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March 2011

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commit/galaxy-central: dan: Allow upload to function on https URLs.
by Bitbucket 14 Mar '11

14 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/425076fe5ea0/ changeset: r5220:425076fe5ea0 user: dan date: 2011-03-15 04:01:11 summary: Allow upload to function on https URLs. affected #: 2 files (142 bytes) --- a/lib/galaxy/tools/parameters/grouping.py Fri Mar 11 17:54:06 2011 -0500 +++ b/lib/galaxy/tools/parameters/grouping.py Mon Mar 14 23:01:11 2011 -0400 @@ -218,12 +218,12 @@ url_paste_file = group_incoming.get( 'url_paste', None ) if url_paste_file is not None: url_paste = open( url_paste_file, 'r' ).read( 1024 ) - if url_paste.lstrip().lower().startswith( 'http://' ) or url_paste.lstrip().lower().startswith( 'ftp://' ): + if url_paste.lstrip().lower().startswith( 'http://' ) or url_paste.lstrip().lower().startswith( 'ftp://' ) or url_paste.lstrip().lower().startswith( 'https://' ): url_paste = url_paste.replace( '\r', '' ).split( '\n' ) for line in url_paste: line = line.strip() if line: - if not line.lower().startswith( 'http://' ) and not line.lower().startswith( 'ftp://' ): + if not line.lower().startswith( 'http://' ) and not line.lower().startswith( 'ftp://' ) and not line.lower().startswith( 'https://' ): continue # non-url line, ignore precreated_name = line dataset_name = override_name --- a/lib/galaxy/web/controllers/tool_runner.py Fri Mar 11 17:54:06 2011 -0500 +++ b/lib/galaxy/web/controllers/tool_runner.py Mon Mar 14 23:01:11 2011 -0400 @@ -237,7 +237,7 @@ line = line.rstrip( '\r\n' ).strip() if not line: continue - elif line.lower().startswith( 'http://' ) or line.lower().startswith( 'ftp://' ): + elif line.lower().startswith( 'http://' ) or line.lower().startswith( 'ftp://' ) or line.lower().startswith( 'https://' ): url = True datasets.append( create_dataset( line ) ) else: 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: kanwei: trackster: Fix BAM reads without cigar string (assume all match); datasets added into a new track browser will now index immediately instead of after changing a chrom
by Bitbucket 11 Mar '11

11 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/98ce387e70ff/ changeset: r5219:98ce387e70ff user: kanwei date: 2011-03-11 23:54:06 summary: trackster: Fix BAM reads without cigar string (assume all match); datasets added into a new track browser will now index immediately instead of after changing a chrom affected #: 4 files (281 bytes) --- a/static/june_2007_style/blue/trackster.css Fri Mar 11 15:57:06 2011 -0500 +++ b/static/june_2007_style/blue/trackster.css Fri Mar 11 17:54:06 2011 -0500 @@ -28,6 +28,7 @@ .track-tile canvas{position:relative;z-index:100;border:solid white;border-width:2px 0px 0px 0px;} .track.error .track-content{background-color:#ECB4AF;background-image:none;padding:2px 0;} .track.nodata .track-content{background-color:#eee;background-image:none;padding:2px 0;} +.track.pending .track-content{background-color:white;background-image:none;padding:2px 0;} .loading{min-height:100px;} .label-track{font-size:10px;border:none;padding:0;margin:0;height:1.5em;overflow:hidden;} .label-track .label{border-left:solid #999 1px;padding:1px;padding-bottom:2px;display:inline-block;} --- a/static/june_2007_style/trackster.css.tmpl Fri Mar 11 15:57:06 2011 -0500 +++ b/static/june_2007_style/trackster.css.tmpl Fri Mar 11 17:54:06 2011 -0500 @@ -177,6 +177,11 @@ background-image: none; padding: 2px 0; } +.track.pending .track-content { + background-color: white; + background-image: none; + padding: 2px 0; +} .loading { min-height: 100px; --- a/static/scripts/packed/trackster.js Fri Mar 11 15:57:06 2011 -0500 +++ b/static/scripts/packed/trackster.js Fri Mar 11 17:54:06 2011 -0500 @@ -1,1 +1,1 @@ -CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. 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NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!==null){$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,j,n){var c=this,o=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=n;this.child_tracks=[];if(c.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});$.each(this.filters,function(t,w){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var v=$("<div/>").addClass("slider-label").appendTo(u);var s=$("<span/>").addClass("name").appendTo(v);s.text(w.name+" ");var r=$("<span/>").addClass("values").appendTo(v);var q=$("<div/>").addClass("slider").appendTo(u);w.control_element=$("<div/>").attr("id",w.name+"-filter-control").appendTo(q);w.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(y,z){var x=z.values;r.text("["+x[0]+"-"+x[1]+"]");w.low=x[0];w.high=x[1];c.draw(true,true)},change:function(x,y){w.control_element.slider("option","slide").call(w.control_element,x,y)}});w.slider=w.control_element;w.slider_label=r;$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(q){q.stopPropagation()}).bind("click",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});var m=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var l=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span class='param-name'>").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span class='param-value'>").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var q=$("<div id='"+s.name+"-param-control'>").appendTo(y);var r=(s.max<=1?0.01:(s.max<=1000?1:5));q.slider({min:s.min,max:s.max,step:r,value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){s.value=B.value}});w.click(function(){var C=t,B=C.text(),A=(s.max<=1?4:s.max.length);C.text("");$("<input type='text'/>").attr("size",A).attr("maxlength",A).attr("value",B).appendTo(C).focus().select().click(function(D){D.stopPropagation()}).blur(function(){$(this).remove();C.text(B)}).keyup(function(F){if(F.keyCode===27){$(this).trigger("blur")}else{if(F.keyCode===13){var D=$(this),E=parseFloat(D.val());if(isNaN(E)||E>s.max||E<s.min){alert("Parameter value must be in the range ["+s.min+"-"+s.max+"]");return $(this)}C.text(E);q.slider("value",E);s.value=E}}})});$("<div style='clear: both;'/>").appendTo(v)});var p=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var k=$("<input type='submit'>").attr("value","Run").appendTo(p);var c=this;k.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(q){c.mode_div.text(q);c.mode=q;c.track_config.values.mode=q;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(q){return function(){d(q)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide Tool":"Show Tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.track_type=="ReadTrack"){var e=(b.show_insertions?"Hide Insertions":"Show Insertions");a[e]=function(){b.show_insertions=!b.show_insertions;b.draw(true);b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},tile_data:function(d,a,g,k,j){var b=this,h=a*DENSITY*d,f=(a+1)*DENSITY*d,e={chrom:this.view.chrom,low:h,high:f,dbkey:this.view.dbkey};if(j===undefined){j=d+"_"+a}var c=b.data_cache.get(j);if(c){return k(c)}$.extend(e,g);$.ajax({url:this.data_url,dataType:"json",data:e,success:function(l){b.data_cache.set(j,l);return k(l)},error:function(m,l,n){console.log(m,l,n)}})},draw:function(a,d){var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}if(d){var k=this;var q=setInterval(function(){if(obj_length(c)===0){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var x=$(v[w]);if(u){x.remove()}else{if(x.children().length!==0){u=true}}}clearInterval(q)}},50)}for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,h,l,c,e,k,m,f){var d=this;var g=function(n){d.tile_cache.set(j,n);d.show_tile(n,k,h,m)};var a=setTimeout(function(){if(h<=d.view.high&&l>=d.view.low){var n;if(!b){n=d.tile_cache.get(j)}if(!n){d.draw_tile(e,c,k,m,function(p){if(p){var o=$("<div class='track-tile'>").prepend(p);n=o}g(n)})}if(n){g(n)}}delete f[a]},50);f[a]=true},show_tile:function(h,j,e,k){var a=this;var c=this.view.high-this.view.low,b=(e-this.view.low)*k;if(this.left_offset){b-=this.left_offset}h.css({position:"absolute",top:0,left:b,height:""});j.append(h);a.max_height=Math.max(a.max_height,h.height());a.content_div.css("height",a.max_height+"px");j.children().css("height",a.max_height+"px");if(a.hidden){return}for(var g=0;g<a.filters.length;g++){a.filters[g].update_ui_elt()}var d=false;if(a.example_feature){for(var g=0;g<a.filters.length;g++){if(a.filters[g].applies_to(a.example_feature)){d=true;break}}}if(a.filters_available!==d){a.filters_available=d;if(!a.filters_available){a.filters_div.hide()}a.make_name_popup_menu()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(c,b,e,g,f){var a=this,d=DENSITY*c;if(g>CHAR_WIDTH_PX){a.tile_data(c,b,{},function(j){if(j===null){a.content_div.css("height","0px");return}var k=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(k)}k=$(k);var h=k.get(0).getContext("2d");k.get(0).width=Math.ceil(d*g+a.left_offset);k.get(0).height=a.height_px;h.font=DEFAULT_FONT;h.textAlign="center";for(var n=0,l=j.length;n<l;n++){var m=Math.round(n*g);h.fillText(j[n],m+a.left_offset,10)}return f(k)})}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(d,a,j,k,h){if(this.vertical_range===undefined){return}var c=this,f=a*DENSITY*d,b=DENSITY*d,g=d+"_"+a,e={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};this.tile_data(d,a,e,function(C){var l=document.createElement("canvas"),q=C.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(l)}l=$(l);l.get(0).width=Math.ceil(b*k);l.get(0).height=c.height_px;var z=l.get(0).getContext("2d"),n=false,B=c.prefs.min_value,v=c.prefs.max_value,A=c.vertical_range,m=c.total_frequency,u=c.height_px,s=c.mode;var r=Math.round(u+B/A*u);z.beginPath();z.moveTo(0,r);z.lineTo(b*k,r);z.fillStyle="#aaa";z.stroke();z.beginPath();z.fillStyle=c.prefs.color;var p,w,x;if(q.length>1){x=Math.ceil((q[1][0]-q[0][0])*k)}else{x=10}for(var o=0,t=q.length;o<t;o++){p=Math.round((q[o][0]-f)*k);w=q[o][1];if(w===null){if(n&&s==="Filled"){z.lineTo(p,u)}n=false;continue}if(w<B){w=B}else{if(w>v){w=v}}if(s==="Histogram"){w=Math.round(w/A*u);z.fillRect(p,r,x,-w)}else{if(s==="Intensity"){w=255-Math.floor((w-B)/A*255);z.fillStyle="rgb("+w+","+w+","+w+")";z.fillRect(p,0,x,u)}else{w=Math.round(u-(w-B)/A*u);if(n){z.lineTo(p,w)}else{n=true;if(s==="Filled"){z.moveTo(p,u);z.lineTo(p,w)}else{z.moveTo(p,w)}}}}}if(s==="Filled"){if(n){z.lineTo(p,r);z.lineTo(0,r)}z.fill()}else{z.stroke()}h(l)})}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2],s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[5],z=x[6],E=x[7],e=x[8];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O-1);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(z,E,l,n,j,d,p){var v=this;if(v.view.reference_track&&n>CHAR_WIDTH_PX&&d===undefined){return v.view.reference_track.tile_data(z,E,{},function(f){v.draw_tile(z,E,l,n,j,f)})}var G=E*DENSITY*z,a=(E+1)*DENSITY*z,s=a-G,H={hda_ldda:v.hda_ldda,dataset_id:v.dataset_id,resolution:this.view.resolution,mode:this.mode};if(p===undefined){var q=this.data_cache.get_data(G,a,this.mode),J=z+"_"+E+"_"+this.mode;if(q===undefined){return v.tile_data(z,E,H,function(f){v.data_cache.set_data(G,a,this.mode,f);v.draw_tile(z,E,l,n,j,d,f)},J)}p=q}var x=Math.ceil(s*n),u=this.mode,K=25,g=this.left_offset,r,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(u==="Auto"){if(p.dataset_type==="summary_tree"){u=p.dataset_type}else{if(p.extra_info==="no_detail"){u="no_detail"}else{var I=p.data;if((I.length&&I.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){u="Squish"}else{u="Pack"}}}}var A=this.get_y_scale(u);if(u==="summary_tree"){h=this.summary_draw_height}if(u==="Dense"){h=K}else{if(u==="no_detail"||u==="Squish"||u==="Pack"){h=this.incremental_slots(n,p.data,u)*A+K;r=this.inc_slots[n]}}c.get(0).width=x+g;c.get(0).height=h;if(p.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}l.parent().css("height",Math.max(this.height_px,h)+"px");var y=c.get(0).getContext("2d");y.fillStyle=this.prefs.block_color;y.font=this.default_font;y.textAlign="right";this.container_div.find(".yaxislabel").remove();if(u==="summary_tree"){this.draw_summary_tree(c,p.data,p.delta,p.max,n,h,G,g);return j(c)}if(p.message){c.css({"border-top":"1px solid red"});y.fillStyle="red";y.textAlign="left";var t=y.textBaseline;y.textBaseline="top";y.fillText(p.message,g,0);y.textBaseline=t;if(!p.data){return j(c)}}this.example_feature=(p.data.length?p.data[0]:undefined);var I=p.data;for(var B=0,D=I.length;B<D;B++){var k=I[B],m=k[0],w=k[1],b=k[2],e=(r&&r[m]!==undefined?r[m]:null);var C=false;var o;for(var F=0;F<this.filters.length;F++){o=this.filters[F];o.update_attrs(k);if(!o.keep(k)){C=true;break}}if(C){continue}if(is_overlap([w,b],[G,a])&&(u=="Dense"||e!==null)){this.draw_element(y,E,u,k,e,G,a,n,A,x,g,d)}}j(c)}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.difference_mode=true;this.show_insertions=false;this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.round(J/2)}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.difference_mode&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file +CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!==-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",b).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var j=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(j/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,k){var f=$(this);var l=k.offsetX-k.current_x;var g=f.scrollTop()-(h.clientY-k.current_height);f.scrollTop(g);k.current_height=h.clientY;k.current_x=k.offsetX;var j=Math.round(l/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}).bind("mousewheel",function(h,k,g,f){if(g){var j=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(k,l){$(l.proxy).css({left:Math.min(k.pageX,l.startX),width:Math.abs(k.pageX-l.startX)});var g=Math.min(k.pageX,l.startX)-a.container.offset().left,f=Math.max(k.pageX,l.startX)-a.container.offset().left,j=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*j)+a.low,Math.round(f/h*j)+a.low)}).bind("dragend",function(l,m){var g=Math.min(l.pageX,m.startX),f=Math.max(l.pageX,m.startX),j=(a.high-a.low),h=a.viewport_container.width(),k=a.low;a.low=Math.round(g/h*j)+k;a.high=Math.round(f/h*j)+k;$(m.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var k=this,a,d,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}k.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,j,n){var c=this,o=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=n;this.child_tracks=[];if(c.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});$.each(this.filters,function(t,w){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var v=$("<div/>").addClass("slider-label").appendTo(u);var s=$("<span/>").addClass("name").appendTo(v);s.text(w.name+" ");var r=$("<span/>").addClass("values").appendTo(v);var q=$("<div/>").addClass("slider").appendTo(u);w.control_element=$("<div/>").attr("id",w.name+"-filter-control").appendTo(q);w.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(y,z){var x=z.values;r.text("["+x[0]+"-"+x[1]+"]");w.low=x[0];w.high=x[1];c.draw(true,true)},change:function(x,y){w.control_element.slider("option","slide").call(w.control_element,x,y)}});w.slider=w.control_element;w.slider_label=r;$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(q){q.stopPropagation()}).bind("click",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});var m=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var l=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span class='param-name'>").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span class='param-value'>").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var q=$("<div id='"+s.name+"-param-control'>").appendTo(y);var r=(s.max<=1?0.01:(s.max<=1000?1:5));q.slider({min:s.min,max:s.max,step:r,value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){s.value=B.value}});w.click(function(){var C=t,B=C.text(),A=(s.max<=1?4:s.max.length);C.text("");$("<input type='text'/>").attr("size",A).attr("maxlength",A).attr("value",B).appendTo(C).focus().select().click(function(D){D.stopPropagation()}).blur(function(){$(this).remove();C.text(B)}).keyup(function(F){if(F.keyCode===27){$(this).trigger("blur")}else{if(F.keyCode===13){var D=$(this),E=parseFloat(D.val());if(isNaN(E)||E>s.max||E<s.min){alert("Parameter value must be in the range ["+s.min+"-"+s.max+"]");return $(this)}C.text(E);q.slider("value",E);s.value=E}}})});$("<div style='clear: both;'/>").appendTo(v)});var p=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var k=$("<input type='submit'>").attr("value","Run").appendTo(p);var c=this;k.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(q){c.mode_div.text(q);c.mode=q;c.track_config.values.mode=q;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(q){return function(){d(q)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide Tool":"Show Tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.track_type=="ReadTrack"){var e=(b.show_insertions?"Hide Insertions":"Show Insertions");a[e]=function(){b.show_insertions=!b.show_insertions;b.draw(true);b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},tile_data:function(d,a,g,k,j){var b=this,h=a*DENSITY*d,f=(a+1)*DENSITY*d,e={chrom:this.view.chrom,low:h,high:f,dbkey:this.view.dbkey};if(j===undefined){j=d+"_"+a}var c=b.data_cache.get(j);if(c){return k(c)}$.extend(e,g);$.ajax({url:this.data_url,dataType:"json",data:e,success:function(l){b.data_cache.set(j,l);return k(l)},error:function(m,l,n){console.log(m,l,n)}})},draw:function(a,d){var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}if(d){var k=this;var q=setInterval(function(){if(obj_length(c)===0){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var x=$(v[w]);if(u){x.remove()}else{if(x.children().length!==0){u=true}}}clearInterval(q)}},50)}for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,h,l,c,e,k,m,f){var d=this;var g=function(n){d.tile_cache.set(j,n);d.show_tile(n,k,h,m)};var a=setTimeout(function(){if(h<=d.view.high&&l>=d.view.low){var n;if(!b){n=d.tile_cache.get(j)}if(!n){d.draw_tile(e,c,k,m,function(p){if(p){var o=$("<div class='track-tile'>").prepend(p);n=o}g(n)})}if(n){g(n)}}delete f[a]},50);f[a]=true},show_tile:function(h,j,e,k){var a=this;var c=this.view.high-this.view.low,b=(e-this.view.low)*k;if(this.left_offset){b-=this.left_offset}h.css({position:"absolute",top:0,left:b,height:""});j.append(h);a.max_height=Math.max(a.max_height,h.height());a.content_div.css("height",a.max_height+"px");j.children().css("height",a.max_height+"px");if(a.hidden){return}for(var g=0;g<a.filters.length;g++){a.filters[g].update_ui_elt()}var d=false;if(a.example_feature){for(var g=0;g<a.filters.length;g++){if(a.filters[g].applies_to(a.example_feature)){d=true;break}}}if(a.filters_available!==d){a.filters_available=d;if(!a.filters_available){a.filters_div.hide()}a.make_name_popup_menu()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(c,b,e,g,f){var a=this,d=DENSITY*c;if(g>CHAR_WIDTH_PX){a.tile_data(c,b,{},function(j){if(j===null){a.content_div.css("height","0px");return}var k=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(k)}k=$(k);var h=k.get(0).getContext("2d");k.get(0).width=Math.ceil(d*g+a.left_offset);k.get(0).height=a.height_px;h.font=DEFAULT_FONT;h.textAlign="center";for(var n=0,l=j.length;n<l;n++){var m=Math.round(n*g);h.fillText(j[n],m+a.left_offset,10)}return f(k)})}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(d,a,j,k,h){if(this.vertical_range===undefined){return}var c=this,f=a*DENSITY*d,b=DENSITY*d,g=d+"_"+a,e={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};this.tile_data(d,a,e,function(C){var l=document.createElement("canvas"),q=C.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(l)}l=$(l);l.get(0).width=Math.ceil(b*k);l.get(0).height=c.height_px;var z=l.get(0).getContext("2d"),n=false,B=c.prefs.min_value,v=c.prefs.max_value,A=c.vertical_range,m=c.total_frequency,u=c.height_px,s=c.mode;var r=Math.round(u+B/A*u);z.beginPath();z.moveTo(0,r);z.lineTo(b*k,r);z.fillStyle="#aaa";z.stroke();z.beginPath();z.fillStyle=c.prefs.color;var p,w,x;if(q.length>1){x=Math.ceil((q[1][0]-q[0][0])*k)}else{x=10}for(var o=0,t=q.length;o<t;o++){p=Math.round((q[o][0]-f)*k);w=q[o][1];if(w===null){if(n&&s==="Filled"){z.lineTo(p,u)}n=false;continue}if(w<B){w=B}else{if(w>v){w=v}}if(s==="Histogram"){w=Math.round(w/A*u);z.fillRect(p,r,x,-w)}else{if(s==="Intensity"){w=255-Math.floor((w-B)/A*255);z.fillStyle="rgb("+w+","+w+","+w+")";z.fillRect(p,0,x,u)}else{w=Math.round(u-(w-B)/A*u);if(n){z.lineTo(p,w)}else{n=true;if(s==="Filled"){z.moveTo(p,u);z.lineTo(p,w)}else{z.moveTo(p,w)}}}}}if(s==="Filled"){if(n){z.lineTo(p,r);z.lineTo(0,r)}z.fill()}else{z.stroke()}h(l)})}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2],s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[5],z=x[6],E=x[7],e=x[8];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O-1);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(z,E,l,n,j,d,p){var v=this;if(v.view.reference_track&&n>CHAR_WIDTH_PX&&d===undefined){return v.view.reference_track.tile_data(z,E,{},function(f){v.draw_tile(z,E,l,n,j,f)})}var G=E*DENSITY*z,a=(E+1)*DENSITY*z,s=a-G,H={hda_ldda:v.hda_ldda,dataset_id:v.dataset_id,resolution:this.view.resolution,mode:this.mode};if(p===undefined){var q=this.data_cache.get_data(G,a,this.mode),J=z+"_"+E+"_"+this.mode;if(q===undefined){return v.tile_data(z,E,H,function(f){v.data_cache.set_data(G,a,this.mode,f);v.draw_tile(z,E,l,n,j,d,f)},J)}p=q}var x=Math.ceil(s*n),u=this.mode,K=25,g=this.left_offset,r,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(u==="Auto"){if(p.dataset_type==="summary_tree"){u=p.dataset_type}else{if(p.extra_info==="no_detail"){u="no_detail"}else{var I=p.data;if((I.length&&I.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){u="Squish"}else{u="Pack"}}}}var A=this.get_y_scale(u);if(u==="summary_tree"){h=this.summary_draw_height}if(u==="Dense"){h=K}else{if(u==="no_detail"||u==="Squish"||u==="Pack"){h=this.incremental_slots(n,p.data,u)*A+K;r=this.inc_slots[n]}}c.get(0).width=x+g;c.get(0).height=h;if(p.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}l.parent().css("height",Math.max(this.height_px,h)+"px");var y=c.get(0).getContext("2d");y.fillStyle=this.prefs.block_color;y.font=this.default_font;y.textAlign="right";this.container_div.find(".yaxislabel").remove();if(u==="summary_tree"){this.draw_summary_tree(c,p.data,p.delta,p.max,n,h,G,g);return j(c)}if(p.message){c.css({"border-top":"1px solid red"});y.fillStyle="red";y.textAlign="left";var t=y.textBaseline;y.textBaseline="top";y.fillText(p.message,g,0);y.textBaseline=t;if(!p.data){return j(c)}}this.example_feature=(p.data.length?p.data[0]:undefined);var I=p.data;for(var B=0,D=I.length;B<D;B++){var k=I[B],m=k[0],w=k[1],b=k[2],e=(r&&r[m]!==undefined?r[m]:null);var C=false;var o;for(var F=0;F<this.filters.length;F++){o=this.filters[F];o.update_attrs(k);if(!o.keep(k)){C=true;break}}if(C){continue}if(is_overlap([w,b],[G,a])&&(u=="Dense"||e!==null)){this.draw_element(y,E,u,k,e,G,a,n,A,x,g,d)}}j(c)}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.difference_mode=true;this.show_insertions=false;this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.round(J/2)}if(!e){e=[[0,o.length]]}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.difference_mode&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file --- a/static/scripts/trackster.js Fri Mar 11 15:57:06 2011 -0500 +++ b/static/scripts/trackster.js Fri Mar 11 17:54:06 2011 -0500 @@ -1067,47 +1067,45 @@ return; } - if ( track.view.chrom !== null ) { - // Get dataset state; if state is fine, enable and draw track. Otherwise, show message - // about track status. - $.getJSON(converted_datasets_state_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, chrom: track.view.chrom}, - function (result) { - if (!result || result === "error" || result.kind === "error") { - track.container_div.addClass("error"); - track.content_div.text(DATA_ERROR); - if (result.message) { - var track_id = track.view.tracks.indexOf(track); - var error_link = $(" <a href='javascript:void(0);'></a>").text("View error").bind("click", function() { - show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } ); - }); - track.content_div.append(error_link); - } - } else if (result === "no converter") { - track.container_div.addClass("error"); - track.content_div.text(DATA_NOCONVERTER); - } else if (result === "no data" || (result.data !== undefined && (result.data === null || result.data.length === 0))) { - track.container_div.addClass("nodata"); - track.content_div.text(DATA_NONE); - } else if (result === "pending") { - track.container_div.addClass("pending"); - track.content_div.text(DATA_PENDING); - setTimeout(function() { track.init(); }, track.data_query_wait); - } else if (result['status'] === "data") { - if (result['valid_chroms']) { - track.valid_chroms = result['valid_chroms']; - track.make_name_popup_menu(); - } - track.content_div.text(DATA_OK); - if (track.view.chrom) { - track.content_div.text(""); - track.content_div.css( "height", track.height_px + "px" ); - track.enabled = true; - // predraw_init may be asynchronous, wait for it and then draw - $.when( track.predraw_init() ).done( function() { track.draw() } ); - } + // Get dataset state; if state is fine, enable and draw track. Otherwise, show message + // about track status. + $.getJSON(converted_datasets_state_url, { hda_ldda: track.hda_ldda, dataset_id: track.dataset_id, chrom: track.view.chrom}, + function (result) { + if (!result || result === "error" || result.kind === "error") { + track.container_div.addClass("error"); + track.content_div.text(DATA_ERROR); + if (result.message) { + var track_id = track.view.tracks.indexOf(track); + var error_link = $(" <a href='javascript:void(0);'></a>").text("View error").bind("click", function() { + show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } ); + }); + track.content_div.append(error_link); } - }); - } + } else if (result === "no converter") { + track.container_div.addClass("error"); + track.content_div.text(DATA_NOCONVERTER); + } else if (result === "no data" || (result.data !== undefined && (result.data === null || result.data.length === 0))) { + track.container_div.addClass("nodata"); + track.content_div.text(DATA_NONE); + } else if (result === "pending") { + track.container_div.addClass("pending"); + track.content_div.text(DATA_PENDING); + setTimeout(function() { track.init(); }, track.data_query_wait); + } else if (result['status'] === "data") { + if (result['valid_chroms']) { + track.valid_chroms = result['valid_chroms']; + track.make_name_popup_menu(); + } + track.content_div.text(DATA_OK); + if (track.view.chrom) { + track.content_div.text(""); + track.content_div.css( "height", track.height_px + "px" ); + track.enabled = true; + // predraw_init may be asynchronous, wait for it and then draw + $.when( track.predraw_init() ).done( function() { track.draw() } ); + } + } + }); }, /** * Additional initialization required before drawing track for the first time. @@ -2779,6 +2777,10 @@ if ((mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { gap = Math.round(w_scale/2); } + if (!cigar) { + // If no cigar string, then assume all matches + cigar = [ [0, orig_seq.length] ] + } for (var cig_id = 0, len = cigar.length; cig_id < len; cig_id++) { var cig = cigar[cig_id], cig_op = "MIDNSHP=X"[cig[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: kanwei: Include
by Bitbucket 11 Mar '11

11 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/760c981e0a8e/ changeset: r5218:760c981e0a8e user: kanwei date: 2011-03-11 21:57:06 summary: Include affected #: 1 file (4 bytes) --- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py Fri Mar 11 14:56:11 2011 -0500 +++ b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py Fri Mar 11 15:57:06 2011 -0500 @@ -2,7 +2,7 @@ from __future__ import division -import sys +import sys, os sys.stderr = open(os.devnull, 'w') # suppress stderr as cython produces warning on some systems: # csamtools.so:6: RuntimeWarning: __builtin__.file size changed 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: greg: Per request from Peter Cock, turn the "Copy data into Galaxy?" check box into a select list that clarifies the behavior. The default is to copy files into Galaxy.
by Bitbucket 11 Mar '11

11 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/70d7d0bfaad6/ changeset: r5217:70d7d0bfaad6 user: greg date: 2011-03-11 20:56:11 summary: Per request from Peter Cock, turn the "Copy data into Galaxy?" check box into a select list that clarifies the behavior. The default is to copy files into Galaxy. affected #: 5 files (617 bytes) --- a/lib/galaxy/tools/actions/upload_common.py Fri Mar 11 13:36:29 2011 -0500 +++ b/lib/galaxy/tools/actions/upload_common.py Fri Mar 11 14:56:11 2011 -0500 @@ -280,7 +280,7 @@ try: link_data_only = uploaded_dataset.link_data_only except: - link_data_only = False + link_data_only = 'copy_files' json = dict( file_type = uploaded_dataset.file_type, ext = uploaded_dataset.ext, name = uploaded_dataset.name, --- a/lib/galaxy/web/controllers/library_common.py Fri Mar 11 13:36:29 2011 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Fri Mar 11 14:56:11 2011 -0500 @@ -717,7 +717,7 @@ space_to_tab = params.get( 'files_0|space_to_tab', '' ) else: space_to_tab = params.get( 'space_to_tab', '' ) - link_data_only = params.get( 'link_data_only', '' ) + link_data_only = params.get( 'link_data_only', 'copy_files' ) dbkey = params.get( 'dbkey', '?' ) if isinstance( dbkey, list ): last_used_build = dbkey[0] @@ -1044,8 +1044,9 @@ if in_folder: uploaded_dataset.in_folder = in_folder uploaded_dataset.data = upload_common.new_upload( trans, cntrller, uploaded_dataset, library_bunch ) - if params.get( 'link_data_only', False ): - uploaded_dataset.link_data_only = True + link_data_only = params.get( 'link_data_only', 'copy_files' ) + uploaded_dataset.link_data_only = link_data_only + if link_data_only == 'link_to_files': uploaded_dataset.data.file_name = os.path.abspath( path ) # Since we are not copying the file into Galaxy's managed # default file location, the dataset should never be purgable. @@ -1059,7 +1060,8 @@ for entry in os.listdir( full_dir ): # Only import regular files path = os.path.join( full_dir, entry ) - if os.path.islink( full_dir ) and params.get( 'link_data_only', False ): + link_data_only = params.get( 'link_data_only', 'copy_files' ) + if os.path.islink( full_dir ) and link_data_only == 'link_to_files': # If we're linking instead of copying and the # sub-"directory" in the import dir is actually a symlink, # dereference the symlink, but not any of its contents. @@ -1068,7 +1070,7 @@ path = os.path.join( link_path, entry ) else: path = os.path.abspath( os.path.join( link_path, entry ) ) - elif os.path.islink( path ) and os.path.isfile( path ) and params.get( 'link_data_only', False ): + elif os.path.islink( path ) and os.path.isfile( path ) and link_data_only == 'link_to_files': # If we're linking instead of copying and the "file" in the # sub-directory of the import dir is actually a symlink, # dereference the symlink (one dereference only, Vasili). @@ -1146,7 +1148,7 @@ space_to_tab = params.get( 'files_0|space_to_tab', '' ) else: space_to_tab = params.get( 'space_to_tab', '' ) - link_data_only = params.get( 'link_data_only', '' ) + link_data_only = params.get( 'link_data_only', 'copy_files' ) dbkey = params.get( 'dbkey', '?' ) if isinstance( dbkey, list ): last_used_build = dbkey[0] --- a/templates/library/common/common.mako Fri Mar 11 13:36:29 2011 -0500 +++ b/templates/library/common/common.mako Fri Mar 11 14:56:11 2011 -0500 @@ -218,33 +218,33 @@ <input type="checkbox" name="preserve_dirs" value="Yes" checked="true" />Yes </div><div class="toolParamHelp" style="clear: both;"> - If checked (default), library subfolders will be used to preserve any subdirectories on the filesystem.<br /> + If checked (default), library sub-folders will be used to preserve any subdirectories on the filesystem. If unchecked, any files in subdirectories on the filesystem will be placed directly in the library folder. </div></div> %endif %if upload_option in ( 'upload_directory', 'upload_paths' ): <div class="form-row"> - <% - if link_data_only == 'No': - checked = ' checked' - else: - checked = '' - link_data_only_field = '<input type="checkbox" name="link_data_only" value="No"%s/>No' % checked - %><label>Copy data into Galaxy?</label><div class="form-row-input"> - ${link_data_only_field} + <select name="link_data_only"> + %if not link_data_only or link_data_only == 'copy_files': + <option value="copy_files" selected>Copy files into Galaxy + <option value="link_to_files">Link to files without copying into Galaxy + %else: + <option value="copy_files">Copy files into Galaxy + <option value="link_to_files" selected>Link to files without copying into Galaxy + %endif + </select></div><div class="toolParamHelp" style="clear: both;"> - Normally data uploaded with this tool is copied into Galaxy's "files" directory - so any later changes to the data will not affect Galaxy. However, this may not - be desired (especially for large NGS datasets), so use of this option will - force Galaxy to always read the data from its original path. + Normally data uploaded with this tool is copied into Galaxy's configured "file_path" location where Galaxy + has a form of control over the data files. However, this may not be desired (especially for large NGS + datasets), so using the option labeled "Link to files without copying into Galaxy" will force Galaxy to + always read the data from its original path. %if upload_option == 'upload_directory': - Any symlinks encountered in the upload directory will be dereferenced once - - that is, Galaxy will point directly to the file that is linked, but no other - symlinks further down the line will be dereferenced. + Any symlinks encountered in the uploaded directory will be dereferenced once. That is, Galaxy will + point directly to the file that is linked, but no other symlinks further down the line will be dereferenced. %endif </div></div> --- a/test/base/twilltestcase.py Fri Mar 11 13:36:29 2011 -0500 +++ b/test/base/twilltestcase.py Fri Mar 11 14:56:11 2011 -0500 @@ -2004,7 +2004,7 @@ # Library dataset stuff def upload_library_dataset( self, cntrller, library_id, folder_id, filename='', server_dir='', replace_id='', upload_option='upload_file', file_type='auto', dbkey='hg18', space_to_tab='', - link_data_only='', preserve_dirs='Yes', roles=[], ldda_message='', hda_ids='', + link_data_only='copy_files', preserve_dirs='Yes', roles=[], ldda_message='', hda_ids='', template_refresh_field_name='1_field_name', template_refresh_field_contents='', template_fields=[], show_deleted='False', strings_displayed=[] ): """Add datasets to library using any upload_option""" @@ -2031,10 +2031,6 @@ tc.fv( "1", "dbkey", dbkey ) if space_to_tab: tc.fv( "1", "space_to_tab", space_to_tab ) - if link_data_only: - tc.fv( "1", "link_data_only", link_data_only ) - if upload_option == 'filesystem_paths' and preserve_dirs == 'Yes': - tc.fv( "1", "preserve_dirs", preserve_dirs ) for role_id in roles: tc.fv( "1", "roles", role_id ) # Refresh the form by selecting the upload_option - we do this here to ensure @@ -2051,18 +2047,21 @@ tc.fv( "add_history_datasets_to_library", "hda_ids", '1' ) tc.submit( 'add_history_datasets_to_library_button' ) else: - if filename: - filename = self.get_filename( filename ) - tc.formfile( "1", "files_0|file_data", filename ) - elif server_dir: + if upload_option == 'filesystem_paths' or upload_option == 'upload_directory': + tc.fv( "1", "link_data_only", link_data_only ) + if upload_option == 'filesystem_paths' and preserve_dirs == 'Yes': + tc.fv( "1", "preserve_dirs", preserve_dirs ) + if upload_option == 'upload_directory' and server_dir: tc.fv( "1", "server_dir", server_dir ) + if upload_option == 'upload_file': + if filename: + filename = self.get_filename( filename ) + tc.formfile( "1", "files_0|file_data", filename ) for check_str in strings_displayed: self.check_page_for_string( check_str ) tc.submit( "runtool_btn" ) # Give the files some time to finish uploading self.library_wait( library_id ) - data = self.last_page() - file( 'greg1.html', 'wb' ).write( data ) self.home() def ldda_permissions( self, cntrller, library_id, folder_id, id, role_ids_str, permissions_in=[], permissions_out=[], strings_displayed=[], ldda_name='' ): --- a/tools/data_source/upload.py Fri Mar 11 13:36:29 2011 -0500 +++ b/tools/data_source/upload.py Fri Mar 11 14:56:11 2011 -0500 @@ -157,6 +157,7 @@ line_count = None converted_path = None stdout = None + link_data_only = dataset.get( 'link_data_only', 'copy_files' ) try: ext = dataset.file_type @@ -334,7 +335,7 @@ return if data_type != 'binary': # don't convert newlines on data we're only going to symlink - if not dataset.get( 'link_data_only', False ): + if link_data_only == 'link_to_files': in_place = True if dataset.type in ( 'server_dir', 'path_paste' ): in_place = False @@ -353,9 +354,7 @@ if ext == 'auto': ext = 'data' # Move the dataset to its "real" path - if dataset.get( 'link_data_only', False ): - pass # data will remain in place - elif dataset.type in ( 'server_dir', 'path_paste' ): + if link_data_only == 'copy_files' and dataset.type in ( 'server_dir', 'path_paste' ): if converted_path is not None: shutil.copy( converted_path, output_path ) try: @@ -365,7 +364,7 @@ else: # this should not happen, but it's here just in case shutil.copy( dataset.path, output_path ) - else: + elif link_data_only == 'copy_files': shutil.move( dataset.path, output_path ) # Write the job info stdout = stdout or 'uploaded %s file' % data_type Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: trackster: Suppress cython warning message causing bam_to_summary_tree to fail. Fix for chroms without 'chr' in front not being displayed
by Bitbucket 11 Mar '11

11 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/faf3b3fda8d6/ changeset: r5216:faf3b3fda8d6 user: kanwei date: 2011-03-11 19:36:29 summary: trackster: Suppress cython warning message causing bam_to_summary_tree to fail. Fix for chroms without 'chr' in front not being displayed affected #: 2 files (251 bytes) --- a/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py Fri Mar 11 10:01:54 2011 -0500 +++ b/lib/galaxy/datatypes/converters/bam_to_summary_tree_converter.py Fri Mar 11 13:36:29 2011 -0500 @@ -3,6 +3,9 @@ from __future__ import division import sys +sys.stderr = open(os.devnull, 'w') # suppress stderr as cython produces warning on some systems: + # csamtools.so:6: RuntimeWarning: __builtin__.file size changed + from galaxy import eggs import pkg_resources --- a/lib/galaxy/visualization/tracks/data_providers.py Fri Mar 11 10:01:54 2011 -0500 +++ b/lib/galaxy/visualization/tracks/data_providers.py Fri Mar 11 13:36:29 2011 -0500 @@ -170,7 +170,7 @@ self.CACHE[filename] = st # Check for data. - return st.chrom_blocks.get(chrom, None) is not None + return st.chrom_blocks.get(chrom, None) is not None or st.chrom_blocks.get(chrom[3:], None) is not None class VcfDataProvider( TracksDataProvider ): """ 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: Apply a corrected version of the patch from Peter Cock that flips the ¬†"Preserve directory structure?" setting when uploading library datasets from filesystem paths.
by Bitbucket 11 Mar '11

11 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/74c4dd43485a/ changeset: r5215:74c4dd43485a user: greg date: 2011-03-11 16:01:54 summary: Apply a corrected version of the patch from Peter Cock that flips the ¬†"Preserve directory structure?" setting when uploading library datasets from filesystem paths. affected #: 3 files (194 bytes) --- a/lib/galaxy/web/controllers/library_common.py Fri Mar 11 09:16:16 2011 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Fri Mar 11 10:01:54 2011 -0500 @@ -1097,9 +1097,7 @@ message = "No paths entered in the upload form" response_code = 400 return None, response_code, message - preserve_dirs = True - if params.get( 'dont_preserve_dirs', False ): - preserve_dirs = False + preserve_dirs = util.string_as_bool( params.get( 'preserve_dirs', False ) ) # locate files bad_paths = [] uploaded_datasets = [] --- a/templates/library/common/common.mako Fri Mar 11 09:16:16 2011 -0500 +++ b/templates/library/common/common.mako Fri Mar 11 10:01:54 2011 -0500 @@ -215,10 +215,11 @@ <div class="form-row"><label>Preserve directory structure?</label><div class="form-row-input"> - <input type="checkbox" name="dont_preserve_dirs" value="No"/>No + <input type="checkbox" name="preserve_dirs" value="Yes" checked="true" />Yes </div><div class="toolParamHelp" style="clear: both;"> - If checked, all files in subdirectories on the filesystem will be placed at the top level of the folder, instead of into subfolders. + If checked (default), library subfolders will be used to preserve any subdirectories on the filesystem.<br /> + If unchecked, any files in subdirectories on the filesystem will be placed directly in the library folder. </div></div> %endif --- a/test/base/twilltestcase.py Fri Mar 11 09:16:16 2011 -0500 +++ b/test/base/twilltestcase.py Fri Mar 11 10:01:54 2011 -0500 @@ -2004,7 +2004,7 @@ # Library dataset stuff def upload_library_dataset( self, cntrller, library_id, folder_id, filename='', server_dir='', replace_id='', upload_option='upload_file', file_type='auto', dbkey='hg18', space_to_tab='', - link_data_only='', dont_preserve_dirs='', roles=[], ldda_message='', hda_ids='', + link_data_only='', preserve_dirs='Yes', roles=[], ldda_message='', hda_ids='', template_refresh_field_name='1_field_name', template_refresh_field_contents='', template_fields=[], show_deleted='False', strings_displayed=[] ): """Add datasets to library using any upload_option""" @@ -2033,8 +2033,8 @@ tc.fv( "1", "space_to_tab", space_to_tab ) if link_data_only: tc.fv( "1", "link_data_only", link_data_only ) - if dont_preserve_dirs: - tc.fv( "1", "dont_preserve_dirs", dont_preserve_dirs ) + if upload_option == 'filesystem_paths' and preserve_dirs == 'Yes': + tc.fv( "1", "preserve_dirs", preserve_dirs ) for role_id in roles: tc.fv( "1", "roles", role_id ) # Refresh the form by selecting the upload_option - we do this here to ensure 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: Apply patch from Ry4an Brase to correct "NoneType dereference on the jobs view" issue.
by Bitbucket 11 Mar '11

11 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0b9bba943c8f/ changeset: r5214:0b9bba943c8f user: greg date: 2011-03-11 15:16:16 summary: Apply patch from Ry4an Brase to correct "NoneType dereference on the jobs view" issue. affected #: 1 file (16 bytes) --- a/templates/admin/jobs.mako Thu Mar 10 17:30:35 2011 -0500 +++ b/templates/admin/jobs.mako Fri Mar 11 09:16:16 2011 -0500 @@ -47,7 +47,7 @@ %endif </td><td>${job.id}</td> - %if job.history.user: + %if job.history and job.history.user: <td>${job.history.user.email}</td> %else: <td>anonymous</td> 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: access to datasets is based on accessibility, not ownership.
by Bitbucket 10 Mar '11

10 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/620da901f5b1/ changeset: r5213:620da901f5b1 user: jgoecks date: 2011-03-10 23:30:35 summary: Trackster: access to datasets is based on accessibility, not ownership. affected #: 1 file (230 bytes) --- a/lib/galaxy/web/controllers/tracks.py Thu Mar 10 16:42:34 2011 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Thu Mar 10 17:30:35 2011 -0500 @@ -408,7 +408,7 @@ """ # Dataset check. - dataset = self.get_dataset( trans, dataset_id ) + dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) msg = self._check_dataset_state( trans, dataset ) if msg: return msg @@ -426,7 +426,7 @@ # TODO: this code is copied from data() -- should refactor. # Dataset check. - dataset = self.get_dataset( trans, dataset_id ) + dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) msg = self._check_dataset_state( trans, dataset ) if not msg: msg = messages.DATA @@ -443,7 +443,7 @@ # Dataset check. if hda_ldda == "hda": - dataset = self.get_dataset( trans, dataset_id ) + dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) else: dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) msg = self._check_dataset_state( trans, dataset ) @@ -488,7 +488,7 @@ # Dataset check. if hda_ldda == "hda": - dataset = self.get_dataset( trans, dataset_id ) + dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) else: dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) msg = self._check_dataset_state( trans, dataset ) @@ -656,7 +656,7 @@ low, high = int( low ), int( high ) # Dataset check. - original_dataset = self.get_dataset( trans, dataset_id ) + original_dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) msg = self._check_dataset_state( trans, original_dataset ) if msg: return to_json_string( msg ) 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: Make shared visualizations work again and pack trackster.js
by Bitbucket 10 Mar '11

10 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/52ead6780d84/ changeset: r5212:52ead6780d84 user: jgoecks date: 2011-03-10 22:42:34 summary: Make shared visualizations work again and pack trackster.js affected #: 4 files (4.0 KB) --- a/lib/galaxy/web/controllers/visualization.py Thu Mar 10 16:11:49 2011 -0500 +++ b/lib/galaxy/web/controllers/visualization.py Thu Mar 10 16:42:34 2011 -0500 @@ -68,7 +68,9 @@ return query.filter( self.model_class.deleted==False ).filter( self.model_class.published==True ) -class VisualizationController( BaseController, Sharable, UsesAnnotations, UsesVisualization, UsesItemRatings ): +class VisualizationController( BaseController, Sharable, UsesAnnotations, + UsesHistoryDatasetAssociation, UsesVisualization, + UsesItemRatings ): _user_list_grid = VisualizationListGrid() _published_list_grid = VisualizationAllPublishedGrid() --- a/static/scripts/packed/trackster.js Thu Mar 10 16:11:49 2011 -0500 +++ b/static/scripts/packed/trackster.js Thu Mar 10 16:42:34 2011 -0500 @@ -1,1 +1,1 @@ -CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!==-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",b).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var j=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(j/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,k){var f=$(this);var l=k.offsetX-k.current_x;var g=f.scrollTop()-(h.clientY-k.current_height);f.scrollTop(g);k.current_height=h.clientY;k.current_x=k.offsetX;var j=Math.round(l/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}).bind("mousewheel",function(h,k,g,f){if(g){var j=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(k,l){$(l.proxy).css({left:Math.min(k.pageX,l.startX),width:Math.abs(k.pageX-l.startX)});var g=Math.min(k.pageX,l.startX)-a.container.offset().left,f=Math.max(k.pageX,l.startX)-a.container.offset().left,j=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*j)+a.low,Math.round(f/h*j)+a.low)}).bind("dragend",function(l,m){var g=Math.min(l.pageX,m.startX),f=Math.max(l.pageX,m.startX),j=(a.high-a.low),h=a.viewport_container.width(),k=a.low;a.low=Math.round(g/h*j)+k;a.high=Math.round(f/h*j)+k;$(m.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var k=this,a,d,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}k.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!==null){$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,j,n){var c=this,o=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=n;this.child_tracks=[];if(c.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});$.each(this.filters,function(t,w){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var v=$("<div/>").addClass("slider-label").appendTo(u);var s=$("<span/>").addClass("name").appendTo(v);s.text(w.name+" ");var r=$("<span/>").addClass("values").appendTo(v);var q=$("<div/>").addClass("slider").appendTo(u);w.control_element=$("<div/>").attr("id",w.name+"-filter-control").appendTo(q);w.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(y,z){var x=z.values;r.text("["+x[0]+"-"+x[1]+"]");w.low=x[0];w.high=x[1];c.draw(true,true)},change:function(x,y){w.control_element.slider("option","slide").call(w.control_element,x,y)}});w.slider=w.control_element;w.slider_label=r;$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(q){q.stopPropagation()}).bind("click",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});var m=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var l=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span class='param-name'>").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span class='param-value'>").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var q=$("<div id='"+s.name+"-param-control'>").appendTo(y);var r=(s.max<=1?0.01:(s.max<=1000?1:5));q.slider({min:s.min,max:s.max,step:r,value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){s.value=B.value}});w.click(function(){var C=t,B=C.text(),A=(s.max<=1?4:s.max.length);C.text("");$("<input type='text'/>").attr("size",A).attr("maxlength",A).attr("value",B).appendTo(C).focus().select().click(function(D){D.stopPropagation()}).blur(function(){$(this).remove();C.text(B)}).keyup(function(F){if(F.keyCode===27){$(this).trigger("blur")}else{if(F.keyCode===13){var D=$(this),E=parseFloat(D.val());if(isNaN(E)||E>s.max||E<s.min){alert("Parameter value must be in the range ["+s.min+"-"+s.max+"]");return $(this)}C.text(E);q.slider("value",E);s.value=E}}})});$("<div style='clear: both;'/>").appendTo(v)});var p=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var k=$("<input type='submit'>").attr("value","Run").appendTo(p);var c=this;k.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(q){c.mode_div.text(q);c.mode=q;c.track_config.values.mode=q;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(q){return function(){d(q)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide Tool":"Show Tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.track_type=="ReadTrack"){var e=(b.show_insertions?"Hide Insertions":"Show Insertions");a[e]=function(){b.show_insertions=!b.show_insertions;b.draw(true);b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},tile_data:function(d,a,g,k,j){var b=this,h=a*DENSITY*d,f=(a+1)*DENSITY*d,e={chrom:this.view.chrom,low:h,high:f,dbkey:this.view.dbkey};if(j===undefined){j=d+"_"+a}var c=b.data_cache.get(j);if(c){return k(c)}$.extend(e,g);$.ajax({url:this.data_url,dataType:"json",data:e,success:function(l){b.data_cache.set(j,l);return k(l)},error:function(m,l,n){console.log(m,l,n)}})},draw:function(a,d){var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}if(d){var k=this;var q=setInterval(function(){console.log("draw_tile_dict_length:",obj_length(c));if(obj_length(c)===0){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var x=$(v[w]);if(u){x.remove()}else{if(x.children().length!==0){u=true}}}clearInterval(q)}},50)}for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,h,l,c,e,k,m,f){var d=this;var g=function(n){d.tile_cache.set(j,n);d.show_tile(n,k,h,m)};var a=setTimeout(function(){if(h<=d.view.high&&l>=d.view.low){var n;if(!b){n=d.tile_cache.get(j)}if(!n){d.draw_tile(e,c,k,m,function(p){if(p){var o=$("<div class='track-tile'>").prepend(p);n=o}g(n)})}if(n){g(n)}}delete f[a]},50);f[a]=true},show_tile:function(h,j,e,k){var a=this;var c=this.view.high-this.view.low,b=(e-this.view.low)*k;if(this.left_offset){b-=this.left_offset}h.css({position:"absolute",top:0,left:b,height:""});j.append(h);a.max_height=Math.max(a.max_height,h.height());a.content_div.css("height",a.max_height+"px");j.children().css("height",a.max_height+"px");if(a.hidden){return}for(var g=0;g<a.filters.length;g++){a.filters[g].update_ui_elt()}var d=false;if(a.example_feature){for(var g=0;g<a.filters.length;g++){if(a.filters[g].applies_to(a.example_feature)){d=true;break}}}if(a.filters_available!==d){a.filters_available=d;if(!a.filters_available){a.filters_div.hide()}a.make_name_popup_menu()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(c,b,e,g,f){var a=this,d=DENSITY*c;if(g>CHAR_WIDTH_PX){a.tile_data(c,b,{},function(j){if(j===null){a.content_div.css("height","0px");return}var k=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(k)}k=$(k);var h=k.get(0).getContext("2d");k.get(0).width=Math.ceil(d*g+a.left_offset);k.get(0).height=a.height_px;h.font=DEFAULT_FONT;h.textAlign="center";for(var n=0,l=j.length;n<l;n++){var m=Math.round(n*g);h.fillText(j[n],m+a.left_offset,10)}return f(k)})}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(d,a,j,k,h){if(this.vertical_range===undefined){return}var c=this,f=a*DENSITY*d,b=DENSITY*d,g=d+"_"+a,e={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};this.tile_data(d,a,e,function(C){var l=document.createElement("canvas"),q=C.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(l)}l=$(l);l.get(0).width=Math.ceil(b*k);l.get(0).height=c.height_px;var z=l.get(0).getContext("2d"),n=false,B=c.prefs.min_value,v=c.prefs.max_value,A=c.vertical_range,m=c.total_frequency,u=c.height_px,s=c.mode;var r=Math.round(u+B/A*u);z.beginPath();z.moveTo(0,r);z.lineTo(b*k,r);z.fillStyle="#aaa";z.stroke();z.beginPath();z.fillStyle=c.prefs.color;var p,w,x;if(q.length>1){x=Math.ceil((q[1][0]-q[0][0])*k)}else{x=10}for(var o=0,t=q.length;o<t;o++){p=Math.round((q[o][0]-f)*k);w=q[o][1];if(w===null){if(n&&s==="Filled"){z.lineTo(p,u)}n=false;continue}if(w<B){w=B}else{if(w>v){w=v}}if(s==="Histogram"){w=Math.round(w/A*u);z.fillRect(p,r,x,-w)}else{if(s==="Intensity"){w=255-Math.floor((w-B)/A*255);z.fillStyle="rgb("+w+","+w+","+w+")";z.fillRect(p,0,x,u)}else{w=Math.round(u-(w-B)/A*u);if(n){z.lineTo(p,w)}else{n=true;if(s==="Filled"){z.moveTo(p,u);z.lineTo(p,w)}else{z.moveTo(p,w)}}}}}if(s==="Filled"){if(n){z.lineTo(p,r);z.lineTo(0,r)}z.fill()}else{z.stroke()}h(l)})}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2],s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[5],z=x[6],E=x[7],e=x[8];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O-1);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(z,E,l,n,j,d,p){var v=this;if(v.view.reference_track&&n>CHAR_WIDTH_PX&&d===undefined){return v.view.reference_track.tile_data(z,E,{},function(f){v.draw_tile(z,E,l,n,j,f)})}var G=E*DENSITY*z,a=(E+1)*DENSITY*z,s=a-G,H={hda_ldda:v.hda_ldda,dataset_id:v.dataset_id,resolution:this.view.resolution,mode:this.mode};if(p===undefined){var q=this.data_cache.get_data(G,a,this.mode),J=z+"_"+E+"_"+this.mode;if(q===undefined){return v.tile_data(z,E,H,function(f){v.data_cache.set_data(G,a,this.mode,f);v.draw_tile(z,E,l,n,j,d,f)},J)}p=q}var x=Math.ceil(s*n),u=this.mode,K=25,g=this.left_offset,r,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(u==="Auto"){if(p.dataset_type==="summary_tree"){u=p.dataset_type}else{if(p.extra_info==="no_detail"){u="no_detail"}else{var I=p.data;if((I.length&&I.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){u="Squish"}else{u="Pack"}}}}var A=this.get_y_scale(u);if(u==="summary_tree"){h=this.summary_draw_height}if(u==="Dense"){h=K}else{if(u==="no_detail"||u==="Squish"||u==="Pack"){h=this.incremental_slots(n,p.data,u)*A+K;r=this.inc_slots[n]}}c.get(0).width=x+g;c.get(0).height=h;if(p.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}l.parent().css("height",Math.max(this.height_px,h)+"px");var y=c.get(0).getContext("2d");y.fillStyle=this.prefs.block_color;y.font=this.default_font;y.textAlign="right";this.container_div.find(".yaxislabel").remove();if(u==="summary_tree"){this.draw_summary_tree(c,p.data,p.delta,p.max,n,h,G,g);return j(c)}if(p.message){c.css({"border-top":"1px solid red"});y.fillStyle="red";y.textAlign="left";var t=y.textBaseline;y.textBaseline="top";y.fillText(p.message,g,0);y.textBaseline=t;if(!p.data){return j(c)}}this.example_feature=(p.data.length?p.data[0]:undefined);var I=p.data;for(var B=0,D=I.length;B<D;B++){var k=I[B],m=k[0],w=k[1],b=k[2],e=(r&&r[m]!==undefined?r[m]:null);var C=false;var o;for(var F=0;F<this.filters.length;F++){o=this.filters[F];o.update_attrs(k);if(!o.keep(k)){C=true;break}}if(C){continue}if(is_overlap([w,b],[G,a])&&(u=="Dense"||e!==null)){this.draw_element(y,E,u,k,e,G,a,n,A,x,g,d)}}j(c)}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.difference_mode=true;this.show_insertions=false;this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.round(J/2)}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.difference_mode&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file +CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!==-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",b).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var j=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(j/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,k){var f=$(this);var l=k.offsetX-k.current_x;var g=f.scrollTop()-(h.clientY-k.current_height);f.scrollTop(g);k.current_height=h.clientY;k.current_x=k.offsetX;var j=Math.round(l/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}).bind("mousewheel",function(h,k,g,f){if(g){var j=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(k,l){$(l.proxy).css({left:Math.min(k.pageX,l.startX),width:Math.abs(k.pageX-l.startX)});var g=Math.min(k.pageX,l.startX)-a.container.offset().left,f=Math.max(k.pageX,l.startX)-a.container.offset().left,j=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*j)+a.low,Math.round(f/h*j)+a.low)}).bind("dragend",function(l,m){var g=Math.min(l.pageX,m.startX),f=Math.max(l.pageX,m.startX),j=(a.high-a.low),h=a.viewport_container.width(),k=a.low;a.low=Math.round(g/h*j)+k;a.high=Math.round(f/h*j)+k;$(m.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var k=this,a,d,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}k.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom!==null){$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})}},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,j,n){var c=this,o=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=n;this.child_tracks=[];if(c.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});$.each(this.filters,function(t,w){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var v=$("<div/>").addClass("slider-label").appendTo(u);var s=$("<span/>").addClass("name").appendTo(v);s.text(w.name+" ");var r=$("<span/>").addClass("values").appendTo(v);var q=$("<div/>").addClass("slider").appendTo(u);w.control_element=$("<div/>").attr("id",w.name+"-filter-control").appendTo(q);w.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(y,z){var x=z.values;r.text("["+x[0]+"-"+x[1]+"]");w.low=x[0];w.high=x[1];c.draw(true,true)},change:function(x,y){w.control_element.slider("option","slide").call(w.control_element,x,y)}});w.slider=w.control_element;w.slider_label=r;$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(q){q.stopPropagation()}).bind("click",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});var m=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var l=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span class='param-name'>").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span class='param-value'>").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var q=$("<div id='"+s.name+"-param-control'>").appendTo(y);var r=(s.max<=1?0.01:(s.max<=1000?1:5));q.slider({min:s.min,max:s.max,step:r,value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){s.value=B.value}});w.click(function(){var C=t,B=C.text(),A=(s.max<=1?4:s.max.length);C.text("");$("<input type='text'/>").attr("size",A).attr("maxlength",A).attr("value",B).appendTo(C).focus().select().click(function(D){D.stopPropagation()}).blur(function(){$(this).remove();C.text(B)}).keyup(function(F){if(F.keyCode===27){$(this).trigger("blur")}else{if(F.keyCode===13){var D=$(this),E=parseFloat(D.val());if(isNaN(E)||E>s.max||E<s.min){alert("Parameter value must be in the range ["+s.min+"-"+s.max+"]");return $(this)}C.text(E);q.slider("value",E);s.value=E}}})});$("<div style='clear: both;'/>").appendTo(v)});var p=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var k=$("<input type='submit'>").attr("value","Run").appendTo(p);var c=this;k.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(q){c.mode_div.text(q);c.mode=q;c.track_config.values.mode=q;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(q){return function(){d(q)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide Tool":"Show Tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.track_type=="ReadTrack"){var e=(b.show_insertions?"Hide Insertions":"Show Insertions");a[e]=function(){b.show_insertions=!b.show_insertions;b.draw(true);b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},tile_data:function(d,a,g,k,j){var b=this,h=a*DENSITY*d,f=(a+1)*DENSITY*d,e={chrom:this.view.chrom,low:h,high:f,dbkey:this.view.dbkey};if(j===undefined){j=d+"_"+a}var c=b.data_cache.get(j);if(c){return k(c)}$.extend(e,g);$.ajax({url:this.data_url,dataType:"json",data:e,success:function(l){b.data_cache.set(j,l);return k(l)},error:function(m,l,n){console.log(m,l,n)}})},draw:function(a,d){var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}if(d){var k=this;var q=setInterval(function(){if(obj_length(c)===0){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var x=$(v[w]);if(u){x.remove()}else{if(x.children().length!==0){u=true}}}clearInterval(q)}},50)}for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,h,l,c,e,k,m,f){var d=this;var g=function(n){d.tile_cache.set(j,n);d.show_tile(n,k,h,m)};var a=setTimeout(function(){if(h<=d.view.high&&l>=d.view.low){var n;if(!b){n=d.tile_cache.get(j)}if(!n){d.draw_tile(e,c,k,m,function(p){if(p){var o=$("<div class='track-tile'>").prepend(p);n=o}g(n)})}if(n){g(n)}}delete f[a]},50);f[a]=true},show_tile:function(h,j,e,k){var a=this;var c=this.view.high-this.view.low,b=(e-this.view.low)*k;if(this.left_offset){b-=this.left_offset}h.css({position:"absolute",top:0,left:b,height:""});j.append(h);a.max_height=Math.max(a.max_height,h.height());a.content_div.css("height",a.max_height+"px");j.children().css("height",a.max_height+"px");if(a.hidden){return}for(var g=0;g<a.filters.length;g++){a.filters[g].update_ui_elt()}var d=false;if(a.example_feature){for(var g=0;g<a.filters.length;g++){if(a.filters[g].applies_to(a.example_feature)){d=true;break}}}if(a.filters_available!==d){a.filters_available=d;if(!a.filters_available){a.filters_div.hide()}a.make_name_popup_menu()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(c,b,e,g,f){var a=this,d=DENSITY*c;if(g>CHAR_WIDTH_PX){a.tile_data(c,b,{},function(j){if(j===null){a.content_div.css("height","0px");return}var k=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(k)}k=$(k);var h=k.get(0).getContext("2d");k.get(0).width=Math.ceil(d*g+a.left_offset);k.get(0).height=a.height_px;h.font=DEFAULT_FONT;h.textAlign="center";for(var n=0,l=j.length;n<l;n++){var m=Math.round(n*g);h.fillText(j[n],m+a.left_offset,10)}return f(k)})}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(d,a,j,k,h){if(this.vertical_range===undefined){return}var c=this,f=a*DENSITY*d,b=DENSITY*d,g=d+"_"+a,e={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};this.tile_data(d,a,e,function(C){var l=document.createElement("canvas"),q=C.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(l)}l=$(l);l.get(0).width=Math.ceil(b*k);l.get(0).height=c.height_px;var z=l.get(0).getContext("2d"),n=false,B=c.prefs.min_value,v=c.prefs.max_value,A=c.vertical_range,m=c.total_frequency,u=c.height_px,s=c.mode;var r=Math.round(u+B/A*u);z.beginPath();z.moveTo(0,r);z.lineTo(b*k,r);z.fillStyle="#aaa";z.stroke();z.beginPath();z.fillStyle=c.prefs.color;var p,w,x;if(q.length>1){x=Math.ceil((q[1][0]-q[0][0])*k)}else{x=10}for(var o=0,t=q.length;o<t;o++){p=Math.round((q[o][0]-f)*k);w=q[o][1];if(w===null){if(n&&s==="Filled"){z.lineTo(p,u)}n=false;continue}if(w<B){w=B}else{if(w>v){w=v}}if(s==="Histogram"){w=Math.round(w/A*u);z.fillRect(p,r,x,-w)}else{if(s==="Intensity"){w=255-Math.floor((w-B)/A*255);z.fillStyle="rgb("+w+","+w+","+w+")";z.fillRect(p,0,x,u)}else{w=Math.round(u-(w-B)/A*u);if(n){z.lineTo(p,w)}else{n=true;if(s==="Filled"){z.moveTo(p,u);z.lineTo(p,w)}else{z.moveTo(p,w)}}}}}if(s==="Filled"){if(n){z.lineTo(p,r);z.lineTo(0,r)}z.fill()}else{z.stroke()}h(l)})}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2],s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[5],z=x[6],E=x[7],e=x[8];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O-1);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(z,E,l,n,j,d,p){var v=this;if(v.view.reference_track&&n>CHAR_WIDTH_PX&&d===undefined){return v.view.reference_track.tile_data(z,E,{},function(f){v.draw_tile(z,E,l,n,j,f)})}var G=E*DENSITY*z,a=(E+1)*DENSITY*z,s=a-G,H={hda_ldda:v.hda_ldda,dataset_id:v.dataset_id,resolution:this.view.resolution,mode:this.mode};if(p===undefined){var q=this.data_cache.get_data(G,a,this.mode),J=z+"_"+E+"_"+this.mode;if(q===undefined){return v.tile_data(z,E,H,function(f){v.data_cache.set_data(G,a,this.mode,f);v.draw_tile(z,E,l,n,j,d,f)},J)}p=q}var x=Math.ceil(s*n),u=this.mode,K=25,g=this.left_offset,r,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(u==="Auto"){if(p.dataset_type==="summary_tree"){u=p.dataset_type}else{if(p.extra_info==="no_detail"){u="no_detail"}else{var I=p.data;if((I.length&&I.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){u="Squish"}else{u="Pack"}}}}var A=this.get_y_scale(u);if(u==="summary_tree"){h=this.summary_draw_height}if(u==="Dense"){h=K}else{if(u==="no_detail"||u==="Squish"||u==="Pack"){h=this.incremental_slots(n,p.data,u)*A+K;r=this.inc_slots[n]}}c.get(0).width=x+g;c.get(0).height=h;if(p.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}l.parent().css("height",Math.max(this.height_px,h)+"px");var y=c.get(0).getContext("2d");y.fillStyle=this.prefs.block_color;y.font=this.default_font;y.textAlign="right";this.container_div.find(".yaxislabel").remove();if(u==="summary_tree"){this.draw_summary_tree(c,p.data,p.delta,p.max,n,h,G,g);return j(c)}if(p.message){c.css({"border-top":"1px solid red"});y.fillStyle="red";y.textAlign="left";var t=y.textBaseline;y.textBaseline="top";y.fillText(p.message,g,0);y.textBaseline=t;if(!p.data){return j(c)}}this.example_feature=(p.data.length?p.data[0]:undefined);var I=p.data;for(var B=0,D=I.length;B<D;B++){var k=I[B],m=k[0],w=k[1],b=k[2],e=(r&&r[m]!==undefined?r[m]:null);var C=false;var o;for(var F=0;F<this.filters.length;F++){o=this.filters[F];o.update_attrs(k);if(!o.keep(k)){C=true;break}}if(C){continue}if(is_overlap([w,b],[G,a])&&(u=="Dense"||e!==null)){this.draw_element(y,E,u,k,e,G,a,n,A,x,g,d)}}j(c)}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.difference_mode=true;this.show_insertions=false;this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.round(J/2)}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.difference_mode&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file --- a/templates/tracks/browser.mako Thu Mar 10 16:11:49 2011 -0500 +++ b/templates/tracks/browser.mako Thu Mar 10 16:42:34 2011 -0500 @@ -10,29 +10,29 @@ </%def><%def name="stylesheets()"> -${parent.stylesheets()} + ${parent.stylesheets()} -${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom" )} + ${h.css( "history", "autocomplete_tagging", "trackster", "overcast/jquery-ui-1.8.5.custom" )} -<style type="text/css"> - #browser-container { - overflow: none; - } - .nav-container { - width: 100%; - ## Overriding styles from trackster.css to push nav up into title bar - height: 0; - text-align: center; - } - .nav { - ## Overriding styles from trackster.css to push nav up into title bar - position: relative; - display: inline-block; - top: -2em; - background: transparent; - border: none; - } -</style> + <style type="text/css"> + #browser-container { + overflow: none; + } + .nav-container { + width: 100%; + ## Overriding styles from trackster.css to push nav up into title bar + height: 0; + text-align: center; + } + .nav { + ## Overriding styles from trackster.css to push nav up into title bar + position: relative; + display: inline-block; + top: -2em; + background: transparent; + border: none; + } + </style></%def><%def name="center_panel()"> --- a/templates/visualization/display.mako Thu Mar 10 16:11:49 2011 -0500 +++ b/templates/visualization/display.mako Thu Mar 10 16:42:34 2011 -0500 @@ -8,17 +8,39 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]--> - ${h.js( "jquery.event.drag", "jquery.autocomplete", "trackster" )} + ${h.js( "jquery.event.drag", "jquery.autocomplete", "jquery.mousewheel", "jquery.autocomplete", "trackster", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic" )} </%def><%def name="stylesheets()"> ${parent.stylesheets()} - + + ## For page: <style type="text/css"> .page-body { padding: 0px; } + </style> + ## For visualization (TODO: copied from browser.mako): + ${h.css( "trackster", "overcast/jquery-ui-1.8.5.custom" )} + <style type="text/css"> + #browser-container { + overflow: none; + } + .nav-container { + width: 100%; + ## Overriding styles from trackster.css to push nav up into title bar + height: 0; + text-align: center; + } + .nav { + ## Overriding styles from trackster.css to push nav up into title bar + position: relative; + display: inline-block; + top: -2em; + background: transparent; + border: none; + } </style></%def> @@ -34,10 +56,19 @@ <div id="${visualization.id}" class="unified-panel-body" style="overflow:none;top:0px;"></div><script type="text/javascript"> - - var data_url = "${h.url_for( controller='/tracks', action='data' )}", + // TODO: much of this code is copied from browser.mako -- create shared base and use in both places. + + // + // Place URLs here so that url_for can be used to generate them. + // + var default_data_url = "${h.url_for( controller='/tracks', action='data' )}", + raw_data_url = "${h.url_for( controller='/tracks', action='raw_data' )}", + run_tool_url = "${h.url_for( controller='/tracks', action='run_tool' )}", reference_url = "${h.url_for( controller='/tracks', action='reference' )}", chrom_url = "${h.url_for( controller='/tracks', action='chroms' )}", + dataset_state_url = "${h.url_for( controller='/tracks', action='dataset_state' )}", + converted_datasets_state_url = "${h.url_for( controller='/tracks', action='converted_datasets_state' )}", + addable_track_types = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack }, view, container_element = $("#${visualization.id}"); @@ -48,12 +79,60 @@ } else { // Viewing just one shared viz $("#right-border").live("click", function() { view.resize_window(); }); } - view = new View( container_element, "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}" ); - %for track in config.get('tracks'): - view.add_track( - new ${track["track_type"]}( "${track['name'] | h}", view, ${track['dataset_id']}, ${track['prefs']} ) - ); - %endfor + + // Create view and add tracks. + var callback; + %if 'viewport' in config: + var callback = function() { view.change_chrom( '${config['viewport']['chrom']}', ${config['viewport']['start']}, ${config['viewport']['end']} ); } + %endif + view = new View(container_element, "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}", callback); + ## A little ugly and redundant, but it gets the job done moving the config from python to JS: + var tracks_config = JSON.parse('${ h.to_json_string( config.get('tracks') ) }'); + var track_config, track, parent_track, parent_obj; + for (var i = 0; i < tracks_config.length; i++) { + track_config = tracks_config[i]; + track = new addable_track_types[track_config["track_type"]]( + track_config['name'], + view, + track_config['hda_ldda'], + track_config['dataset_id'], + track_config['prefs'], + track_config['filters'], + track_config['tool'], + (track_config.is_child ? parent_track : undefined)); + parent_obj = view; + if (track_config.is_child) { + parent_obj = parent_track; + } + else { + // New parent track is this track. + parent_track = track; + } + parent_obj.add_track(track); + } + + // + // Keyboard navigation. Scroll ~7% of height when scrolling up/down. + // + $(document).keydown(function(e) { + // Key codes: left == 37, up == 38, right == 39, down == 40 + switch(e.which) { + case 37: + view.move_fraction(0.25); + break + case 38: + var change = Math.round(view.viewport_container.height()/15.0); + view.viewport_container.scrollTo('-=' + change + 'px'); + break; + case 39: + view.move_fraction(-0.25); + break; + case 40: + var change = Math.round(view.viewport_container.height()/15.0); + view.viewport_container.scrollTo('+=' + change + 'px'); + break; + } + }); }); </script> 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 10 Mar '11

10 Mar '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d69e36d1d2f6/ changeset: r5210:d69e36d1d2f6 user: kanwei date: 2011-03-10 22:09:03 summary: Make workflow run_complete.mako modern affected #: 1 file (621 bytes) --- a/templates/workflow/run_complete.mako Thu Mar 10 15:48:00 2011 -0500 +++ b/templates/workflow/run_complete.mako Thu Mar 10 16:09:03 2011 -0500 @@ -1,38 +1,20 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> -<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<%inherit file="/base.mako"/> -<head> -<link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> -<script> -if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history' ) }"; -} -</script> -</head> - -<body> - <div class="donemessage"> - <p> - Successfully ran workflow "${workflow.name}", the following datasets have - been added to the queue. - %if new_history: - These datasets will appear in a new history: - <a target='galaxy_history' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(new_history.id), use_panels=False, show_deleted=False )}"> - '${h.to_unicode(new_history.name)}'. - </a> - %endif - </p> - <div style="padding-left: 10px;"> - %for step_outputs in outputs.itervalues(): - %for data in step_outputs.itervalues(): - %if not new_history or data.history == new_history: - <p><b>${data.hid}</b>: ${data.name}</p> - %endif - %endfor +<div class="donemessagelarge"> + Successfully ran workflow "${workflow.name}". The following datasets have been added to the queue: + %if new_history: + These datasets will appear in a new history: + <a target='galaxy_history' href="${h.url_for( controller='history', action='list', operation="Switch", id=trans.security.encode_id(new_history.id), use_panels=False, show_deleted=False )}"> + '${h.to_unicode(new_history.name)}'. + </a> + %endif + <div style="padding-left: 10px;"> + %for step_outputs in outputs.itervalues(): + %for data in step_outputs.itervalues(): + %if not new_history or data.history == new_history: + <p><strong>${data.hid}</strong>: ${data.name}</p> + %endif %endfor - </div> + %endfor </div> -</body> - -</html> +</div> \ No newline at end of file http://bitbucket.org/galaxy/galaxy-central/changeset/394e58a5e63c/ changeset: r5211:394e58a5e63c user: kanwei date: 2011-03-10 22:11:49 summary: merge affected #: 0 files (0 bytes) --- a/tool-data/shared/ucsc/manual_builds.txt Thu Mar 10 16:09:03 2011 -0500 +++ b/tool-data/shared/ucsc/manual_builds.txt Thu Mar 10 16:11:49 2011 -0500 @@ -696,3 +696,5 @@ Spur_v2.6 Purple Sea Urchin (Strongylocentrotus purpuratus) v2.6 Ptrichocarpa_156 Poplar (Populus trichocarpa) Hydra_JCVI Hydra magnipapillata str. 105 +Araly1 Arabidopsis lyrata +Zea_mays_B73_RefGen_v2 Maize (Zea mays) chr1=301354135,chr2=237068928,chr3=232140222,chr4=241473566,chr5=217872898,chr6=169174371,chr7=176764813,chr8=175793772,chr9=156750718,chr10=150189513,chr11=7140224 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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