - # Don't visit .hg directories - should be impossible since we don't - # allow uploaded archives that contain .hg dirs, but just in case... - dirs.remove( '.hg' ) - if 'hgrc' in files: - # Don't include hgrc files in commit. - files.remove( 'hgrc' ) + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: + for undesirable_dir in undesirable_dirs: + if undesirable_dir in dirs: + dirs.remove( undesirable_dir ) + undesirable_dirs_removed += 1 + for undesirable_file in undesirable_files: + if undesirable_file in files: + files.remove( undesirable_file ) + undesirable_files_removed += 1 for name in files: full_name = os.path.join( root, name ) if full_name not in filenames_in_archive: @@ -286,7 +306,7 @@ # See if the content of the change set was valid. admin_only = len( repository.downloadable_revisions ) != 1 handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only ) - return True, '', files_to_remove, content_alert_str + return True, '', files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): if isgzip: self.__handle_gzip( repository, uploaded_file_name ) 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 this email.

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commit/galaxy-central: greg: Fix for rerunning a tool where the correct id / version are available.
by Bitbucket 12 Mar '12

12 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/48b64ce958b4/ changeset: 48b64ce958b4 user: greg date: 2012-03-12 20:30:37 summary: Fix for rerunning a tool where the correct id / version are available. affected #: 1 file diff -r b199460443afeb3023f1c160f23b2215ba42add4 -r 48b64ce958b4ed9ec28639c1057adc67f70ae016 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -246,9 +246,15 @@ if tool_id in self.tools_by_id: tool = self.tools_by_id[ tool_id ] if tool_version and tool.version == tool_version: - return tool + if get_all_versions: + return [ tool ] + else: + return tool else: - return tool + if get_all_versions: + return [ tool ] + else: + return tool tv = self.__get_tool_version( tool_id ) if tv: tool_version_ids = tv.get_version_ids( self.app ) 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 this email.

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commit/galaxy-central: greg: Check potential tool config files to ensure they are text before attempting to load them in tool shed repositories, and a fix handling for tools contained in a repository that don't peoperly load into Galaxy because they are missing a required entry in the tool_data_table.conf file.
by Bitbucket 12 Mar '12

12 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b199460443af/ changeset: b199460443af user: greg date: 2012-03-12 18:51:07 summary: Check potential tool config files to ensure they are text before attempting to load them in tool shed repositories, and a fix handling for tools contained in a repository that don't peoperly load into Galaxy because they are missing a required entry in the tool_data_table.conf file. affected #: 6 files diff -r 02f55e34ccfeef865d5d0811664a1f95635ec609 -r b199460443afeb3023f1c160f23b2215ba42add4 lib/galaxy/tool_shed/migrate/check.py --- a/lib/galaxy/tool_shed/migrate/check.py +++ b/lib/galaxy/tool_shed/migrate/check.py @@ -63,7 +63,7 @@ raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output ) elif missing_tool_configs: msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>" - msg += "\n\nThe list of files at the end of this message refer to tools that are configured to load into the tool panel for\n" + msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n" msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools can be automatically installed\n" msg += "from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n" msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n" diff -r 02f55e34ccfeef865d5d0811664a1f95635ec609 -r b199460443afeb3023f1c160f23b2215ba42add4 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -2,6 +2,7 @@ from datetime import date, datetime, timedelta from time import strftime from galaxy import util +from galaxy.datatypes.checkers import * from galaxy.util.json import * from galaxy.tools.search import ToolBoxSearch from galaxy.model.orm import * @@ -11,6 +12,7 @@ from elementtree.ElementTree import Element, SubElement log = logging.getLogger( __name__ ) + def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ): # A tool shed repository is being installed so change the shed_tool_conf file. Parse the config file to generate the entire list # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have @@ -320,14 +322,15 @@ # Find all tool configs. if name != 'datatypes_conf.xml' and name.endswith( '.xml' ): full_path = os.path.abspath( os.path.join( root, name ) ) - try: - tool = toolbox.load_tool( full_path ) - except Exception, e: - tool = None - if tool is not None: - tool_config = os.path.join( root, name ) - guid = generate_tool_guid( repository_clone_url, tool ) - metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) + if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] + or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): + try: + tool = toolbox.load_tool( full_path ) + except Exception, e: + tool = None + if tool is not None: + tool_config = os.path.join( root, name ) + metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) # Find all exported workflows elif name.endswith( '.ga' ): relative_path = os.path.join( root, name ) @@ -642,10 +645,14 @@ repository_tools_tups = [] if 'tools' in metadata_dict: for tool_dict in metadata_dict[ 'tools' ]: - relative_path = tool_dict[ 'tool_config' ] - guid = tool_dict[ 'guid' ] - tool = app.toolbox.load_tool( os.path.abspath( relative_path ), guid=guid ) - repository_tools_tups.append( ( relative_path, guid, tool ) ) + relative_path = tool_dict.get( 'tool_config', None ) + guid = tool_dict.get( 'guid', None ) + if relative_path and guid: + tool = app.toolbox.load_tool( os.path.abspath( relative_path ), guid=guid ) + else: + tool = None + if tool: + repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups def get_tool_panel_config_tool_path_install_dir( app, repository ): # Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the @@ -745,6 +752,7 @@ missing_data_table_entry = True break if missing_data_table_entry: + sample_file = None # The repository must contain a tool_data_table_conf.xml.sample file that includes all required entries for all tools in the repository. for sample_file in sample_files: head, tail = os.path.split( sample_file ) @@ -753,10 +761,10 @@ error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_file ) if error: # TODO: Do more here than logging an exception. - log.debug( exception_msg ) + log.debug( correction_msg ) # Reload the tool into the local list of repository_tools_tups. repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) - repository_tools_tups[ index ] = ( tup_path, repository_tool ) + repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) return repository_tools_tups def handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups ): """Inspect each tool to see if it has any input parameters that are dynamically generated select lists that depend on a .loc file.""" @@ -781,6 +789,46 @@ repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) return repository_tools_tups +def handle_sample_tool_data_table_conf_file( app, filename ): + """ + Parse the incoming filename and add new entries to the in-memory + app.tool_data_tables dictionary as well as appending them to the + shed's tool_data_table_conf.xml file on disk. + """ + error = False + message = '' + try: + new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( filename ) + except Exception, e: + message = str( e ) + error = True + if not error: + # Add an entry to the end of the tool_data_table_conf.xml file. + tdt_config = "%s/tool_data_table_conf.xml" % app.config.root + if os.path.exists( tdt_config ): + # Make a backup of the file since we're going to be changing it. + today = date.today() + backup_date = today.strftime( "%Y_%m_%d" ) + tdt_config_copy = '%s/tool_data_table_conf.xml_%s_backup' % ( app.config.root, backup_date ) + shutil.copy( os.path.abspath( tdt_config ), os.path.abspath( tdt_config_copy ) ) + # Write each line of the tool_data_table_conf.xml file, except the last line to a temp file. + fh = tempfile.NamedTemporaryFile( 'wb' ) + tmp_filename = fh.name + fh.close() + new_tdt_config = open( tmp_filename, 'wb' ) + for i, line in enumerate( open( tdt_config, 'rb' ) ): + if line.find( '</tables>' ) >= 0: + for new_table_elem in new_table_elems: + new_tdt_config.write( ' %s\n' % util.xml_to_string( new_table_elem ).rstrip( '\n' ) ) + new_tdt_config.write( '</tables>\n' ) + else: + new_tdt_config.write( line ) + new_tdt_config.close() + shutil.move( tmp_filename, os.path.abspath( tdt_config ) ) + else: + message = "The required file named tool_data_table_conf.xml does not exist in the Galaxy install directory." + error = True + return error, message def handle_tool_dependencies( current_working_dir, repo_files_dir, repository_tools_tups ): """ Inspect each tool to see if it includes a "requirement" that refers to a fabric diff -r 02f55e34ccfeef865d5d0811664a1f95635ec609 -r b199460443afeb3023f1c160f23b2215ba42add4 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -2464,46 +2464,6 @@ id = trans.security.decode_id( id ) quota = trans.sa_session.query( trans.model.Quota ).get( id ) return quota -def handle_sample_tool_data_table_conf_file( app, filename ): - """ - Parse the incoming filename and add new entries to the in-memory - app.tool_data_tables dictionary as well as appending them to the - shed's tool_data_table_conf.xml file on disk. - """ - error = False - message = '' - try: - new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( filename ) - except Exception, e: - message = str( e ) - error = True - if not error: - # Add an entry to the end of the tool_data_table_conf.xml file. - tdt_config = "%s/tool_data_table_conf.xml" % app.config.root - if os.path.exists( tdt_config ): - # Make a backup of the file since we're going to be changing it. - today = date.today() - backup_date = today.strftime( "%Y_%m_%d" ) - tdt_config_copy = '%s/tool_data_table_conf.xml_%s_backup' % ( app.config.root, backup_date ) - shutil.copy( os.path.abspath( tdt_config ), os.path.abspath( tdt_config_copy ) ) - # Write each line of the tool_data_table_conf.xml file, except the last line to a temp file. - fh = tempfile.NamedTemporaryFile( 'wb' ) - tmp_filename = fh.name - fh.close() - new_tdt_config = open( tmp_filename, 'wb' ) - for i, line in enumerate( open( tdt_config, 'rb' ) ): - if line.find( '</tables>' ) >= 0: - for new_table_elem in new_table_elems: - new_tdt_config.write( ' %s\n' % util.xml_to_string( new_table_elem ).rstrip( '\n' ) ) - new_tdt_config.write( '</tables>\n' ) - else: - new_tdt_config.write( line ) - new_tdt_config.close() - shutil.move( tmp_filename, os.path.abspath( tdt_config ) ) - else: - message = "The required file named tool_data_table_conf.xml does not exist in the Galaxy install directory." - error = True - return error, message def tool_shed_encode( val ): if isinstance( val, dict ): value = simplejson.dumps( val ) diff -r 02f55e34ccfeef865d5d0811664a1f95635ec609 -r b199460443afeb3023f1c160f23b2215ba42add4 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1,10 +1,12 @@ import os, string, socket, logging, simplejson, binascii from time import strftime from datetime import * +from galaxy.datatypes.checkers import * from galaxy.tools import * from galaxy.util.json import from_json_string, to_json_string from galaxy.util.hash_util import * from galaxy.util.shed_util import copy_sample_loc_file, generate_datatypes_metadata, generate_tool_metadata, generate_workflow_metadata +from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -314,19 +316,21 @@ # Find all tool configs. if name != 'datatypes_conf.xml' and name.endswith( '.xml' ): full_path = os.path.abspath( os.path.join( root, name ) ) - try: - tool = load_tool( trans, full_path ) - valid = True - except Exception, e: - valid = False - invalid_files.append( ( name, str( e ) ) ) - if valid and tool is not None: - can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) - if can_set_metadata: - # Update the list of metadata dictionaries for tools in metadata_dict. - tool_config = os.path.join( root, name ) - repository_clone_url = generate_clone_url( trans, id ) - metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) + if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] + or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): + try: + tool = load_tool( trans, full_path ) + valid = True + except Exception, e: + valid = False + invalid_files.append( ( name, str( e ) ) ) + if valid and tool is not None: + can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) + if can_set_metadata: + # Update the list of metadata dictionaries for tools in metadata_dict. + tool_config = os.path.join( root, name ) + repository_clone_url = generate_clone_url( trans, id ) + metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) # Find all exported workflows elif name.endswith( '.ga' ): try: @@ -381,22 +385,24 @@ fh = open( tmp_filename, 'w' ) fh.write( fctx.data() ) fh.close() - try: - tool = load_tool( trans, tmp_filename ) - valid = True - except Exception, e: - invalid_files.append( ( filename, str( e ) ) ) - valid = False - if valid and tool is not None: - # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename - # here is the relative path to the config file within the change set context, something - # like filtering.xml, but when the change set was the repository tip, the value was - # something like database/community_files/000/repo_1/filtering.xml. This shouldn't break - # anything, but may result in a bit of confusion when maintaining the code / data over time. - # IMPORTANT NOTE: Here we are assuming that since the current change set is not the repository - # tip, we do not have to handle any .loc.sample files since they would have been handled previously. - repository_clone_url = generate_clone_url( trans, id ) - metadata_dict = generate_tool_metadata( filename, tool, repository_clone_url, metadata_dict ) + if not ( check_binary( tmp_filename ) or check_image( tmp_filename ) or check_gzip( tmp_filename )[ 0 ] + or check_bz2( tmp_filename )[ 0 ] or check_zip( tmp_filename ) ): + try: + tool = load_tool( trans, tmp_filename ) + valid = True + except Exception, e: + invalid_files.append( ( filename, str( e ) ) ) + valid = False + if valid and tool is not None: + # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename + # here is the relative path to the config file within the change set context, something + # like filtering.xml, but when the change set was the repository tip, the value was + # something like database/community_files/000/repo_1/filtering.xml. This shouldn't break + # anything, but may result in a bit of confusion when maintaining the code / data over time. + # IMPORTANT NOTE: Here we are assuming that since the current change set is not the repository + # tip, we do not have to handle any .loc.sample files since they would have been handled previously. + repository_clone_url = generate_clone_url( trans, id ) + metadata_dict = generate_tool_metadata( filename, tool, repository_clone_url, metadata_dict ) try: os.unlink( tmp_filename ) except: diff -r 02f55e34ccfeef865d5d0811664a1f95635ec609 -r b199460443afeb3023f1c160f23b2215ba42add4 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -856,13 +856,15 @@ fh = open( tmp_filename, 'w' ) fh.write( fctx.data() ) fh.close() - try: - tool = load_tool( trans, tmp_filename ) - valid = True - except: - valid = False - if valid and tool is not None: - tool_guids.append( generate_tool_guid( trans, repository, tool ) ) + if not ( check_binary( tmp_filename ) or check_image( tmp_filename ) or check_gzip( tmp_filename )[ 0 ] + or check_bz2( tmp_filename )[ 0 ] or check_zip( tmp_filename ) ): + try: + tool = load_tool( trans, tmp_filename ) + valid = True + except: + valid = False + if valid and tool is not None: + tool_guids.append( generate_tool_guid( trans, repository, tool ) ) try: os.unlink( tmp_filename ) except: diff -r 02f55e34ccfeef865d5d0811664a1f95635ec609 -r b199460443afeb3023f1c160f23b2215ba42add4 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -3,6 +3,7 @@ from galaxy.model.orm import * from galaxy.datatypes.checkers import * from common import * +from galaxy.util.shed_util import handle_sample_tool_data_table_conf_file from mercurial import hg, ui, commands log = logging.getLogger( __name__ ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: 6 new changesets
by Bitbucket 12 Mar '12

12 Mar '12

6 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4a7374937251/ changeset: 4a7374937251 user: jgoecks date: 2012-03-11 16:47:06 summary: Trackster: enable resizing of feature tracks. Added generic framework for resizing tracks. affected #: 3 files diff -r e1c0cd5ed76766e4bf18f5342bf6cd395fca4732 -r 4a7374937251e31761b3e2cf052d3a6405b75179 static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -27,7 +27,7 @@ .track{background:white;} .track-header{text-align:left;padding:4px 0px;color:#666;} .track-header .menubutton{margin-left:0px;} -.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('../images/tracks/diag_bg.gif');min-height:16px;position:relative;} +.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('../images/tracks/diag_bg.gif');min-height:16px;position:relative;overflow:hidden;} .track-name{float:left;margin-top:2px;height:16px;} .label-track .track-content{background:white;} .track-tile{background:white;} diff -r e1c0cd5ed76766e4bf18f5342bf6cd395fca4732 -r 4a7374937251e31761b3e2cf052d3a6405b75179 static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -178,6 +178,7 @@ background: #eee url('../images/tracks/diag_bg.gif'); min-height: 16px; position: relative; + overflow: hidden; } .track-name { diff -r e1c0cd5ed76766e4bf18f5342bf6cd395fca4732 -r 4a7374937251e31761b3e2cf052d3a6405b75179 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -3149,12 +3149,20 @@ this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT); this.dataset_check_url = converted_datasets_state_url; this.data_manager = ('data_manager' in obj_dict ? obj_dict.data_manager : new DataManager(DATA_CACHE_SIZE, this)); - + + // Height attributes: min height, max height, and visible height. + this.min_height_px = 16; + this.max_height_px = 800; + this.visible_height_px = 0; + // // Create content div, which is where track is displayed, and add to container if available. // this.content_div = $("<div class='track-content'>").appendTo(this.container_div); - if (this.container) { this.container.content_div.append(this.container_div); } + if (this.container) { + this.container.content_div.append(this.container_div); + this.add_resize_handle(); + } }; extend(Track.prototype, Drawable.prototype, { @@ -3236,6 +3244,46 @@ return header_div; }, /** + * Action to take during resize. + */ + on_resize: function() {}, + /** + * Add resizing handle to drawable's container_div. + */ + add_resize_handle: function () { + var track = this; + var in_handle = false; + var in_drag = false; + var drag_control = $( "<div class='track-resize'>" ) + // Control shows on hover over track, stays while dragging + $(track.container_div).hover( function() { + if ( track.content_visible ) { + in_handle = true; + drag_control.show(); + } + }, function() { + in_handle = false; + if ( ! in_drag ) { drag_control.hide(); } + }); + // Update height and force redraw of current view while dragging, + // clear cache to force redraw of other tiles. + drag_control.hide().bind( "dragstart", function( e, d ) { + in_drag = true; + d.original_height = $(track.content_div).height(); + }).bind( "drag", function( e, d ) { + var new_height = Math.min( Math.max( d.original_height + d.deltaY, track.min_height_px ), track.max_height_px ); + $(track.content_div).css( 'height', new_height ); + track.visible_height_px = (track.max_height_px === new_height ? 0 : new_height); + track.on_resize(); + }).bind( "dragend", function( e, d ) { + track.tile_cache.clear(); + in_drag = false; + if (!in_handle) { drag_control.hide(); } + track.config.values.height = track.visible_height_px; + track.changed(); + }).appendTo(track.container_div); + }, + /** * Set track's modes and update mode icon popup. */ set_display_modes: function(new_modes, init_mode) { @@ -3380,7 +3428,7 @@ track.content_div.text(DATA_OK); if (track.view.chrom) { track.content_div.text(""); - track.content_div.css( "height", track.height_px + "px" ); + track.content_div.css( "height", track.visible_height_px + "px" ); track.enabled = true; // predraw_init may be asynchronous, wait for it and then draw $.when(track.predraw_init()).done(function() { @@ -3556,6 +3604,10 @@ this.view.request_redraw(false, force, clear_after, this); }, /** + * Actions to be taken before drawing. + */ + before_draw: function() {}, + /** * Draw track. It is possible to force a redraw rather than use cached tiles and/or clear old * tiles after drawing new tiles. * NOTE: this function should never be called directly; use request_draw() so that requestAnimationFrame @@ -3578,6 +3630,8 @@ resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / TILE_SIZE ) / Math.log(RESOLUTION) )); w_scale = width / (view.max_high - view.max_low); } + + this.before_draw(); // // Method for moving and/or removing tiles: @@ -3591,7 +3645,6 @@ // Step (a) for (re)moving tiles. this.content_div.children().addClass("remove"); - this.max_height = 0; var // Index of first tile that overlaps visible region. tile_index = Math.floor( low / (resolution * TILE_SIZE) ), @@ -3738,7 +3791,7 @@ * number of pixels required. */ get_canvas_height: function(result, mode, w_scale, canvas_width) { - return this.height_px; + return this.visible_height_px; }, /** * Draw a track tile. @@ -3785,12 +3838,13 @@ parent_element.append(tile_element); } - // Set track height. - 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"); + track.after_show_tile(tile); }, /** + * Actions to be taken after showing tile. + */ + after_show_tile: function(tile) {}, + /** * Returns tile bounds--tile low and tile high--based on a tile index. Return value is an array * with values tile_low and tile_high. */ @@ -4183,7 +4237,7 @@ view.reference_track = this; this.left_offset = 200; - this.height_px = 12; + this.visible_height_px = 12; this.container_div.addClass("reference-track"); this.content_div.css("background", "none"); this.content_div.css("min-height", "0px"); @@ -4231,10 +4285,6 @@ this.mode = "Histogram"; TiledTrack.call(this, view, container, obj_dict); - this.min_height_px = 16; - this.max_height_px = 400; - // Default height for new tracks, should be a defined constant? - this.height_px = 32; this.hda_ldda = obj_dict.hda_ldda; this.dataset_id = obj_dict.dataset_id; this.original_dataset_id = this.dataset_id; @@ -4249,7 +4299,7 @@ { 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 } + { key: 'height', type: 'int', default_value: 32, hidden: true } ], saved_values: obj_dict.prefs, onchange: function() { @@ -4261,13 +4311,17 @@ }); this.prefs = this.config.values; - this.height_px = this.config.values.height; + this.visible_height_px = this.config.values.height; this.vertical_range = this.config.values.max_value - this.config.values.min_value; - - this.add_resize_handle(); }; extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, { /** + * Action to take during resize. + */ + on_resize: function() { + this.request_draw(true); + }, + /** * Set track minimum value. */ set_min_value: function(new_val) { @@ -4285,41 +4339,6 @@ this.tile_cache.clear(); this.request_draw(); }, - add_resize_handle: function () { - // Add control for resizing - // Trickery here to deal with the hovering drag handle, can probably be - // pulled out and reused. - var track = this; - var in_handle = false; - var in_drag = false; - var drag_control = $( "<div class='track-resize'>" ) - // Control shows on hover over track, stays while dragging - $(track.container_div).hover( function() { - if ( track.content_visible ) { - in_handle = true; - drag_control.show(); - } - }, function() { - in_handle = false; - if ( ! in_drag ) { drag_control.hide(); } - }); - // Update height and force redraw of current view while dragging, - // clear cache to force redraw of other tiles. - drag_control.hide().bind( "dragstart", function( e, d ) { - in_drag = true; - d.original_height = $(track.content_div).height(); - }).bind( "drag", function( e, d ) { - var new_height = Math.min( Math.max( d.original_height + d.deltaY, track.min_height_px ), track.max_height_px ); - $(track.content_div).css( 'height', new_height ); - track.height_px = new_height; - track.request_draw(true); - }).bind( "dragend", function( e, d ) { - track.tile_cache.clear(); - in_drag = false; - if (!in_handle) { drag_control.hide(); } - track.config.values.height = track.height_px; - }).appendTo(track.container_div); - }, predraw_init: function() { var track = this; @@ -4429,6 +4448,7 @@ { key: 'connector_style', label: 'Connector style', type: 'select', default_value: 'fishbones', options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, + { key: 'height', type: 'int', default_value: this.visible_height_px, hidden: true} ], saved_values: obj_dict.prefs, onchange: function() { @@ -4439,8 +4459,8 @@ } }); this.prefs = this.config.values; - - this.height_px = 0; + this.visible_height_px = this.config.values.height; + this.container_div.addClass( "feature-track" ); this.hda_ldda = obj_dict.hda_ldda; this.dataset_id = obj_dict.dataset_id; @@ -4464,6 +4484,30 @@ } }, /** + * Actions to be taken before drawing. + */ + before_draw: function() { + // Clear because this is set when drawing. + this.max_height_px = 0; + }, + /** + * Actions to be taken after showing tile. + */ + after_show_tile: function(tile) { + // Update max height based on current tile. + this.max_height_px = Math.max(this.max_height_px, tile.html_elt.height()); + + // Update height for all tiles based on max height. + tile.html_elt.parent().children().css("height", this.max_height_px + "px"); + + // Update track height based on max height and visible height. + var track_height = this.max_height_px; + if (this.visible_height_px !== 0) { + track_height = Math.min(this.max_height_px, this.visible_height_px); + } + this.content_div.css("height", track_height + "px"); + }, + /** * Actions to be taken after draw has been completed. Draw is completed when all tiles have been * drawn/fetched and shown. */ https://bitbucket.org/galaxy/galaxy-central/changeset/b6231600bc71/ changeset: b6231600bc71 user: jgoecks date: 2012-03-11 17:06:33 summary: Update .hgignore to include new config files, tool data, and jars. affected #: 1 file diff -r 4a7374937251e31761b3e2cf052d3a6405b75179 -r b6231600bc71c9d7c09d914e1953919c9a12e02d .hgignore --- a/.hgignore +++ b/.hgignore @@ -26,9 +26,27 @@ # Config files universe_wsgi.ini reports_wsgi.ini +community_wsgi.ini + datatypes_conf.xml tool_conf.xml +external_service_types_conf.xml +migrated_tools_conf.xml +shed_tool_conf.xml +tool_data_table_conf.xml +tool_sheds_conf.xml static/welcome.html.* +static/welcome.html + +# Tool data. +tool-data/annotation_profiler_options.xml +tool-data/annotation_profiler_valid_builds.txt +tool-data/gatk_annotations.txt +tool-data/gd.restriction_enzymes.txt +tool-data/gd.species.txt +tool-data/shared/igv/igv_build_sites.txt +tool-data/shared/rviewer/rviewer_build_sites.txt +tool-data/shared/ucsc/builds.txt tool-data/*.loc # Test output @@ -40,6 +58,9 @@ # Chrom len files *.len +# Jars +tool-data/shared/jars/ + # Misc *.orig .DS_Store https://bitbucket.org/galaxy/galaxy-central/changeset/8e9d2b492c4c/ changeset: 8e9d2b492c4c user: jgoecks date: 2012-03-12 16:56:29 summary: Fix feature popup functionality broken in 4a7374937251 by separating track content into tiles and overlay and using different CSS rules to manage them. Pack trackster script. affected #: 5 files diff -r b6231600bc71c9d7c09d914e1953919c9a12e02d -r 8e9d2b492c4cabea37cab72c4bc4f7b384e4183b lib/galaxy/web/controllers/visualization.py --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -32,7 +32,7 @@ operations = [ grids.GridOperation( "View/Edit", allow_multiple=False, url_args=dict( controller='tracks', action='browser' ) ), grids.GridOperation( "Edit Attributes", allow_multiple=False, url_args=dict( action='edit') ), - grids.GridOperation( "Clone", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False, url_args=dict( action='clone') ), + grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False, url_args=dict( action='clone') ), grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True, confirm="Are you sure you want to delete this visualization?" ), ] diff -r b6231600bc71c9d7c09d914e1953919c9a12e02d -r 8e9d2b492c4cabea37cab72c4bc4f7b384e4183b static/june_2007_style/blue/trackster.css --- a/static/june_2007_style/blue/trackster.css +++ b/static/june_2007_style/blue/trackster.css @@ -27,9 +27,11 @@ .track{background:white;} .track-header{text-align:left;padding:4px 0px;color:#666;} .track-header .menubutton{margin-left:0px;} -.track-content{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('../images/tracks/diag_bg.gif');min-height:16px;position:relative;overflow:hidden;} +.tiles{text-align:center;border-top:1px solid #eee;border-bottom:2px solid #eee;background:#eee url('../images/tracks/diag_bg.gif');min-height:16px;position:relative;overflow:hidden;} +.overlay{position:absolute;left:0;top:0;} .track-name{float:left;margin-top:2px;height:16px;} .label-track .track-content{background:white;} +.track-content{position:relative;} .track-tile{background:white;} .track-tile canvas{position:relative;z-index:100;} .tile-message{border-bottom:solid 1px red;text-align:center;color:red;background-color:white;} diff -r b6231600bc71c9d7c09d914e1953919c9a12e02d -r 8e9d2b492c4cabea37cab72c4bc4f7b384e4183b static/june_2007_style/trackster.css.tmpl --- a/static/june_2007_style/trackster.css.tmpl +++ b/static/june_2007_style/trackster.css.tmpl @@ -171,7 +171,7 @@ margin-left: 0px; } -.track-content { +.tiles { text-align: center; border-top: 1px solid #eee; border-bottom: 2px solid #eee; @@ -181,6 +181,12 @@ overflow: hidden; } +.overlay { + position: absolute; + left: 0; + top: 0; +} + .track-name { float: left; margin-top: 2px; @@ -211,6 +217,11 @@ background-color: #ECB4AF; background-image: none; } + +.track-content { + position: relative; +} + .track.nodata .track-content { background-color: #eee; background-image: none; diff -r b6231600bc71c9d7c09d914e1953919c9a12e02d -r 8e9d2b492c4cabea37cab72c4bc4f7b384e4183b static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});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/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").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_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").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();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.content_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.content_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;ac<ag.length;ac++){if(!this._keep_val(ag[ac])){ae=false;break}}return ae}else{return this._keep_val(ad[this.index])}},update_attrs:function(ad){var ac=false;if(!this.applies_to(ad)){return ac}if(ad[this.index]<this.min){this.min=Math.floor(ad[this.index]);ac=true}if(ad[this.index]>this.max){this.max=Math.ceil(ad[this.index]);ac=true}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(ad.html_elt).parent());var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display 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$("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.content_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.content_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.content_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.content_div.text(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.content_div.text(V);if(ad.view.chrom){ad.content_div.text("");ad.content_div.css("height",ad.height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.content_div.children().addClass("remove");this.max_height=0;var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.content_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.content_div.children(".remove").remove()}var af=this;if(ak){this.content_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.max_height=Math.max(ad.max_height,ac.height());ad.content_div.css("height",ad.max_height+"px");ag.children().css("height",ad.max_height+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={todo:"label",todo:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,"reference",ac,{content_div:ac.top_labeltrack},{});ac.reference_track=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_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false)};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){af.content_div.css("height","0px");return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}return new b(af,ad,ag,ae,ak)}this.content_div.css("height","0px")}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{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:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,K.prototype,{set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.content_div).css("height",ag);ac.height_px=ag;ac.request_draw(true)}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.height_px}).appendTo(ac.container_div)},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".tipsy").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});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/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").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_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").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();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.content_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.content_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data 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style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;ac<ag.length;ac++){if(!this._keep_val(ag[ac])){ae=false;break}}return ae}else{return this._keep_val(ad[this.index])}},update_attrs:function(af){var ac=false;if(!this.applies_to(af)){return ac}var ad=af[this.index];if(!(ad instanceof Array)){ad=[ad]}for(var ae=0;ae<ad.length;ae++){var ag=ad[ae];if(ag<this.min){this.min=Math.floor(ag);ac=true}if(ag>this.max){this.max=Math.ceil(ag);ac=true}}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);this.add_resize_handle()}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.tiles_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.tiles_div.text(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.tiles_div.text(V);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.after_show_tile(ae)},after_show_tile:function(ac){},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={todo:"label",todo:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,"reference",ac,{content_div:ac.top_labeltrack},{});ac.reference_track=this;this.left_offset=200;this.visible_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_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false)};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){af.content_div.css("height","0px");return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}return new b(af,ad,ag,ae,ak)}this.content_div.css("height","0px")}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{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:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};p(j.prototype,q.prototype,K.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},after_show_tile:function(ac){this.max_height_px=Math.max(this.max_height_px,ac.html_elt.height());ac.html_elt.parent().children().css("height",this.max_height_px+"px");var ad=this.max_height_px;if(this.visible_height_px!==0){ad=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ad+"px")},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".tipsy").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r b6231600bc71c9d7c09d914e1953919c9a12e02d -r 8e9d2b492c4cabea37cab72c4bc4f7b384e4183b static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1098,11 +1098,11 @@ return header_div; }, hide_contents: function () { - this.content_div.hide(); + this.tiles_div.hide(); }, show_contents: function() { // Show the contents div and labels (if present) - this.content_div.show(); + this.tiles_div.show(); // Request a redraw of the content this.request_draw(); }, @@ -3039,7 +3039,7 @@ }, function() { this.hovered = false; // Clear popup if it is still hanging around (this is probably not needed) - $(this).siblings(".feature-popup").remove(); + $(this).parents(".track-content").children(".overlay").children(".feature-popup").remove(); } ).mousemove(function (e) { // Use the hover plugin to get a delay before showing popup if ( !this.hovered ) { return; } @@ -3051,7 +3051,7 @@ feature_data = tile.feature_mapper.get_feature_data(offsetX, offsetY), feature_uid = (feature_data ? feature_data[0] : null); // Hide visible popup if not over a feature or over a different feature. - $(this).siblings(".feature-popup").each(function() { + $(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function() { if ( !feature_uid || $(this).attr("id") !== feature_uid.toString() ) { $(this).remove(); @@ -3096,8 +3096,8 @@ popups[feature_uid] = popup; } - // Attach popup to canvas's parent. - popup.appendTo($(tile.html_elt).parent()); + // Attach popup to track's overlay. + popup.appendTo( $(this).parents(".track-content").children(".overlay") ); // Offsets are within canvas, but popup must be positioned relative to parent element. // parseInt strips "px" from left, top measurements. +7 so that mouse pointer does not @@ -3117,7 +3117,7 @@ } }) .mouseleave(function() { - $(this).siblings(".feature-popup").remove(); + $(this).parents(".track-content").children(".overlay").children(".feature-popup").remove(); }); }; @@ -3272,7 +3272,7 @@ d.original_height = $(track.content_div).height(); }).bind( "drag", function( e, d ) { var new_height = Math.min( Math.max( d.original_height + d.deltaY, track.min_height_px ), track.max_height_px ); - $(track.content_div).css( 'height', new_height ); + $(track.tiles_div).css( 'height', new_height ); track.visible_height_px = (track.max_height_px === new_height ? 0 : new_height); track.on_resize(); }).bind( "dragend", function( e, d ) { @@ -3385,7 +3385,7 @@ } */ // Remove old track content (e.g. tiles, messages). - track.content_div.children().remove(); + track.tiles_div.children().remove(); track.container_div.removeClass("nodata error pending"); // @@ -3403,32 +3403,32 @@ function (result) { if (!result || result === "error" || result.kind === "error") { track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); + track.tiles_div.text(DATA_ERROR); if (result.message) { var error_link = $(" <a href='javascript:void(0);'></a>").text("View error").click(function() { show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } ); }); - track.content_div.append(error_link); + track.tiles_div.append(error_link); } } else if (result === "no converter") { track.container_div.addClass("error"); - track.content_div.text(DATA_NOCONVERTER); + track.tiles_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); + track.tiles_div.text(DATA_NONE); } else if (result === "pending") { track.container_div.addClass("pending"); - track.content_div.text(DATA_PENDING); + track.tiles_div.text(DATA_PENDING); setTimeout(function() { track.init(); }, track.data_query_wait); } else if (result['status'] === "data") { if (result['valid_chroms']) { track.valid_chroms = result['valid_chroms']; track.update_icons(); } - track.content_div.text(DATA_OK); + track.tiles_div.text(DATA_OK); if (track.view.chrom) { - track.content_div.text(""); - track.content_div.css( "height", track.visible_height_px + "px" ); + track.tiles_div.text(""); + track.tiles_div.css( "height", track.visible_height_px + "px" ); track.enabled = true; // predraw_init may be asynchronous, wait for it and then draw $.when(track.predraw_init()).done(function() { @@ -3482,6 +3482,10 @@ } } + // Add tiles_div, overlay_div to content_div. + this.tiles_div = $("<div/>").addClass("tiles").appendTo(this.content_div); + this.overlay_div = $("<div/>").addClass("overlay").appendTo(this.content_div); + if (obj_dict.mode) { this.change_mode(obj_dict.mode); } @@ -3643,7 +3647,7 @@ // // Step (a) for (re)moving tiles. - this.content_div.children().addClass("remove"); + this.tiles_div.children().addClass("remove"); var // Index of first tile that overlaps visible region. @@ -3654,7 +3658,7 @@ is_tile = function(o) { return (o && 'track' in o) }; // Draw tiles. while ( ( tile_index * TILE_SIZE * resolution ) < high ) { - var draw_result = this.draw_helper( force, width, tile_index, resolution, this.content_div, w_scale ); + var draw_result = this.draw_helper( force, width, tile_index, resolution, this.tiles_div, w_scale ); if ( is_tile(draw_result) ) { drawn_tiles.push( draw_result ); } else { @@ -3664,13 +3668,13 @@ } // Step (c) for (re)moving tiles when clear_after is false. - if (!clear_after) { this.content_div.children(".remove").remove(); } + if (!clear_after) { this.tiles_div.children(".remove").remove(); } // Use interval to check if tiles have been drawn. When all tiles are drawn, call post-draw actions. var track = this; if (all_tiles_drawn) { // Step (c) for (re)moving tiles when clear_after is true: - this.content_div.children(".remove").remove(); + this.tiles_div.children(".remove").remove(); track.postdraw_actions(drawn_tiles, width, w_scale, clear_after); } }, @@ -4505,7 +4509,7 @@ if (this.visible_height_px !== 0) { track_height = Math.min(this.max_height_px, this.visible_height_px); } - this.content_div.css("height", track_height + "px"); + this.tiles_div.css("height", track_height + "px"); }, /** * Actions to be taken after draw has been completed. Draw is completed when all tiles have been https://bitbucket.org/galaxy/galaxy-central/changeset/f2d52761856c/ changeset: f2d52761856c user: jgoecks date: 2012-03-12 16:57:52 summary: Another config file addition to .hgignore affected #: 1 file diff -r 8e9d2b492c4cabea37cab72c4bc4f7b384e4183b -r f2d52761856cbf38656a029ef361da7ff905c9dd .hgignore --- a/.hgignore +++ b/.hgignore @@ -35,6 +35,8 @@ shed_tool_conf.xml tool_data_table_conf.xml tool_sheds_conf.xml +integrated_tool_panel.xml + static/welcome.html.* static/welcome.html https://bitbucket.org/galaxy/galaxy-central/changeset/1285c240c467/ changeset: 1285c240c467 user: jgoecks date: 2012-03-12 16:59:41 summary: Update converter name to be more descriptive. affected #: 1 file diff -r f2d52761856cbf38656a029ef361da7ff905c9dd -r 1285c240c46764b667942f2031302d0ec19f4e40 lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml @@ -1,4 +1,4 @@ -<tool id="CONVERTER_wig_to_bigwig" name="wig->bigwig for Trackster. Needs 'wigToBigWig' tool in path." hidden="true"> +<tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" hidden="true"><command>wigToBigWig $input $chromInfo $output</command><inputs> https://bitbucket.org/galaxy/galaxy-central/changeset/02f55e34ccfe/ changeset: 02f55e34ccfe user: jgoecks date: 2012-03-12 16:59:52 summary: Merge. affected #: 3 files diff -r 1285c240c46764b667942f2031302d0ec19f4e40 -r 02f55e34ccfeef865d5d0811664a1f95635ec609 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -241,7 +241,7 @@ os.close( fd ) shutil.move( filename, os.path.abspath( self.integrated_tool_panel_config ) ) os.chmod( self.integrated_tool_panel_config, 0644 ) - def get_tool( self, tool_id, tool_version=None ): + def get_tool( self, tool_id, tool_version=None, get_all_versions=False ): """Attempt to locate a tool in the tool box.""" if tool_id in self.tools_by_id: tool = self.tools_by_id[ tool_id ] @@ -252,6 +252,12 @@ tv = self.__get_tool_version( tool_id ) if tv: tool_version_ids = tv.get_version_ids( self.app ) + if get_all_versions: + available_tool_versions = [] + for tool_version_id in tool_version_ids: + if tool_version_id in self.tools_by_id: + available_tool_versions.append( self.tools_by_id[ tool_version_id ] ) + return available_tool_versions for tool_version_id in tool_version_ids: if tool_version_id in self.tools_by_id: tool = self.tools_by_id[ tool_version_id ] diff -r 1285c240c46764b667942f2031302d0ec19f4e40 -r 02f55e34ccfeef865d5d0811664a1f95635ec609 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py +++ b/lib/galaxy/web/controllers/tool_runner.py @@ -109,16 +109,49 @@ raise Exception("Failed to get job information for dataset hid %d" % data.hid) # Get the tool object tool_id = job.tool_id + tool_version = job.tool_version try: # Load the tool toolbox = self.get_toolbox() - tool = toolbox.get_tool( tool_id ) + tools = toolbox.get_tool( tool_id, tool_version=tool_version, get_all_versions=True ) + if len( tools ) > 1: + tool_id_select_field = self.build_tool_id_select_field( tools, tool_id ) + for tool in tools: + if tool.id == tool_id: + break + else: + tool = tools[ 0 ] + tool_id_version_message = 'This job was initially run with tool id "%s", version "%s", and multiple derivations ' % ( job.tool_id, job.tool_version ) + tool_id_version_message += 'of this tool are available. Rerun the job with the selected tool or choose another derivation of the tool.' + else: + tool_id_select_field = None + tool = tools[ 0 ] + if tool.id == job.tool_id and tool.version == job.tool_version: + tool_id_version_message = '' + elif tool.id == job.tool_id: + if job.tool_version == None: + # For some reason jobs don't always keep track of the tool version. + tool_id_version_message = '' + else: + if len( tools ) > 1: + tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version + tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.' + else: + tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version + tool_id_version_message += 'You can rerun the job with this tool version, which is a derivation of the original tool.' + else: + if len( tools ) > 1: + tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version + tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.' + else: + tool_id_version_message = 'This job was initially run with tool id "%s", version "%s", which is not ' % ( job.tool_id, job.tool_version ) + tool_id_version_message += 'currently available. You can rerun the job with this tool, which is a derivation of the original tool.' assert tool is not None, 'Requested tool has not been loaded.' except: - #this is expected, so not an exception + # This is expected so not an exception. + tool_id_version_message = '' error( "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id ) - # Can't rerun upload, external data sources, et cetera. Workflow - # compatible will proxy this for now + # Can't rerun upload, external data sources, et cetera. Workflow compatible will proxy this for now if not tool.is_workflow_compatible: error( "The '%s' tool does not currently support rerunning." % tool.name ) # Get the job's parameters @@ -163,7 +196,30 @@ if from_noframe is not None: add_frame.wiki_url = trans.app.config.wiki_url add_frame.from_noframe = True - return trans.fill_template( "tool_form.mako", history=history, toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars ) + return trans.fill_template( "tool_form.mako", + history=history, + toolbox=toolbox, + tool_id_select_field=tool_id_select_field, + tool=tool, + util=util, + add_frame=add_frame, + tool_id_version_message=tool_id_version_message, + **vars ) + def build_tool_id_select_field( self, tools, selected_tool_id ): + """Build a SelectField whose options are the ids for the received list of tools.""" + options = [] + refresh_on_change_values = [] + for tool in tools: + options.append( ( tool.id, tool.id ) ) + refresh_on_change_values.append( tool.id ) + select_field = SelectField( name='tool_id', refresh_on_change=True, refresh_on_change_values=refresh_on_change_values ) + for option_tup in options: + selected = option_tup[0] == selected_tool_id + if selected: + select_field.add_option( option_tup[0], option_tup[1], selected=True ) + else: + select_field.add_option( option_tup[0], option_tup[1] ) + return select_field @web.expose def redirect( self, trans, redirect_url=None, **kwd ): if not redirect_url: @@ -251,7 +307,6 @@ datasets.append( create_dataset( 'Pasted Entry' ) ) break return [ d.id for d in datasets ] - @web.expose def upload_async_message( self, trans, **kwd ): # might be more appropriate in a different controller diff -r 1285c240c46764b667942f2031302d0ec19f4e40 -r 02f55e34ccfeef865d5d0811664a1f95635ec609 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -1,4 +1,5 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /><%namespace file="/base_panels.mako" import="overlay" /><%def name="stylesheets()"> @@ -274,10 +275,11 @@ assert len(tool.action) == 2 tool_url = tool.action[0] + h.url_for(tool.action[1]) %> -%if message: - <div class="errormessage">${message}</div> - <br/> + +%if tool_id_version_message: + ${render_msg( tool_id_version_message, 'error' )} %endif + <div class="toolForm" id="${tool.id}"> %if tool.has_multiple_pages: <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div> @@ -286,7 +288,18 @@ %endif <div class="toolFormBody"><form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> - <input type="hidden" name="tool_id" value="${tool.id}"> + %if tool_id_select_field: + <div class="form-row"> + <label>Tool id:</label> + ${tool_id_select_field.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Select a different derivation of this tool to rerun the job. + </div> + </div> + <div style="clear: both"></div> + %else: + <input type="hidden" name="tool_id" value="${tool.id}"> + %endif <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> %if tool.display_by_page[tool_state.page]: ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Handle tool versions with job reruns.
by Bitbucket 12 Mar '12

12 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2cd1bacf5e04/ changeset: 2cd1bacf5e04 user: greg date: 2012-03-12 15:20:56 summary: Handle tool versions with job reruns. affected #: 3 files diff -r e1c0cd5ed76766e4bf18f5342bf6cd395fca4732 -r 2cd1bacf5e0463bd804bf5fc7ac79a3ddf142937 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -241,7 +241,7 @@ os.close( fd ) shutil.move( filename, os.path.abspath( self.integrated_tool_panel_config ) ) os.chmod( self.integrated_tool_panel_config, 0644 ) - def get_tool( self, tool_id, tool_version=None ): + def get_tool( self, tool_id, tool_version=None, get_all_versions=False ): """Attempt to locate a tool in the tool box.""" if tool_id in self.tools_by_id: tool = self.tools_by_id[ tool_id ] @@ -252,6 +252,12 @@ tv = self.__get_tool_version( tool_id ) if tv: tool_version_ids = tv.get_version_ids( self.app ) + if get_all_versions: + available_tool_versions = [] + for tool_version_id in tool_version_ids: + if tool_version_id in self.tools_by_id: + available_tool_versions.append( self.tools_by_id[ tool_version_id ] ) + return available_tool_versions for tool_version_id in tool_version_ids: if tool_version_id in self.tools_by_id: tool = self.tools_by_id[ tool_version_id ] diff -r e1c0cd5ed76766e4bf18f5342bf6cd395fca4732 -r 2cd1bacf5e0463bd804bf5fc7ac79a3ddf142937 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py +++ b/lib/galaxy/web/controllers/tool_runner.py @@ -109,16 +109,49 @@ raise Exception("Failed to get job information for dataset hid %d" % data.hid) # Get the tool object tool_id = job.tool_id + tool_version = job.tool_version try: # Load the tool toolbox = self.get_toolbox() - tool = toolbox.get_tool( tool_id ) + tools = toolbox.get_tool( tool_id, tool_version=tool_version, get_all_versions=True ) + if len( tools ) > 1: + tool_id_select_field = self.build_tool_id_select_field( tools, tool_id ) + for tool in tools: + if tool.id == tool_id: + break + else: + tool = tools[ 0 ] + tool_id_version_message = 'This job was initially run with tool id "%s", version "%s", and multiple derivations ' % ( job.tool_id, job.tool_version ) + tool_id_version_message += 'of this tool are available. Rerun the job with the selected tool or choose another derivation of the tool.' + else: + tool_id_select_field = None + tool = tools[ 0 ] + if tool.id == job.tool_id and tool.version == job.tool_version: + tool_id_version_message = '' + elif tool.id == job.tool_id: + if job.tool_version == None: + # For some reason jobs don't always keep track of the tool version. + tool_id_version_message = '' + else: + if len( tools ) > 1: + tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version + tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.' + else: + tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version + tool_id_version_message += 'You can rerun the job with this tool version, which is a derivation of the original tool.' + else: + if len( tools ) > 1: + tool_id_version_message = 'This job was initially run with tool version "%s", which is not currently available. ' % job.tool_version + tool_id_version_message += 'You can rerun the job with the selected tool or choose another derivation of the tool.' + else: + tool_id_version_message = 'This job was initially run with tool id "%s", version "%s", which is not ' % ( job.tool_id, job.tool_version ) + tool_id_version_message += 'currently available. You can rerun the job with this tool, which is a derivation of the original tool.' assert tool is not None, 'Requested tool has not been loaded.' except: - #this is expected, so not an exception + # This is expected so not an exception. + tool_id_version_message = '' error( "This dataset was created by an obsolete tool (%s). Can't re-run." % tool_id ) - # Can't rerun upload, external data sources, et cetera. Workflow - # compatible will proxy this for now + # Can't rerun upload, external data sources, et cetera. Workflow compatible will proxy this for now if not tool.is_workflow_compatible: error( "The '%s' tool does not currently support rerunning." % tool.name ) # Get the job's parameters @@ -163,7 +196,30 @@ if from_noframe is not None: add_frame.wiki_url = trans.app.config.wiki_url add_frame.from_noframe = True - return trans.fill_template( "tool_form.mako", history=history, toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars ) + return trans.fill_template( "tool_form.mako", + history=history, + toolbox=toolbox, + tool_id_select_field=tool_id_select_field, + tool=tool, + util=util, + add_frame=add_frame, + tool_id_version_message=tool_id_version_message, + **vars ) + def build_tool_id_select_field( self, tools, selected_tool_id ): + """Build a SelectField whose options are the ids for the received list of tools.""" + options = [] + refresh_on_change_values = [] + for tool in tools: + options.append( ( tool.id, tool.id ) ) + refresh_on_change_values.append( tool.id ) + select_field = SelectField( name='tool_id', refresh_on_change=True, refresh_on_change_values=refresh_on_change_values ) + for option_tup in options: + selected = option_tup[0] == selected_tool_id + if selected: + select_field.add_option( option_tup[0], option_tup[1], selected=True ) + else: + select_field.add_option( option_tup[0], option_tup[1] ) + return select_field @web.expose def redirect( self, trans, redirect_url=None, **kwd ): if not redirect_url: @@ -251,7 +307,6 @@ datasets.append( create_dataset( 'Pasted Entry' ) ) break return [ d.id for d in datasets ] - @web.expose def upload_async_message( self, trans, **kwd ): # might be more appropriate in a different controller diff -r e1c0cd5ed76766e4bf18f5342bf6cd395fca4732 -r 2cd1bacf5e0463bd804bf5fc7ac79a3ddf142937 templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -1,4 +1,5 @@ <%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /><%namespace file="/base_panels.mako" import="overlay" /><%def name="stylesheets()"> @@ -274,10 +275,11 @@ assert len(tool.action) == 2 tool_url = tool.action[0] + h.url_for(tool.action[1]) %> -%if message: - <div class="errormessage">${message}</div> - <br/> + +%if tool_id_version_message: + ${render_msg( tool_id_version_message, 'error' )} %endif + <div class="toolForm" id="${tool.id}"> %if tool.has_multiple_pages: <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div> @@ -286,7 +288,18 @@ %endif <div class="toolFormBody"><form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}"> - <input type="hidden" name="tool_id" value="${tool.id}"> + %if tool_id_select_field: + <div class="form-row"> + <label>Tool id:</label> + ${tool_id_select_field.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Select a different derivation of this tool to rerun the job. + </div> + </div> + <div style="clear: both"></div> + %else: + <input type="hidden" name="tool_id" value="${tool.id}"> + %endif <input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}"> %if tool.display_by_page[tool_state.page]: ${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Clean up temp files.
by Bitbucket 09 Mar '12

09 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e1c0cd5ed767/ changeset: e1c0cd5ed767 user: jgoecks date: 2012-03-09 22:11:21 summary: Clean up temp files. affected #: 1 file diff -r 3c32b4a448c6d042d39eb2225ddfe2476a18de0f -r e1c0cd5ed76766e4bf18f5342bf6cd395fca4732 tools/extract/extract_genomic_dna.py --- a/tools/extract/extract_genomic_dna.py +++ b/tools/extract/extract_genomic_dna.py @@ -279,5 +279,10 @@ if skipped_lines: # Error message includes up to the first 10 skipped lines. print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, '\n'.join( invalid_lines[:10] ) ) + + # Clean up temp file. + if fasta_file: + os.remove( seq_path ) + os.remove( tmp_name ) if __name__ == "__main__": __main__() 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 this email.

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commit/galaxy-central: dannon: Workflows: Add run workflow directly to the editor's menu.
by Bitbucket 08 Mar '12

08 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3c32b4a448c6/ changeset: 3c32b4a448c6 user: dannon date: 2012-03-08 20:05:40 summary: Workflows: Add run workflow directly to the editor's menu. affected #: 1 file diff -r 796d08ce13d092321a1c629fcb66ea225676da99 -r 3c32b4a448c6d042d39eb2225ddfe2476a18de0f templates/workflow/editor.mako --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -236,6 +236,9 @@ make_popupmenu( $("#workflow-options-button"), { "Save" : save_current_workflow, + "Run": function() { + window.location = "${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id(stored.id))}"; + }, ##"Create New" : create_new_workflow_dialog, "Edit Attributes" : edit_workflow_attributes, ##"Edit Workflow Outputs": edit_workflow_outputs, 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 this email.

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commit/galaxy-central: jgoecks: Trackster: bug fixes for read filtering.
by Bitbucket 08 Mar '12

08 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/796d08ce13d0/ changeset: 796d08ce13d0 user: jgoecks date: 2012-03-08 18:29:13 summary: Trackster: bug fixes for read filtering. affected #: 2 files diff -r 91a437977be1b1ae6eabd510e553f86f86f74ac0 -r 796d08ce13d092321a1c629fcb66ea225676da99 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -718,7 +718,7 @@ else: results.append( [ "%i_%s" % ( read.pos, qname ), read.pos, read.pos + read_len, qname, - read.cigar, strand, read.seq, [read.mapq, 125] ] ) + read.cigar, strand, read.seq, read.mapq ] ) # Take care of reads whose mates are out of range. # TODO: count paired reads when adhering to max_vals? diff -r 91a437977be1b1ae6eabd510e553f86f86f74ac0 -r 796d08ce13d092321a1c629fcb66ea225676da99 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2480,14 +2480,27 @@ return updated; } + // // Update filter's min, max based on element values. - if (element[this.index] < this.min) { - this.min = Math.floor(element[this.index]); - updated = true; - } - if (element[this.index] > this.max) { - this.max = Math.ceil(element[this.index]); - updated = true; + // + + // Make value(s) into an Array. + var values = element[this.index]; + if (!(values instanceof Array)) { + values = [values]; + } + + // Loop through values and update min, max. + for (var i = 0; i < values.length; i++) { + var value = values[i]; + if (value < this.min) { + this.min = Math.floor(value); + updated = true; + } + if (value > this.max) { + this.max = Math.ceil(value); + updated = true; + } } return updated; }, 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 this email.

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commit/galaxy-central: jgoecks: Enable fasta_to_len conversion to use only first word in title; this is standards compliant and used by default for automatic conversion.
by Bitbucket 08 Mar '12

08 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/91a437977be1/ changeset: 91a437977be1 user: jgoecks date: 2012-03-08 17:09:14 summary: Enable fasta_to_len conversion to use only first word in title; this is standards compliant and used by default for automatic conversion. affected #: 2 files diff -r 5ffd9f8983538741cf0597e6e61ccc70256ad585 -r 91a437977be1b1ae6eabd510e553f86f86f74ac0 lib/galaxy/datatypes/converters/fasta_to_len.py --- a/lib/galaxy/datatypes/converters/fasta_to_len.py +++ b/lib/galaxy/datatypes/converters/fasta_to_len.py @@ -9,7 +9,7 @@ assert sys.version_info[:2] >= ( 2, 4 ) -def compute_fasta_length( fasta_file, out_file, keep_first_char ): +def compute_fasta_length( fasta_file, out_file, keep_first_char, keep_first_word=False ): infile = fasta_file out = open( out_file, 'w') @@ -32,6 +32,8 @@ continue if line[0] == '>': if first_entry == False: + if keep_first_word: + fasta_title = fasta_title.split()[0] out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) ) else: first_entry = False @@ -41,8 +43,10 @@ seq_len += len(line) # last fasta-entry + if keep_first_word: + fasta_title = fasta_title.split()[0] out.write( "%s\t%d\n" % ( fasta_title[ 1:keep_first_char ], seq_len ) ) out.close() -if __name__ == "__main__" : - compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3] ) \ No newline at end of file +if __name__ == "__main__" : + compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], True ) \ No newline at end of file diff -r 5ffd9f8983538741cf0597e6e61ccc70256ad585 -r 91a437977be1b1ae6eabd510e553f86f86f74ac0 tools/fasta_tools/fasta_compute_length.py --- a/tools/fasta_tools/fasta_compute_length.py +++ b/tools/fasta_tools/fasta_compute_length.py @@ -6,4 +6,4 @@ import sys from galaxy.datatypes.converters.fasta_to_len import compute_fasta_length -compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3]) \ No newline at end of file +compute_fasta_length( sys.argv[1], sys.argv[2], sys.argv[3], False ) \ No newline at end of file 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 this email.

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commit/galaxy-central: dannon: branch close
by Bitbucket 08 Mar '12

08 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f61e924a5463/ changeset: f61e924a5463 branch: import_workflow_api_script user: dannon date: 2012-03-08 16:17:40 summary: branch close affected #: 0 files 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 this email.

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commit/galaxy-central: jgoecks: Add necessary space after threads option in Cuffmerge.
by Bitbucket 08 Mar '12

08 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/04ff82b2ce0c/ changeset: 04ff82b2ce0c user: jgoecks date: 2012-03-08 14:37:20 summary: Add necessary space after threads option in Cuffmerge. affected #: 1 file diff -r 40f1816d685794f4a2ddb139ca25803f2da9b0de -r 04ff82b2ce0c9e4788e87691ef871c078b47a424 tools/ngs_rna/cuffmerge_wrapper.py --- a/tools/ngs_rna/cuffmerge_wrapper.py +++ b/tools/ngs_rna/cuffmerge_wrapper.py @@ -82,7 +82,7 @@ # Add options. if options.num_threads: - cmd += ( " -p %i" % int ( options.num_threads ) ) + cmd += ( " -p %i " % int ( options.num_threads ) ) if options.ref_annotation: cmd += " -g %s " % options.ref_annotation if options.use_seq_data: 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 this email.

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commit/galaxy-central: greg: Fix for populating the tool panel and generating the integrated_tool_panel.xml file.
by Bitbucket 07 Mar '12

07 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/40f1816d6857/ changeset: 40f1816d6857 user: greg date: 2012-03-07 19:35:34 summary: Fix for populating the tool panel and generating the integrated_tool_panel.xml file. affected #: 1 file diff -r 1d73ef1ce3cd9040a808511c0f69ae04a514d635 -r 40f1816d685794f4a2ddb139ca25803f2da9b0de lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -72,6 +72,13 @@ self.init_tools( config_filename ) except: log.exception( "Error loading tools defined in config %s", config_filename ) + if self.integrated_tool_panel_config_has_contents: + # Load self.tool_panel based on the order in self.integrated_tool_panel. + self.load_tool_panel() + # Always write the current in-memory integrated_tool_panel to the integrated_tool_panel.xml file. + # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel + # config files, adding or removing locally developed tools or workflows. + self.write_integrated_tool_panel_config_file() def init_tools( self, config_filename ): """ Read the configuration file and load each tool. The following tags are currently supported: @@ -121,13 +128,6 @@ tool_path=tool_path, config_elems=config_elems ) self.shed_tool_confs.append( shed_tool_conf_dict ) - if self.integrated_tool_panel_config_has_contents: - # Load self.tool_panel based on the order in self.integrated_tool_panel. - self.load_tool_panel() - # Always write the current in-memory integrated_tool_panel to the integrated_tool_panel.xml file. - # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel - # config files, adding or removing locally developed tools or workflows. - self.write_integrated_tool_panel_config_file() def load_tool_panel( self ): for key, val in self.integrated_tool_panel.items(): if key.startswith( 'tool_' ): 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 this email.

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commit/galaxy-central: dannon: Workflows: Multiple run workflows now copy input datasets to newly created histories when used.
by Bitbucket 07 Mar '12

07 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1d73ef1ce3cd/ changeset: 1d73ef1ce3cd user: dannon date: 2012-03-07 19:13:58 summary: Workflows: Multiple run workflows now copy input datasets to newly created histories when used. affected #: 1 file diff -r c2a2ae70c05183e8c66c0c6e7a4c2c9ea30f03ec -r 1d73ef1ce3cd9040a808511c0f69ae04a514d635 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1502,7 +1502,6 @@ job = None if step.type == 'tool' or step.type is None: tool = trans.app.toolbox.get_tool( step.tool_id ) - input_values = step.state.inputs # Connect up def callback( input, value, prefixed_name, prefixed_label ): if isinstance( input, DataToolParameter ): @@ -1531,6 +1530,11 @@ else: job, out_data = step.module.execute( trans, step.state ) outputs[ step.id ] = out_data + if new_history: + for input_dataset_hda in out_data.values(): + new_hda = input_dataset_hda.copy( copy_children=True ) + new_history.add_dataset(new_hda) + outputs[ step.id ]['input_ds_copy'] = new_hda # Record invocation workflow_invocation_step = model.WorkflowInvocationStep() workflow_invocation_step.workflow_invocation = workflow_invocation 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 this email.

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commit/galaxy-central: greg: Fix for generating ToolSectionLabels in the integrated_tool_panel.xml file.
by Bitbucket 06 Mar '12

06 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c2a2ae70c051/ changeset: c2a2ae70c051 user: greg date: 2012-03-06 23:15:38 summary: Fix for generating ToolSectionLabels in the integrated_tool_panel.xml file. affected #: 2 files diff -r 5a6ec71bd0fff451944785d19f3112ac3e43c413 -r c2a2ae70c05183e8c66c0c6e7a4c2c9ea30f03ec lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -1,8 +1,6 @@ """ -Manage automatic installation of tools configured in tool_shed_install.xml, all of which were -at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool -shed. Tools included in tool_shed_install.xml that have already been installed will not be -re-installed. +Manage automatic installation of tools configured in the xxx.xml files in ~/scripts/migrate_tools (e.g., 0002_tools.xml). +All of the tools were at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool shed. """ import logging, urllib2 from galaxy.tools import ToolSection @@ -13,8 +11,8 @@ class InstallManager( object ): def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config ): """ - Check tool settings in tool_shed_install_config and install all tools that are not already installed. The tool panel - configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml. + Check tool settings in tool_shed_install_config and install all repositories that are not already installed. The tool + panel configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml. """ self.app = app self.toolbox = self.app.toolbox diff -r 5a6ec71bd0fff451944785d19f3112ac3e43c413 -r c2a2ae70c05183e8c66c0c6e7a4c2c9ea30f03ec lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -232,6 +232,9 @@ if section_item: os.write( fd, ' <workflow id="%s" />\n' % section_item.id ) elif section_key.startswith( 'label_' ): + label_id = section_item.id or '' + label_text = section_item.text or '' + label_version = section_item.version or '' os.write( fd, ' <label id="%s" text="%s" version="%s" />\n' % ( label_id, label_text, label_version ) ) os.write( fd, ' </section>\n' ) os.write( fd, '</toolbox>\n' ) 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 this email.

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commit/galaxy-central: jgoecks: Editable text support: (a) use jQuery function style and (b) add support for tipsy. Trackster: add help/tipsy text when setting line track/histogram max/min. Pack scripts.
by Bitbucket 06 Mar '12

06 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5a6ec71bd0ff/ changeset: 5a6ec71bd0ff user: jgoecks date: 2012-03-06 22:30:03 summary: Editable text support: (a) use jQuery function style and (b) add support for tipsy. Trackster: add help/tipsy text when setting line track/histogram max/min. Pack scripts. affected #: 4 files diff -r 8de1ee93943b06bbdbf21a11bf574db4d38793d7 -r 5a6ec71bd0fff451944785d19f3112ac3e43c413 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -331,21 +331,23 @@ } /** - * Returns editable text element. Element is a div with text: (a) when user clicks on text, a textbox/area - * enables user to edit text; (b) when user presses enter key, element's text is set. + * Make an element with text editable: (a) when user clicks on text, a textbox/area + * is provided for editing; (b) when enter key pressed, element's text is set and on_finish + * is called. */ // TODO: use this function to implement async_save_text (implemented below). -function get_editable_text_elt(text, use_textarea, num_cols, num_rows, on_finish) { - // Set defaults if necessary. - if (num_cols === undefined) { - num_cols = 30; - } - if (num_rows === undefined) { - num_rows = 4; - } +$.fn.make_text_editable = function(config_dict) { + // Get config options. + var num_cols = ("num_cols" in config_dict ? config_dict.num_cols : 30), + num_rows = ("num_rows" in config_dict ? config_dict.num_rows : 4), + use_textarea = ("use_textarea" in config_dict ? config_dict.use_textarea : false), + on_finish = ("on_finish" in config_dict ? config_dict.on_finish : null), + help_text = ("help_text" in config_dict ? config_dict.help_text : null); + - // Create div for element. - var container = $("<div/>").addClass("editable-text").text(text).click(function(e) { + // Add element behavior. + var container = $(this); + container.addClass("editable-text").click(function(e) { // If there's already an input element, editing is active, so do nothing. if ($(this).children(":input").length > 0) { return; @@ -354,7 +356,7 @@ container.removeClass("editable-text"); // Handler for setting element text. - var set_text = function(new_text, do_on_finish) { + var set_text = function(new_text) { container.find(":input").remove(); if (new_text != "") { @@ -366,7 +368,7 @@ } container.addClass("editable-text"); - if (do_on_finish && on_finish) { + if (on_finish) { on_finish(new_text); } }; @@ -383,7 +385,7 @@ } }); button_elt = $("<button/>").text("Done").click(function() { - set_text(input_elt.val(), true); + set_text(input_elt.val()); // Return false so that click does not propogate to container. return false; }); @@ -398,7 +400,7 @@ $(this).trigger("blur"); } else if (e.keyCode === 13) { // Enter key. - set_text($(this).val(), true); + set_text($(this).val()); } }); } @@ -415,6 +417,12 @@ // Do not propogate to elements below b/c that blurs input and prevents it from being used. e.stopPropagation(); }); + + // Add help text if there some. + if (help_text) { + container.attr("title", help_text).tipsy( { gravity: 's' } ); + } + return container; } diff -r 8de1ee93943b06bbdbf21a11bf574db4d38793d7 -r 5a6ec71bd0fff451944785d19f3112ac3e43c413 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return 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a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var 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d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});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/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").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_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").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();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.content_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.content_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;ac<ag.length;ac++){if(!this._keep_val(ag[ac])){ae=false;break}}return ae}else{return this._keep_val(ad[this.index])}},update_attrs:function(ad){var ac=false;if(!this.applies_to(ad)){return ac}if(ad[this.index]<this.min){this.min=Math.floor(ad[this.index]);ac=true}if(ad[this.index]>this.max){this.max=Math.ceil(ad[this.index]);ac=true}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(ad.html_elt).parent());var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.content_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.content_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.content_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.content_div.text(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.content_div.text(V);if(ad.view.chrom){ad.content_div.text("");ad.content_div.css("height",ad.height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.content_div.children().addClass("remove");this.max_height=0;var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.content_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.content_div.children(".remove").remove()}var af=this;if(ak){this.content_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.max_height=Math.max(ad.max_height,ac.height());ad.content_div.css("height",ad.max_height+"px");ag.children().css("height",ad.max_height+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={todo:"label",todo:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,"reference",ac,{content_div:ac.top_labeltrack},{});ac.reference_track=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_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false)};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){af.content_div.css("height","0px");return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}return new b(af,ad,ag,ae,ak)}this.content_div.css("height","0px")}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{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:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,K.prototype,{set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.content_div).css("height",ag);ac.height_px=ag;ac.request_draw(true)}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.height_px}).appendTo(ac.container_div)},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=get_editable_text_elt(W(ac.prefs.min_value,3),false,6,null,function(aj){var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=get_editable_text_elt(W(ac.prefs.max_value,3),false,6,null,function(aj){var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=get_editable_text_elt(ak,false,12,0,function(av){var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});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/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").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_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").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();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.content_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.content_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;ac<ag.length;ac++){if(!this._keep_val(ag[ac])){ae=false;break}}return ae}else{return this._keep_val(ad[this.index])}},update_attrs:function(ad){var ac=false;if(!this.applies_to(ad)){return ac}if(ad[this.index]<this.min){this.min=Math.floor(ad[this.index]);ac=true}if(ad[this.index]>this.max){this.max=Math.ceil(ad[this.index]);ac=true}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(ad.html_elt).parent());var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.content_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.content_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.content_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.content_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.content_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.content_div.text(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.content_div.text(V);if(ad.view.chrom){ad.content_div.text("");ad.content_div.css("height",ad.height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.content_div.children().addClass("remove");this.max_height=0;var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.content_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.content_div.children(".remove").remove()}var af=this;if(ak){this.content_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.max_height=Math.max(ad.max_height,ac.height());ad.content_div.css("height",ad.max_height+"px");ag.children().css("height",ad.max_height+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={todo:"label",todo:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,"reference",ac,{content_div:ac.top_labeltrack},{});ac.reference_track=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_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false)};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){af.content_div.css("height","0px");return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}return new b(af,ad,ag,ae,ak)}this.content_div.css("height","0px")}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{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:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,K.prototype,{set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.content_div).css("height",ag);ac.height_px=ag;ac.request_draw(true)}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.height_px}).appendTo(ac.container_div)},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".tipsy").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r 8de1ee93943b06bbdbf21a11bf574db4d38793d7 -r 5a6ec71bd0fff451944785d19f3112ac3e43c413 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -4340,20 +4340,31 @@ track.container_div.find(".yaxislabel").remove(); // Add min, max labels. - var min_label = get_editable_text_elt(round(track.prefs.min_value, 3), false, 6, null, function(new_val) { - var new_val = parseFloat(new_val); - if (!isNaN(new_val)) { - track.set_min_value(new_val); - } - } ).addClass('yaxislabel bottom').attr("id", 'linetrack_' + track.dataset_id + '_minval') - .prependTo(track.container_div), - max_label = get_editable_text_elt(round(track.prefs.max_value, 3), false, 6, null, function(new_val) { - var new_val = parseFloat(new_val); - if (!isNaN(new_val)) { - track.set_max_value(new_val); - } - } ).addClass('yaxislabel top').attr("id", 'linetrack_' + track.dataset_id + '_maxval') - .prependTo(track.container_div); + var + min_label = $("<div/>").text(round(track.prefs.min_value, 3)).make_text_editable({ + num_cols: 6, + on_finish: function(new_val) { + $(".tipsy").remove(); + var new_val = parseFloat(new_val); + if (!isNaN(new_val)) { + track.set_min_value(new_val); + } + }, + help_text: "Set min value" + }).addClass('yaxislabel bottom').attr("id", 'linetrack_' + track.dataset_id + '_minval') + .prependTo(track.container_div), + max_label = $("<div/>").text(round(track.prefs.max_value, 3)).make_text_editable({ + num_cols: 6, + on_finish: function(new_val) { + $(".tipsy").remove(); + var new_val = parseFloat(new_val); + if (!isNaN(new_val)) { + track.set_max_value(new_val); + } + }, + help_text: "Set max value" + }).addClass('yaxislabel top').attr("id", 'linetrack_' + track.dataset_id + '_maxval') + .prependTo(track.container_div); }); }, /** @@ -4515,15 +4526,17 @@ var first_tile = tiles[0]; if (first_tile instanceof SummaryTreeTile) { var max_val = (this.prefs.histogram_max ? this.prefs.histogram_max : first_tile.max_val), - max_label = - get_editable_text_elt(max_val, false, 12, 0, function(new_val) { + max_label = $("<div/>").text(max_val).make_text_editable({ + num_cols: 12, + on_finish: function(new_val) { + $(".tipsy").remove(); var new_val = parseFloat(new_val); track.prefs.histogram_max = (!isNaN(new_val) ? new_val : null); track.tile_cache.clear(); track.request_draw(); - }) - .addClass('yaxislabel top') - .css("color", this.prefs.label_color); + }, + help_text: "Set max value; leave blank to use default" + }).addClass('yaxislabel top').css("color", this.prefs.label_color); this.container_div.prepend(max_label); } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for Error 349 (net::ERR_RESPONSE_HEADERS_MULTIPLE_CONTENT_DISPOSITION) when downloading exported histories.
by Bitbucket 06 Mar '12

06 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8de1ee93943b/ changeset: 8de1ee93943b user: dan date: 2012-03-06 21:43:32 summary: Fix for Error 349 (net::ERR_RESPONSE_HEADERS_MULTIPLE_CONTENT_DISPOSITION) when downloading exported histories. affected #: 1 file diff -r c7192cd00414c7452bc6ee1547ad9622c3840e25 -r 8de1ee93943b06bbdbf21a11bf574db4d38793d7 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -657,12 +657,13 @@ valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' hname = history.name hname = ''.join(c in valid_chars and c or '_' for c in hname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy-History-%s.tar" % ( hname ) + hname = "Galaxy-History-%s.tar" % ( hname ) if jeha.compressed: - trans.response.headers["Content-Disposition"] += ".gz" + hname += ".gz" trans.response.set_content_type( 'application/x-gzip' ) else: trans.response.set_content_type( 'application/x-tar' ) + trans.response.headers["Content-Disposition"] = 'attachment; filename="%s"' % ( hname ) return trans.app.object_store.get_data(jeha.dataset) elif jeha.job.state in [ model.Job.states.RUNNING, model.Job.states.QUEUED, model.Job.states.WAITING ]: return trans.show_message( "Still exporting history %(n)s; please check back soon. Link: <a href='%(s)s'>%(s)s</a>" \ 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 this email.

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