[galaxy-commits] commit/galaxy-central: jgoecks: UI framework enhancements: (a) upgrade to jQuery UI 1.9.1; (b) remove version information from jQuery UI file names; (c) add generic jQueryUI search+select combobox widget; (d) use combobox widget for choosing dbkey in Trackster visualizations. Also pack scripts.

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/394c3bd89926/ changeset: 394c3bd89926 user: jgoecks date: 2012-10-30 14:07:29 summary: UI framework enhancements: (a) upgrade to jQuery UI 1.9.1; (b)= remove version information from jQuery UI file names; (c) add generic jQue= ryUI search+select combobox widget; (d) use combobox widget for choosing db= key in Trackster visualizations. Also pack scripts. affected #: 27 files

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/june_2007_style/blue/jquery-ui/smoothness/images/u= i-bg_glass_55_fbf9ee_1x400.png Binary file static/june_2007_style/blue/jquery-ui/smoothness/images/ui-bg_g= lass_55_fbf9ee_1x400.png has changed

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/june_2007_style/blue/jquery-ui/smoothness/images/u= i-icons_2e83ff_256x240.png Binary file static/june_2007_style/blue/jquery-ui/smoothness/images/ui-icon= s_2e83ff_256x240.png has changed

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/june_2007_style/blue/jquery-ui/smoothness/jquery-u= i-1.8.23.custom.css --- a/static/june_2007_style/blue/jquery-ui/smoothness/jquery-ui-1.8.23.cus= tom.css +++ /dev/null @@ -1,363 +0,0 @@ -/*! - * jQuery UI CSS Framework 1.8.23 - * - * Copyright 2012, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Theming/API - */ - -/* Layout helpers -----------------------------------*/ -.ui-helper-hidden { display: none; } -.ui-helper-hidden-accessible { position: absolute !important; clip: rect(1= px 1px 1px 1px); clip: rect(1px,1px,1px,1px); } -.ui-helper-reset { margin: 0; padding: 0; border: 0; outline: 0; line-heig= ht: 1.3; text-decoration: none; font-size: 100%; list-style: none; } -.ui-helper-clearfix:before, .ui-helper-clearfix:after { content: ""; displ= ay: table; } -.ui-helper-clearfix:after { clear: both; } -.ui-helper-clearfix { zoom: 1; } -.ui-helper-zfix { width: 100%; height: 100%; top: 0; left: 0; position: ab= solute; opacity: 0; filter:Alpha(Opacity=3D0); } - - -/* Interaction Cues -----------------------------------*/ -.ui-state-disabled { cursor: default !important; } - - -/* Icons -----------------------------------*/ - -/* states and images */ -.ui-icon { display: block; text-indent: -99999px; overflow: hidden; backgr= ound-repeat: no-repeat; } - - -/* Misc visuals -----------------------------------*/ - -/* Overlays */ -.ui-widget-overlay { position: absolute; top: 0; left: 0; width: 100%; hei= ght: 100%; } - - -/*! - * jQuery UI CSS Framework 1.8.23 - * - * Copyright 2012, AUTHORS.txt (http://jqueryui.com/about) - * Dual licensed under the MIT or GPL Version 2 licenses. - * http://jquery.org/license - * - * http://docs.jquery.com/UI/Theming/API - * - * To view and modify this theme, visit http://jqueryui.com/themeroller/?f= fDefault=3DVerdana,Arial,sans-serif&fwDefault=3Dnormal&fsDefault=3D1.1em&co= rnerRadius=3D4px&bgColorHeader=3Dcccccc&bgTextureHeader=3D03_highlight_soft= .png&bgImgOpacityHeader=3D75&borderColorHeader=3Daaaaaa&fcHeader=3D222222&i= conColorHeader=3D222222&bgColorContent=3Dffffff&bgTextureContent=3D01_flat.= png&bgImgOpacityContent=3D75&borderColorContent=3Daaaaaa&fcContent=3D222222= &iconColorContent=3D222222&bgColorDefault=3De6e6e6&bgTextureDefault=3D02_gl= ass.png&bgImgOpacityDefault=3D75&borderColorDefault=3Dd3d3d3&fcDefault=3D55= 5555&iconColorDefault=3D888888&bgColorHover=3Ddadada&bgTextureHover=3D02_gl= ass.png&bgImgOpacityHover=3D75&borderColorHover=3D999999&fcHover=3D212121&i= conColorHover=3D454545&bgColorActive=3Dffffff&bgTextureActive=3D02_glass.pn= g&bgImgOpacityActive=3D65&borderColorActive=3Daaaaaa&fcActive=3D212121&icon= ColorActive=3D454545&bgColorHighlight=3Dfbf9ee&bgTextureHighlight=3D02_glas= s.png&bgImgOpacityHighlight=3D55&borderColorHighlight=3Dfcefa1&fcHighlight= =3D363636&iconColorHighlight=3D2e83ff&bgColorError=3Dfef1ec&bgTextureError= =3D02_glass.png&bgImgOpacityError=3D95&borderColorError=3Dcd0a0a&fcError=3D= cd0a0a&iconColorError=3Dcd0a0a&bgColorOverlay=3Daaaaaa&bgTextureOverlay=3D0= 1_flat.png&bgImgOpacityOverlay=3D0&opacityOverlay=3D30&bgColorShadow=3Daaaa= aa&bgTextureShadow=3D01_flat.png&bgImgOpacityShadow=3D0&opacityShadow=3D30&= thicknessShadow=3D8px&offsetTopShadow=3D-8px&offsetLeftShadow=3D-8px&corner= RadiusShadow=3D8px - */ - - -/* Component containers -----------------------------------*/ -.ui-widget { font-family: Verdana,Arial,sans-serif; 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diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/libs/jquery/jquery-ui-combobox.js --- /dev/null +++ b/static/scripts/libs/jquery/jquery-ui-combobox.js @@ -0,0 +1,142 @@ +/** + * A generic search + select combobox based on jQueryUI button and autocom= plete. + * Code is derived from http://jqueryui.com/autocomplete/ + *=20 + * Options: + * appendTo - element to attach autocomplete options to; default is <body> + * size - text input's size; default is 20 + */ + +(function( $ ) { + $.widget( "ui.combobox", { + _create: function() { + var input, + that =3D this, + select =3D this.element.hide(), + selected =3D select.children( ":selected" ), + value =3D selected.val() ? selected.text() : "", + wrapper =3D this.wrapper =3D $( "<span>" ) + .addClass( "ui-combobox" ) + .insertAfter( select ); + + function removeIfInvalid(element) { + var value =3D $( element ).val(), + matcher =3D new RegExp( "^" + $.ui.autocomplete.escape= Regex( value ) + "$", "i" ), + valid =3D false; + select.children( "option" ).each(function() { + if ( $( this ).text().match( matcher ) ) { + this.selected =3D valid =3D true; + return false; + } + }); + if ( !valid ) { + // remove invalid value, as it didn't match anything + $( element ) + .val( "" ) + .attr( "title", value + " didn't match any item" ) + .tooltip( "open" ); + select.val( "" ); + setTimeout(function() { + input.tooltip( "close" ).attr( "title", "" ); + }, 2500 ); + input.data( "autocomplete" ).term =3D ""; + return false; + } + } + + var size =3D ( this.options.size ? this.options.size : 20 ); + input =3D $( "<input>" ) + .appendTo( wrapper ) + .val( value ) + .click( function() { + this.select(); + }) + .attr( "title", "" ) + .attr( "size", size ) + .addClass( "ui-state-default ui-combobox-input" ) + .autocomplete({ + appendTo: this.options.appendTo, + delay: 0, + minLength: 0, + source: function( request, response ) { + var matcher =3D new RegExp( $.ui.autocomplete.esca= peRegex(request.term), "i" ); + response( select.children( "option" ).map(function= () { + var text =3D $( this ).text(); + if ( this.value && ( !request.term || matcher.= test(text) ) ) + return { + label: text.replace( + new RegExp( + "(?![^&;]+;)(?!<[^<>]*)(" + + $.ui.autocomplete.escapeRegex(= request.term) + + ")(?![^<>]*>)(?![^&;]+;)", "gi" + ), "<strong>$1</strong>" ), + value: text, + option: this + }; + }) ); + }, + select: function( event, ui ) { + ui.item.option.selected =3D true; + that._trigger( "selected", event, { + item: ui.item.option + }); + }, + change: function( event, ui ) { + if ( !ui.item ) + return removeIfInvalid( this ); + } + }) + .addClass( "ui-widget ui-widget-content ui-corner-left" ); + + input.data( "autocomplete" )._renderItem =3D function( ul, ite= m ) { + return $( "<li>" ) + .data( "item.autocomplete", item ) + .append( "<a>" + item.label + "</a>" ) + .appendTo( ul ); + }; + + $( "<a>" ) + .attr( "tabIndex", -1 ) + .attr( "title", "Show All Items" ) + .tooltip() + .appendTo( wrapper ) + .button({ + icons: { + primary: "ui-icon-triangle-1-s" + }, + text: false + }) + .removeClass( "ui-corner-all" ) + .addClass( "ui-corner-right ui-combobox-toggle" ) + .click(function() { + // close if already visible + if ( input.autocomplete( "widget" ).is( ":visible" ) )= { + input.autocomplete( "close" ); + removeIfInvalid( input ); + return; + } + + // work around a bug (likely same cause as #5265) + $( this ).blur(); + + // pass empty string as value to search for, displayin= g all results + input.autocomplete( "search", "" ); + input.focus(); + }); + + input + .tooltip({ + position: { + of: this.button + }, + tooltipClass: "ui-state-highlight" + }); + }, + + destroy: function() { + this.wrapper.remove(); + this.element.show(); + $.Widget.prototype.destroy.call( this ); + } + }); +})( jQuery ); \ No newline at end of file

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diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=3DBackbone.Model.extend({defaults:{title:"",icon_class:"",o= n_click:null,tooltip_config:{},isMenuButton:true,id:null,href:null,target:n= ull,enabled:true,visible:true}});var IconButtonView=3DBackbone.View.extend(= {initialize:function(){this.model.attributes.tooltip_config=3D{placement:"b= ottom"};this.model.bind("change",this.render,this)},render:function(){this.= $el.tooltip("hide");var a=3D$(Handlebars.partials.iconButton(this.model.toJ= SON()));a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a)= ;this.setElement(a);return this},events:{click:"click"},click:function(a){i= f(this.model.attributes.on_click){this.model.attributes.on_click(a);return = false}return true}});IconButtonView.templates=3D{iconButton:Handlebars.part= ials.iconButton};var IconButtonCollection=3DBackbone.Collection.extend({mod= el:IconButton});var IconButtonMenuView=3DBackbone.View.extend({tagName:"div= ",initialize:function(){this.render()},render:function(){var a=3Dthis;this.= collection.each(function(c){var b=3D$("<a/>").attr("href","javascript:void(= 0)").attr("title",c.attributes.title).addClass("icon-button menu-button").a= ddClass(c.attributes.icon_class).appendTo(a.$el).click(c.attributes.on_clic= k);if(c.attributes.tooltip_config){b.tooltip(c.attributes.tooltip_config)}}= );return this}});var create_icon_buttons_menu=3Dfunction(b,a){if(!a){a=3D{}= }var c=3Dnew IconButtonCollection(_.map(b,function(d){return new IconButton= (_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid= =3DBackbone.Collection.extend({});var GridView=3DBackbone.View.extend({});v= ar GalaxyPaths=3DBackbone.Model.extend({defaults:{root_path:"",image_path:"= "}}); \ No newline at end of file +var IconButton=3DBackbone.Model.extend({defaults:{title:"",icon_class:"",o= n_click:null,menu_options:null,tooltip_config:{},isMenuButton:true,id:null,= href:null,target:null,enabled:true,visible:true}});var IconButtonView=3DBac= kbone.View.extend({initialize:function(){this.model.attributes.tooltip_conf= ig=3D{placement:"bottom"};this.model.bind("change",this.render,this)},rende= r:function(){this.$el.tooltip("hide");var a=3D$(Handlebars.partials.iconBut= ton(this.model.toJSON()));a.tooltip(this.model.get("tooltip_config"));this.= $el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},c= lick:function(a){if(this.model.attributes.on_click){this.model.attributes.o= n_click(a);return false}return true}});IconButtonView.templates=3D{iconButt= on:Handlebars.partials.iconButton};var IconButtonCollection=3DBackbone.Coll= ection.extend({model:IconButton});var IconButtonMenuView=3DBackbone.View.ex= tend({tagName:"div",initialize:function(){this.render()},render:function(){= var a=3Dthis;this.collection.each(function(d){var b=3D$("<a/>").attr("href"= ,"javascript:void(0)").attr("title",d.attributes.title).addClass("icon-butt= on menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.= attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes= .tooltip_config)}var c=3Dd.get("options");if(c){make_popupmenu(b,c)}});retu= rn this}});var create_icon_buttons_menu=3Dfunction(b,a){if(!a){a=3D{}}var c= =3Dnew IconButtonCollection(_.map(b,function(d){return new IconButton(_.ext= end(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=3DBack= bone.Collection.extend({});var GridView=3DBackbone.View.extend({});var Gala= xyPaths=3DBackbone.Model.extend({defaults:{root_path:"",image_path:""}}); \ No newline at end of file

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -define(["libs/underscore","libs/d3","viz/visualization"],function(g,j,h){v= ar k=3DBackbone.Model.extend({is_visible:function(o,l){var m=3Do.getBoundin= gClientRect(),n=3D$("svg")[0].getBoundingClientRect();if(m.right<0||m.left>= n.right||m.bottom<0||m.top>n.bottom){return false}return true}});var c=3DBa= ckbone.Model.extend({defaults:{prefs:{color:"#ccc"}}});var a=3DBackbone.Vie= w.extend({className:"circster",initialize:function(l){this.total_gap=3Dl.to= tal_gap;this.genome=3Dl.genome;this.dataset_arc_height=3Dl.dataset_arc_heig= ht;this.track_gap=3D5;this.label_arc_height=3D20;this.scale=3D1;this.track_= views=3Dnull;this.model.get("tracks").on("add",this.add_track,this);this.mo= del.get("tracks").on("remove",this.remove_track,this)},get_tracks_bounds:fu= nction(){var n=3Dthis.dataset_arc_height,l=3DMath.min(this.$el.width(),this= .$el.height()),p=3Dl/2-this.model.get("tracks").length*(this.dataset_arc_he= ight+this.track_gap)-(this.label_arc_height+this.track_gap),o=3Dj.range(p,l= /2,this.dataset_arc_height+this.track_gap);var m=3Dthis;return g.map(o,func= tion(q){return[q,q+m.dataset_arc_height]})},render:function(){var o=3Dthis,= q=3Dthis.dataset_arc_height,r=3Do.$el.width(),l=3Do.$el.height(),p=3Dthis.m= odel.get("tracks"),s=3Dthis.get_tracks_bounds(),n=3Dj.select(o.$el[0]).appe= nd("svg").attr("width",r).attr("height",l).attr("pointer-events","all").app= end("svg:g").call(j.behavior.zoom().on("zoom",function(){var t=3Dj.event.sc= ale;n.attr("transform","translate("+j.event.translate+") scale("+t+")");if(= o.scale!=3D=3Dt){if(o.zoom_drag_timeout){clearTimeout(o.zoom_drag_timeout)}= o.zoom_drag_timeout=3DsetTimeout(function(){g.each(o.track_views,function(u= ){u.update_scale(t)})},400)}})).attr("transform","translate("+r/2+","+l/2+"= )").append("svg:g").attr("class","tracks");this.track_views=3Dp.map(functio= n(t,u){track_view_class=3D(t.get("track_type")=3D=3D=3D"LineTrack"?d:e);ret= urn new track_view_class({el:n.append("g")[0],track:t,radius_bounds:s[u],ge= nome:o.genome,total_gap:o.total_gap})});g.each(this.track_views,function(t)= {t.render()});var m=3Ds[p.length];m[1]=3Dm[0];this.label_track_view=3Dnew b= ({el:n.append("g")[0],track:new c(),radius_bounds:m,genome:o.genome,total_g= ap:o.total_gap});this.label_track_view.render()},add_track:function(p){var = o=3Dthis.get_tracks_bounds();g.each(this.track_views,function(r,s){r.update= _radius_bounds(o[s])});var n=3Dthis.track_views.length,q=3D(p.get("track_ty= pe")=3D=3D=3D"LineTrack"?d:e),l=3Dnew q({el:j.select("g.tracks").append("g"= )[0],track:p,radius_bounds:o[n],genome:this.genome,total_gap:this.total_gap= });l.render();this.track_views.push(l);var m=3Do[o.length-1];m[1]=3Dm[0];th= is.label_track_view.update_radius_bounds(m)},remove_track:function(m,o,n){v= ar l=3Dthis.track_views[n.index];this.track_views.splice(n.index,1);l.$el.r= emove();var p=3Dthis.get_tracks_bounds();g.each(this.track_views,function(q= ,r){q.update_radius_bounds(p[r])})}});var i=3DBackbone.View.extend({tagName= :"g",initialize:function(l){this.bg_stroke=3D"ccc";this.loading_bg_fill=3D"= 000";this.bg_fill=3D"ccc";this.total_gap=3Dl.total_gap;this.track=3Dl.track= ;this.radius_bounds=3Dl.radius_bounds;this.genome=3Dl.genome;this.chroms_la= yout=3Dthis._chroms_layout();this.data_bounds=3D[];this.scale=3D1;this.pare= nt_elt=3Dj.select(this.$el[0])},render:function(){var p=3Dthis.parent_elt;i= f(!p){console.log("no parent elt")}var o=3Dthis.chroms_layout,r=3Dj.svg.arc= ().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),l= =3Dp.selectAll("g").data(o).enter().append("svg:g"),n=3Dl.append("path").at= tr("d",r).attr("class","chrom-background").style("stroke",this.bg_stroke).s= tyle("fill",this.loading_bg_fill);n.append("title").text(function(t){return= t.data.chrom});var m=3Dthis,q=3Dm.track.get("data_manager"),s=3D(q?q.data_= is_ready():true);$.when(s).then(function(){$.when(m._render_data(p)).then(f= unction(){n.style("fill",m.bg_fill)})})},update_radius_bounds:function(m){t= his.radius_bounds=3Dm;var l=3Dj.svg.arc().innerRadius(this.radius_bounds[0]= ).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chro= m-background").transition().duration(1000).attr("d",l);this._transition_chr= om_data()},update_scale:function(o){var n=3Dthis.scale;this.scale=3Do;if(o<= =3Dn){return}var m=3Dthis,l=3Dnew k();this.parent_elt.selectAll("path.chrom= -data").filter(function(q,p){return l.is_visible(this)}).each(function(v,r)= {var u=3Dj.select(this),q=3Du.attr("chrom"),t=3Dm.genome.get_chrom_region(q= ),s=3Dm.track.get("data_manager"),p;if(!s.can_get_more_detailed_data(t)){re= turn}p=3Dm.track.get("data_manager").get_more_detailed_data(t,"Coverage",0,= o);$.when(p).then(function(z){u.remove();m._update_data_bounds();var y=3Dg.= find(m.chroms_layout,function(A){return A.data.chrom=3D=3D=3Dq});var w=3Dm.= track.get("prefs"),x=3Dw.block_color;if(!x){x=3Dw.color}m._render_chrom_dat= a(m.parent_elt,y,z).style("stroke",x).style("fill",x)})});return m},_transi= tion_chrom_data:function(){var m=3Dthis.track,o=3Dthis.chroms_layout,l=3Dth= is.parent_elt.selectAll("g>path.chrom-data"),p=3Dl[0].length;if(p>0){var n= =3Dthis;$.when(m.get("data_manager").get_genome_wide_data(this.genome)).the= n(function(r){var q=3Dg.reject(g.map(r,function(s,t){var u=3Dnull,v=3Dn._ge= t_path_function(o[t],s);if(v){u=3Dv(s.data)}return u}),function(s){return s= =3D=3D=3Dnull});l.each(function(t,s){j.select(this).transition().duration(1= 000).attr("d",q[s])})})}},_update_data_bounds:function(){var l=3Dthis.data_= bounds;this.data_bounds=3Dthis.get_data_bounds(this.track.get("data_manager= ").get_genome_wide_data(this.genome));if(this.data_bounds[0]<l[0]||this.dat= a_bounds[1]>l[1]){this._transition_chrom_data()}},_render_data:function(o){= var n=3Dthis,m=3Dthis.chroms_layout,l=3Dthis.track,p=3D$.Deferred();$.when(= l.get("data_manager").get_genome_wide_data(this.genome)).then(function(s){n= .data_bounds=3Dn.get_data_bounds(s);layout_and_data=3Dg.zip(m,s),chroms_dat= a_layout=3Dg.map(layout_and_data,function(t){var u=3Dt[0],v=3Dt[1];return n= ._render_chrom_data(o,u,v)});var q=3Dl.get("config"),r=3Dq.get_value("block= _color");if(!r){r=3Dq.get_value("color")}n.parent_elt.selectAll("path.chrom= -data").style("stroke",r).style("fill",r);p.resolve(o)});return p},_render_= chrom_data:function(l,m,n){},_get_path_function:function(m,l){},_chroms_lay= out:function(){var m=3Dthis.genome.get_chroms_info(),o=3Dj.layout.pie().val= ue(function(q){return q.len}).sort(null),p=3Do(m),l=3Dthis.total_gap/m.leng= th,n=3Dg.map(p,function(s,r){var q=3Ds.endAngle-l;s.endAngle=3D(q>s.startAn= gle?q:s.startAngle);return s});return n}});var b=3Di.extend({initialize:fun= ction(l){i.prototype.initialize.call(this,l);this.bg_stroke=3D"fff";this.bg= _fill=3D"fff"},_render_data:function(m){var l=3Dm.selectAll("g");l.selectAl= l("path").attr("id",function(n){return"label-"+n.data.chrom});l.append("svg= :text").filter(function(n){return n.endAngle-n.startAngle>0.08}).attr("text= -anchor","middle").append("svg:textPath").attr("xlink:href",function(n){ret= urn"#label-"+n.data.chrom}).attr("startOffset","25%").text(function(n){retu= rn n.data.chrom})}});var f=3Di.extend({_render_chrom_data:function(l,o,m){v= ar p=3Dthis._get_path_function(o,m);if(!p){return null}var n=3Dl.datum(m.da= ta),q=3Dn.append("path").attr("class","chrom-data").attr("chrom",o.data.chr= om).attr("d",p);return q},_get_path_function:function(o,n){if(typeof n=3D= =3D=3D"string"||!n.data||n.data.length=3D=3D=3D0){return null}var l=3Dj.sca= le.linear().domain(this.data_bounds).range(this.radius_bounds);var p=3Dj.sc= ale.linear().domain([0,n.data.length]).range([o.startAngle,o.endAngle]);var= m=3Dj.svg.line.radial().interpolate("linear").radius(function(q){return l(= q[1])}).angle(function(r,q){return p(q)});return j.svg.area.radial().interp= olate(m.interpolate()).innerRadius(l(0)).outerRadius(m.radius()).angle(m.an= gle())},get_data_bounds:function(l){}});var e=3Df.extend({get_data_bounds:f= unction(m){var l=3Dg.map(m,function(n){if(typeof n=3D=3D=3D"string"||!n.max= ){return 0}return n.max});return[0,(l&&typeof l!=3D=3D"string"?g.max(l):0)]= }});var d=3Df.extend({get_data_bounds:function(m){var l=3Dg.flatten(g.map(m= ,function(n){if(n){return g.map(n.data,function(o){return o[1]})}else{retur= n 0}}));return[g.min(l),g.max(l)]}});return{CircsterView:a}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/visualization"],function(g,k,h){v= ar l=3DBackbone.Model.extend({is_visible:function(p,m){var n=3Dp.getBoundin= gClientRect(),o=3D$("svg")[0].getBoundingClientRect();if(n.right<0||n.left>= o.right||n.bottom<0||n.top>o.bottom){return false}return true}});var c=3DBa= ckbone.Model.extend({defaults:{prefs:{color:"#ccc"}}});var a=3DBackbone.Vie= w.extend({className:"circster",initialize:function(m){this.total_gap=3Dm.to= tal_gap;this.genome=3Dm.genome;this.dataset_arc_height=3Dm.dataset_arc_heig= ht;this.track_gap=3D5;this.label_arc_height=3D20;this.scale=3D1;this.circul= ar_views=3Dnull;this.chords_views=3Dnull;this.model.get("tracks").on("add",= this.add_track,this);this.model.get("tracks").on("remove",this.remove_track= ,this);this.get_circular_tracks()},get_circular_tracks:function(){return th= is.model.get("tracks").filter(function(m){return m.get("track_type")!=3D=3D= "DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get= ("tracks").filter(function(m){return m.get("track_type")=3D=3D=3D"DiagonalH= eatmapTrack"})},get_tracks_bounds:function(){var n=3Dthis.get_circular_trac= ks();dataset_arc_height=3Dthis.dataset_arc_height,min_dimension=3DMath.min(= this.$el.width(),this.$el.height()),radius_start=3Dmin_dimension/2-n.length= *(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track= _gap),tracks_start_radii=3Dk.range(radius_start,min_dimension/2,this.datase= t_arc_height+this.track_gap);var m=3Dthis;return g.map(tracks_start_radii,f= unction(o){return[o,o+m.dataset_arc_height]})},render:function(){var u=3Dth= is,p=3Dthis.dataset_arc_height,m=3Du.$el.width(),t=3Du.$el.height(),r=3Dthi= s.get_circular_tracks(),o=3Dthis.get_chord_tracks(),q=3Dthis.get_tracks_bou= nds(),n=3Dk.select(u.$el[0]).append("svg").attr("width",m).attr("height",t)= .attr("pointer-events","all").append("svg:g").call(k.behavior.zoom().on("zo= om",function(){var v=3Dk.event.scale;n.attr("transform","translate("+k.even= t.translate+") scale("+v+")");if(u.scale!=3D=3Dv){if(u.zoom_drag_timeout){c= learTimeout(u.zoom_drag_timeout)}u.zoom_drag_timeout=3DsetTimeout(function(= ){g.each(u.circular_views,function(w){w.update_scale(v)})},400)}})).attr("t= ransform","translate("+m/2+","+t/2+")").append("svg:g").attr("class","track= s");this.circular_views=3Dr.map(function(w,x){var y=3D(w.get("track_type")= =3D=3D=3D"LineTrack"?d:e),v=3Dnew y({el:n.append("g")[0],track:w,radius_bou= nds:q[x],genome:u.genome,total_gap:u.total_gap});v.render();return v});this= .chords_views=3Do.map(function(w){var v=3Dnew i({el:n.append("g")[0],track:= w,radius_bounds:q[0],genome:u.genome,total_gap:u.total_gap});v.render();ret= urn v});var s=3Dq[r.length];s[1]=3Ds[0];this.label_track_view=3Dnew b({el:n= .append("g")[0],track:new c(),radius_bounds:s,genome:u.genome,total_gap:u.t= otal_gap});this.label_track_view.render()},add_track:function(s){if(s.get("= track_type")=3D=3D=3D"DiagonalHeatmapTrack"){var o=3Dthis.circular_views[0]= .radius_bounds,r=3Dnew i({el:k.select("g.tracks").append("g")[0],track:s,ra= dius_bounds:o,genome:this.genome,total_gap:this.total_gap});r.render();this= .chords_views.push(r)}else{var q=3Dthis.get_tracks_bounds();g.each(this.cir= cular_views,function(u,v){u.update_radius_bounds(q[v])});g.each(this.chords= _views,function(u){u.update_radius_bounds(q[0])});var p=3Dthis.circular_vie= ws.length,t=3D(s.get("track_type")=3D=3D=3D"LineTrack"?d:e),m=3Dnew t({el:k= .select("g.tracks").append("g")[0],track:s,radius_bounds:q[p],genome:this.g= enome,total_gap:this.total_gap});m.render();this.circular_views.push(m);var= n=3Dq[q.length-1];n[1]=3Dn[0];this.label_track_view.update_radius_bounds(n= )}},remove_track:function(n,p,o){var m=3Dthis.circular_views[o.index];this.= circular_views.splice(o.index,1);m.$el.remove();var q=3Dthis.get_tracks_bou= nds();g.each(this.circular_views,function(r,s){r.update_radius_bounds(q[s])= })}});var j=3DBackbone.View.extend({tagName:"g",initialize:function(m){this= .bg_stroke=3D"ccc";this.loading_bg_fill=3D"000";this.bg_fill=3D"ccc";this.t= otal_gap=3Dm.total_gap;this.track=3Dm.track;this.radius_bounds=3Dm.radius_b= ounds;this.genome=3Dm.genome;this.chroms_layout=3Dthis._chroms_layout();thi= s.data_bounds=3D[];this.scale=3D1;this.parent_elt=3Dk.select(this.$el[0])},= get_fill_color:function(){var m=3Dthis.track.get("config").get_value("block= _color");if(!m){m=3Dthis.track.get("config").get_value("color")}return m},r= ender:function(){var q=3Dthis.parent_elt;if(!q){console.log("no parent elt"= )}var p=3Dthis.chroms_layout,s=3Dk.svg.arc().innerRadius(this.radius_bounds= [0]).outerRadius(this.radius_bounds[1]),m=3Dq.selectAll("g").data(p).enter(= ).append("svg:g"),o=3Dm.append("path").attr("d",s).attr("class","chrom-back= ground").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);= o.append("title").text(function(u){return u.data.chrom});var n=3Dthis,r=3Dn= .track.get("data_manager"),t=3D(r?r.data_is_ready():true);$.when(t).then(fu= nction(){$.when(n._render_data(q)).then(function(){o.style("fill",n.bg_fill= )})})},update_radius_bounds:function(n){this.radius_bounds=3Dn;var m=3Dk.sv= g.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1= ]);this.parent_elt.selectAll("g>path.chrom-background").transition().durati= on(1000).attr("d",m);this._transition_chrom_data()},update_scale:function(p= ){var o=3Dthis.scale;this.scale=3Dp;if(p<=3Do){return}var n=3Dthis,m=3Dnew = l();this.parent_elt.selectAll("path.chrom-data").filter(function(r,q){retur= n m.is_visible(this)}).each(function(w,s){var v=3Dk.select(this),r=3Dv.attr= ("chrom"),u=3Dn.genome.get_chrom_region(r),t=3Dn.track.get("data_manager"),= q;if(!t.can_get_more_detailed_data(u)){return}q=3Dn.track.get("data_manager= ").get_more_detailed_data(u,"Coverage",0,p);$.when(q).then(function(z){v.re= move();n._update_data_bounds();var y=3Dg.find(n.chroms_layout,function(A){r= eturn A.data.chrom=3D=3D=3Dr});var x=3Dn.get_fill_color();n._render_chrom_d= ata(n.parent_elt,y,z).style("stroke",x).style("fill",x)})});return n},_tran= sition_chrom_data:function(){var n=3Dthis.track,p=3Dthis.chroms_layout,m=3D= this.parent_elt.selectAll("g>path.chrom-data"),q=3Dm[0].length;if(q>0){var = 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tAll("path.chrom-data").style("stroke",r).style("fill",r);q.resolve(p)});re= turn q},_render_chrom_data:function(m,n,o){},_get_path_function:function(n,= m){},_chroms_layout:function(){var n=3Dthis.genome.get_chroms_info(),p=3Dk.= layout.pie().value(function(r){return r.len}).sort(null),q=3Dp(n),m=3Dthis.= total_gap/n.length,o=3Dg.map(q,function(t,s){var r=3Dt.endAngle-m;t.endAngl= e=3D(r>t.startAngle?r:t.startAngle);return t});return o}});var b=3Dj.extend= ({initialize:function(m){j.prototype.initialize.call(this,m);this.bg_stroke= =3D"fff";this.bg_fill=3D"fff"},_render_data:function(n){var m=3Dn.selectAll= ("g");m.selectAll("path").attr("id",function(o){return"label-"+o.data.chrom= });m.append("svg:text").filter(function(o){return o.endAngle-o.startAngle>0= .08}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href"= ,function(o){return"#label-"+o.data.chrom}).attr("startOffset","25%").text(= function(o){return o.data.chrom})}});var f=3Dj.extend({_render_chrom_data:f= 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[0]))},_get_region_angle:function(o,m){var n=3Dg.find(this.chroms_layout,fu= nction(p){return p.data.chrom=3D=3D=3Do});return n.endAngle-((n.endAngle-n.= startAngle)*(n.data.len-m)/n.data.len)}});return{CircsterView:a}}); \ No newline at end of file

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/scatterplot.js --- a/static/scripts/packed/viz/scatterplot.js +++ b/static/scripts/packed/viz/scatterplot.js @@ -1,1 +1,1 @@ -define(["../libs/underscore","../mvc/base-mvc","../utils/LazyDataLoader","= ../templates/compiled/template-visualization-scatterplotControlForm","../te= mplates/compiled/template-visualization-statsTable","../templates/compiled/= template-visualization-chartSettings","../libs/d3","../libs/bootstrap","../= libs/jquery/jquery-ui-1.8.23.custom.min"],function(){function a(f){var d=3D= 10,h=3D7,g=3D10,e=3D8,c=3D5;this.log=3Dfunction(){if(this.debugging&&consol= e&&console.debug){var i=3DArray.prototype.slice.call(arguments);i.unshift(t= his.toString());console.debug.apply(console,i)}};this.log("new TwoVarScatte= rplot:",f);this.defaults=3D{id:"TwoVarScatterplot",containerSelector:"body"= ,maxDataPoints:30000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTick= s:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:= 50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:nu= ll,yMax:null,xLabel:"X",yLabel:"Y"};this.config=3D_.extend({},this.defaults= ,f);this.updateConfig=3Dfunction(i,j){_.extend(this.config,i)};this.toStrin= g=3Dfunction(){return this.config.id};this.translateStr=3Dfunction(i,j){ret= urn"translate("+i+","+j+")"};this.rotateStr=3Dfunction(j,i,k){return"rotate= ("+j+","+i+","+k+")"};this.svg=3Dd3.select(this.config.containerSelector).a= ppend("svg:svg").attr("class","chart");this.content=3Dthis.svg.append("svg:= g").attr("class","content").attr("id",this.config.id);this.xAxis=3Dthis.con= tent.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel= =3Dthis.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-l= abel");this.yAxis=3Dthis.content.append("g").attr("class","axis").attr("id"= ,"y-axis");this.yAxisLabel=3Dthis.yAxis.append("text").attr("class","axis-l= abel").attr("id","y-axis-label");this.adjustChartDimensions=3Dfunction(l,j,= i,k){l=3Dl||0;j=3Dj||0;i=3Di||0;k=3Dk||0;this.svg.attr("width",this.config.= width+(this.config.marginRight+j)+(this.config.marginLeft+k)).attr("height"= ,this.config.height+(this.config.marginTop+l)+(this.config.marginBottom+i))= .style("display","block");this.content=3Dthis.svg.select("g.content").attr(= "transform",this.translateStr(this.config.marginLeft+k,this.config.marginTo= p+l))};this.preprocessData=3Dfunction(k,j,i){return(k.length>this.config.ma= xDataPoints)?(k.slice(0,this.config.maxDataPoints)):(k)};this.setUpDomains= =3Dfunction(i,k,j){this.xMin=3Dthis.config.xMin||(j)?(j[0].min):(d3.min(i))= ;this.xMax=3Dthis.config.xMax||(j)?(j[0].max):(d3.max(i));this.yMin=3Dthis.= config.yMin||(j)?(j[1].min):(d3.min(k));this.yMax=3Dthis.config.yMax||(j)?(= j[1].max):(d3.max(k))};this.setUpScales=3Dfunction(){this.xScale=3Dd3.scale= .linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.y= Scale=3Dd3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.= height,0])};this.setUpXAxis=3Dfunction(){this.xAxisFn=3Dd3.svg.axis().scale= (this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr= ("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);th= is.xLongestLabel=3Dd3.max(_.map([this.xMin,this.xMax],function(i){return(St= ring(i)).length}));if(this.xLongestLabel>=3Dc){this.xAxis.selectAll("g").fi= lter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",th= is.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor"= ,"middle").text(this.config.xLabel)};this.setUpYAxis=3Dfunction(){this.yAxi= sFn=3Dd3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient(= "left");this.yAxis.call(this.yAxisFn);var i=3Dthis.yAxis.selectAll("text").= filter(function(m,l){return l!=3D=3D0});this.yLongestLabel=3Dd3.max(i[0].ma= p(function(m,l){return(d3.select(m).text()).length}))||0;var j=3Dd+(this.yL= ongestLabel*h)+e+g;this.config.yAxisLabelBumpX=3D-(j-g);if(this.config.marg= inLeft<j){var k=3D(j)-this.config.marginLeft;k=3D(k<0)?(0):(k);this.adjustC= hartDimensions(0,0,0,k)}this.yAxisLabel.attr("x",this.config.yAxisLabelBump= X).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transf= orm",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).= text(this.config.yLabel)};this.renderGrid=3Dfunction(){this.vGridLines=3Dth= is.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisF= n.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-lin= e v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).at= tr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().r= emove();this.hGridLines=3Dthis.content.selectAll("line.h-grid-line").data(t= his.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("= svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",= 0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScal= e);this.hGridLines.exit().remove()};this.glyphEnterState=3Dfunction(i){};th= is.glyphFinalState=3Dfunction(i){};this.glyphExitState=3Dfunction(i){};this= .renderDatapoints=3Dfunction(i,l,j){this.log(this+".renderDatapoints",argum= ents);var k=3D0;this.datapoints=3Dthis.addDatapoints(i,l,j,".glyph");this.d= atapoints.exit().each(function(){k+=3D1}).transition().duration(this.config= .animDuration).attr("cy",this.config.height).attr("r",0).remove();this.log(= k," glyphs removed")};this.addDatapoints=3Dfunction(m,k,i,l){this.log(this+= ".addDatapoints",arguments);var p=3Dthis,o=3D0,q=3Dfunction(s,r){return p.x= Scale(m[r])},j=3Dfunction(s,r){return p.yScale(k[r])};var n=3Dthis.content.= selectAll(l);this.log("existing datapoints:",n);n=3Dn.data(m);o=3D0;n.enter= ().append("svg:circle").each(function(){o+=3D1}).classed("glyph",true).attr= ("cx",q).attr("cy",j).attr("r",0);this.log(o," new glyphs created");o=3D0;n= .transition().duration(this.config.animDuration).each(function(){o+=3D1}).a= ttr("cx",q).attr("cy",j).attr("r",p.config.datapointSize);this.log(o," exis= ting glyphs transitioned");if(i){n.attr("data",function(s,r){return(i[r])})= }n.attr("title",function(s,r){return((i)?(i[r]+": "):(""))+m[r]+", "+k[r]})= ;n.on("mouseover",function(){var r=3Dd3.select(this);r.style("fill","red").= style("fill-opacity",1);p.content.append("line").attr("stroke","red").attr(= "stroke-width",1).attr("x1",r.attr("cx")).attr("y1",r.attr("cy")).attr("x2"= ,0).attr("y2",r.attr("cy")).classed("hoverline",true);p.content.append("lin= e").attr("stroke","red").attr("stroke-width",1).attr("x1",r.attr("cx")).att= r("y1",r.attr("cy")).attr("x2",r.attr("cx")).attr("y2",p.config.height).cla= ssed("hoverline",true)}).on("mouseout",function(){d3.select(this).style("fi= ll","black").style("fill-opacity",0.2);d3.selectAll(".hoverline").remove()}= 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ls:e})}});$(this.loader).bind("error",function(g,e,f){c.log("ERROR:",e,f);a= lert("ERROR fetching data:\n"+e+"\n"+f);c.hideLoadingIndicator()})},render:= function(){var c=3Dthis,d=3D{config:this.chartConfig,allColumns:[],numericC= olumns:[],loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this= .loadingIndicatorImage};_.each(this.dataset.metadata_column_types,function(= g,f){var e=3D"column "+(f+1);if(c.dataset.metadata_column_names){e=3Dc.data= set.metadata_column_names[f]}if(g=3D=3D=3D"int"||g=3D=3D=3D"float"){d.numer= icColumns.push({index:f,name:e})}d.allColumns.push({index:f,name:e})});this= .$el.append(b.templates.form(d));this.$dataSettingsPanel=3Dthis.$el.find(".= tab-pane#data-settings");this.$chartSettingsPanel=3Dthis._render_chartSetti= ngs();this.$statsPanel=3Dthis.$el.find(".tab-pane#chart-stats");return this= },_render_chartSettings:function(){var c=3Dthis,d=3Dthis.$el.find(".tab-pan= e#chart-settings"),e=3D{datapointSize:{min:2,max:10,step:1},width:{min:200,= max:800,step:20},height:{min:200,max:800,step:20}};d.append(b.templates.cha= rtSettings(this.chartConfig));d.find(".numeric-slider-input").each(function= (){var h=3D$(this),g=3Dh.find(".slider-output"),i=3Dh.find(".slider"),j=3Dh= .attr("id");function f(){var l=3D$(this),k=3Dl.slider("value");g.text(k)}i.= slider(_.extend(e[j],{value:c.chartConfig[j],change:f,slide:f}))});return d= },events:{"click #include-id-checkbox":"toggleThirdColumnSelector","click #= data-settings #render-button":"renderPlot","click #chart-settings #render-b= utton":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el= .find('select[name=3D"ID"]').parent().toggle()},showLoadingIndicator:functi= on(d,e){d=3Dd||"";var c=3Dthis.$el.find("div#loading-indicator");messageBox= =3Dc.find(".loading-message");if(c.is(":visible")){if(d){messageBox.fadeOut= ("fast",function(){messageBox.text(d);messageBox.fadeIn("fast",e)})}else{e(= )}}else{if(d){messageBox.text(d)}c.fadeIn("fast",e)}},hideLoadingIndicator:= function(c){this.$el.find("div#loading-indicator").fadeOut("fast",c)},rende= rPlot:function(){var c=3Dthis;c.data=3Dnull;c.meta=3Dnull;_.extend(this.cha= rtConfig,this.getGraphSettings());this.log("this.chartConfig:",this.chartCo= nfig);this.plot.updateConfig(this.chartConfig,false);this.loader.url=3Dthis= .dataURL+"&"+jQuery.param(this.getDataSettings());this.log("this.loader, ur= l:",this.loader.url,"total:",this.loader.total);$(this.loader).bind("loaded= .new",function(e,d){c.log(c+" loaded.new",d);c.postProcessDataFetchResponse= (d);c.log("postprocessed data:",c.data,"meta:",c.meta);c.showLoadingIndicat= or("Rendering...",function(){c.$el.find("ul.nav").find('a[href=3D"#chart-st= ats"]').tab("show");c.plot.render(c.data,c.meta);c.renderStats(c.data,c.met= a);c.hideLoadingIndicator()})});$(this.loader).bind("complete",function(d,e= ){c.log("complete",e);$(c.loader).unbind()});c.showLoadingIndicator("Fetchi= ng data...",function(){c.loader.load()})},renderStats:function(){this.$stat= sPanel.html(b.templates.statsTable({stats:[{name:"Count",xval:this.meta[0].= count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.= meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name= :"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.= meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].media= n,yval:this.meta[1].median}]}))},changeChartSettings:function(){var c=3Dthi= s;newGraphSettings=3Dthis.getGraphSettings();this.log("newGraphSettings:",n= ewGraphSettings);_.extend(this.chartConfig,newGraphSettings);this.log("this= .chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,fa= lse);if(c.data&&c.meta){c.showLoadingIndicator("Rendering...",function(){c.= plot.render(c.data,c.meta);c.hideLoadingIndicator()})}else{this.renderPlot(= )}},postProcessDataFetchResponse:function(c){this.postProcessData(c.data);t= his.postProcessMeta(c.meta)},postProcessData:function(d){var c=3Dthis;if(c.= data){_.each(d,function(f,e){c.data[e]=3Dc.data[e].concat(f)})}else{c.data= =3Dd}},postProcessMeta:function(e){var c=3Dthis,d=3Dthis.dataset.metadata_c= olumn_types;if(c.meta){_.each(e,function(g,f){var k=3Dc.meta[f],i=3Dd[f];c.= log(f+" postprocessing meta:",g);k.count+=3D(g.count)?(g.count):(0);c.log(f= ,"count:",k.count);if((i=3D=3D=3D"int")||(i=3D=3D=3D"float")){k.min=3DMath.= min(g.min,k.min);k.max=3DMath.max(g.max,k.max);k.sum=3Dg.sum+k.sum;k.mean= =3D(k.count)?(k.sum/k.count):(null);var h=3Dc.data[f].slice().sort(),j=3DMa= th.floor(h.length/2);if(h.length%2=3D=3D=3D0){k.median=3D((h[j]+h[(j+1)])/2= )}else{k.median=3Dh[j]}}})}else{c.meta=3De;c.log("initial meta:",c.meta)}},= getDataSettings:function(){var d=3Dthis.getColumnSelections(),c=3D[];this.l= og("columnSelections:",d);c=3D[d.X.colIndex,d.Y.colIndex];if(this.$dataSett= ingsPanel.find("#include-id-checkbox").attr("checked")){c.push(d.ID.colInde= x)}var e=3D{data_type:"raw_data",columns:"["+c+"]"};this.log("params:",e);r= eturn e},getColumnSelections:function(){var c=3D{};this.$dataSettingsPanel.= find("div.column-select select").each(function(){var d=3D$(this),e=3Dd.val(= );c[d.attr("name")]=3D{colIndex:e,colName:d.children('[value=3D"'+e+'"]').t= ext()}});return c},getGraphSettings:function(){var e=3D{},f=3Dthis.getColum= nSelections();e.datapointSize=3Dthis.$chartSettingsPanel.find("#datapointSi= ze.numeric-slider-input").find(".slider").slider("value");e.width=3Dthis.$c= hartSettingsPanel.find("#width.numeric-slider-input").find(".slider").slide= r("value");e.height=3Dthis.$chartSettingsPanel.find("#height.numeric-slider= -input").find(".slider").slider("value");var d=3Dthis.$chartSettingsPanel.f= ind("input#X-axis-label").val(),c=3Dthis.$chartSettingsPanel.find("input#Y-= axis-label").val();e.xLabel=3D(d=3D=3D=3D"X")?(f.X.colName):(d);e.yLabel=3D= (c=3D=3D=3D"Y")?(f.Y.colName):(c);e.animDuration=3D10;if(this.$chartSetting= sPanel.find("#animDuration.checkbox-input").is(":checked")){e.animDuration= =3D500}this.log("graphSettings:",e);return e},toString:function(){return"Sc= atterplotControlForm("+this.dataset.id+")"}});b.templates=3D{form:Handlebar= s.templates["template-visualization-scatterplotControlForm"],statsTable:Han= dlebars.templates["template-visualization-statsTable"],chartSettings:Handle= bars.templates["template-visualization-chartSettings"]};return{LazyDataLoad= er:LazyDataLoader,TwoVarScatterplot:a,ScatterplotControlForm:b}}); \ No newline at end of file +define(["../libs/underscore","../mvc/base-mvc","../utils/LazyDataLoader","= ../templates/compiled/template-visualization-scatterplotControlForm","../te= mplates/compiled/template-visualization-statsTable","../templates/compiled/= template-visualization-chartSettings","../libs/d3","../libs/bootstrap","../= libs/jquery/jquery-ui"],function(){function a(f){var d=3D10,h=3D7,g=3D10,e= =3D8,c=3D5;this.log=3Dfunction(){if(this.debugging&&console&&console.debug)= {var i=3DArray.prototype.slice.call(arguments);i.unshift(this.toString());c= onsole.debug.apply(console,i)}};this.log("new TwoVarScatterplot:",f);this.d= efaults=3D{id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30= 000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBu= mpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50= ,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLab= el:"X",yLabel:"Y"};this.config=3D_.extend({},this.defaults,f);this.updateCo= nfig=3Dfunction(i,j){_.extend(this.config,i)};this.toString=3Dfunction(){re= turn this.config.id};this.translateStr=3Dfunction(i,j){return"translate("+i= +","+j+")"};this.rotateStr=3Dfunction(j,i,k){return"rotate("+j+","+i+","+k+= ")"};this.svg=3Dd3.select(this.config.containerSelector).append("svg:svg").= attr("class","chart");this.content=3Dthis.svg.append("svg:g").attr("class",= "content").attr("id",this.config.id);this.xAxis=3Dthis.content.append("g").= attr("class","axis").attr("id","x-axis");this.xAxisLabel=3Dthis.xAxis.appen= d("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis= =3Dthis.content.append("g").attr("class","axis").attr("id","y-axis");this.y= AxisLabel=3Dthis.yAxis.append("text").attr("class","axis-label").attr("id",= "y-axis-label");this.adjustChartDimensions=3Dfunction(l,j,i,k){l=3Dl||0;j= =3Dj||0;i=3Di||0;k=3Dk||0;this.svg.attr("width",this.config.width+(this.con= fig.marginRight+j)+(this.config.marginLeft+k)).attr("height",this.config.he= ight+(this.config.marginTop+l)+(this.config.marginBottom+i)).style("display= ","block");this.content=3Dthis.svg.select("g.content").attr("transform",thi= s.translateStr(this.config.marginLeft+k,this.config.marginTop+l))};this.pre= processData=3Dfunction(k,j,i){return(k.length>this.config.maxDataPoints)?(k= .slice(0,this.config.maxDataPoints)):(k)};this.setUpDomains=3Dfunction(i,k,= j){this.xMin=3Dthis.config.xMin||(j)?(j[0].min):(d3.min(i));this.xMax=3Dthi= s.config.xMax||(j)?(j[0].max):(d3.max(i));this.yMin=3Dthis.config.yMin||(j)= ?(j[1].min):(d3.min(k));this.yMax=3Dthis.config.yMax||(j)?(j[1].max):(d3.ma= x(k))};this.setUpScales=3Dfunction(){this.xScale=3Dd3.scale.linear().domain= ([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=3Dd3.scale= .linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this= .setUpXAxis=3Dfunction(){this.xAxisFn=3Dd3.svg.axis().scale(this.xScale).ti= cks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",thi= s.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel= =3Dd3.max(_.map([this.xMin,this.xMax],function(i){return(String(i)).length}= ));if(this.xLongestLabel>=3Dc){this.xAxis.selectAll("g").filter(":nth-child= (odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/= 2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(= this.config.xLabel)};this.setUpYAxis=3Dfunction(){this.yAxisFn=3Dd3.svg.axi= s().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAx= is.call(this.yAxisFn);var i=3Dthis.yAxis.selectAll("text").filter(function(= m,l){return l!=3D=3D0});this.yLongestLabel=3Dd3.max(i[0].map(function(m,l){= return(d3.select(m).text()).length}))||0;var j=3Dd+(this.yLongestLabel*h)+e= +g;this.config.yAxisLabelBumpX=3D-(j-g);if(this.config.marginLeft<j){var k= =3D(j)-this.config.marginLeft;k=3D(k<0)?(0):(k);this.adjustChartDimensions(= 0,0,0,k)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",thi= s.config.height/2).attr("text-anchor","middle").attr("transform",this.rotat= eStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.confi= g.yLabel)};this.renderGrid=3Dfunction(){this.vGridLines=3Dthis.content.sele= ctAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));= this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",= true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xS= cale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hG= ridLines=3Dthis.content.selectAll("line.h-grid-line").data(this.yScale.tick= s(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").clas= sed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",th= is.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLi= nes.exit().remove()};this.glyphEnterState=3Dfunction(i){};this.glyphFinalSt= ate=3Dfunction(i){};this.glyphExitState=3Dfunction(i){};this.renderDatapoin= ts=3Dfunction(i,l,j){this.log(this+".renderDatapoints",arguments);var k=3D0= ;this.datapoints=3Dthis.addDatapoints(i,l,j,".glyph");this.datapoints.exit(= ).each(function(){k+=3D1}).transition().duration(this.config.animDuration).= attr("cy",this.config.height).attr("r",0).remove();this.log(k," glyphs remo= ved")};this.addDatapoints=3Dfunction(m,k,i,l){this.log(this+".addDatapoints= ",arguments);var p=3Dthis,o=3D0,q=3Dfunction(s,r){return p.xScale(m[r])},j= =3Dfunction(s,r){return p.yScale(k[r])};var n=3Dthis.content.selectAll(l);t= his.log("existing datapoints:",n);n=3Dn.data(m);o=3D0;n.enter().append("svg= :circle").each(function(){o+=3D1}).classed("glyph",true).attr("cx",q).attr(= "cy",j).attr("r",0);this.log(o," new glyphs created");o=3D0;n.transition().= duration(this.config.animDuration).each(function(){o+=3D1}).attr("cx",q).at= tr("cy",j).attr("r",p.config.datapointSize);this.log(o," existing glyphs tr= ansitioned");if(i){n.attr("data",function(s,r){return(i[r])})}n.attr("title= ",function(s,r){return((i)?(i[r]+": "):(""))+m[r]+", "+k[r]});n.on("mouseov= er",function(){var r=3Dd3.select(this);r.style("fill","red").style("fill-op= acity",1);p.content.append("line").attr("stroke","red").attr("stroke-width"= ,1).attr("x1",r.attr("cx")).attr("y1",r.attr("cy")).attr("x2",0).attr("y2",= r.attr("cy")).classed("hoverline",true);p.content.append("line").attr("stro= ke","red").attr("stroke-width",1).attr("x1",r.attr("cx")).attr("y1",r.attr(= "cy")).attr("x2",r.attr("cx")).attr("y2",p.config.height).classed("hoverlin= e",true)}).on("mouseout",function(){d3.select(this).style("fill","black").s= tyle("fill-opacity",0.2);d3.selectAll(".hoverline").remove()});return n};th= is.render=3Dfunction(k,l){this.log(this+".render",arguments);var i=3Dk[0],m= =3Dk[1],j=3D(k.length>2)?(k[2]):(undefined);i=3Dthis.preprocessData(i);m=3D= this.preprocessData(m);this.log("xCol len",i.length,"yCol len",m.length);th= is.setUpDomains(i,m,l);this.setUpScales();this.adjustChartDimensions();this= .setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(i,m= ,j)}}var b=3DBaseView.extend(LoggableMixin).extend({className:"scatterplot-= settings-form",dataLoadDelay:500,dataLoadSize:3001,loadingIndicatorImage:"l= oading_large_white_bg.gif",initialize:function(c){if(this.logger){window.fo= rm=3Dthis}this.dataset=3Dnull;this.chartConfig=3Dnull;this.plot=3Dnull;this= .loader=3Dnull;this.$statsPanel=3Dnull;this.$chartSettingsPanel=3Dnull;this= .$dataSettingsPanel=3Dnull;this.dataFetch=3Dnull;this.initializeFromAttribu= tes(c);this.initializeChart(c);this.initializeDataLoader(c)},initializeFrom= Attributes:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires = a dataset")}else{this.dataset=3Dc.dataset}if(jQuery.type(this.dataset.metad= ata_column_types)=3D=3D=3D"string"){this.dataset.metadata_column_types=3Dth= is.dataset.metadata_column_types.split(", ")}this.log("dataset:",this.datas= et);if(!c.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL= ")}else{this.dataURL=3Dc.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("t= his.dataURL:",this.dataURL)},initializeChart:function(c){this.chartConfig= =3Dc.chartConfig||{};if(this.logger){this.chartConfig.debugging=3Dtrue}this= .log("initial chartConfig:",this.chartConfig);this.plot=3Dnew a(this.chartC= onfig);this.chartConfig=3Dthis.plot.config},initializeDataLoader:function(d= ){var c=3Dthis;this.loader=3Dnew LazyDataLoader({logger:(this.logger)?(this= .logger):(null),url:null,start:d.start||0,total:d.total||this.dataset.metad= ata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:fun= ction(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})}});$(= this.loader).bind("error",function(g,e,f){c.log("ERROR:",e,f);alert("ERROR = fetching data:\n"+e+"\n"+f);c.hideLoadingIndicator()})},render:function(){v= ar c=3Dthis,d=3D{config:this.chartConfig,allColumns:[],numericColumns:[],lo= adingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndi= catorImage};_.each(this.dataset.metadata_column_types,function(g,f){var e= =3D"column "+(f+1);if(c.dataset.metadata_column_names){e=3Dc.dataset.metada= ta_column_names[f]}if(g=3D=3D=3D"int"||g=3D=3D=3D"float"){d.numericColumns.= push({index:f,name:e})}d.allColumns.push({index:f,name:e})});this.$el.appen= d(b.templates.form(d));this.$dataSettingsPanel=3Dthis.$el.find(".tab-pane#d= ata-settings");this.$chartSettingsPanel=3Dthis._render_chartSettings();this= .$statsPanel=3Dthis.$el.find(".tab-pane#chart-stats");return this},_render_= chartSettings:function(){var c=3Dthis,d=3Dthis.$el.find(".tab-pane#chart-se= ttings"),e=3D{datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,st= ep:20},height:{min:200,max:800,step:20}};d.append(b.templates.chartSettings= (this.chartConfig));d.find(".numeric-slider-input").each(function(){var h= =3D$(this),g=3Dh.find(".slider-output"),i=3Dh.find(".slider"),j=3Dh.attr("i= d");function f(){var l=3D$(this),k=3Dl.slider("value");g.text(k)}i.slider(_= .extend(e[j],{value:c.chartConfig[j],change:f,slide:f}))});return d},events= :{"click #include-id-checkbox":"toggleThirdColumnSelector","click #data-set= tings #render-button":"renderPlot","click #chart-settings #render-button":"= changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('s= elect[name=3D"ID"]').parent().toggle()},showLoadingIndicator:function(d,e){= d=3Dd||"";var c=3Dthis.$el.find("div#loading-indicator");messageBox=3Dc.fin= d(".loading-message");if(c.is(":visible")){if(d){messageBox.fadeOut("fast",= function(){messageBox.text(d);messageBox.fadeIn("fast",e)})}else{e()}}else{= if(d){messageBox.text(d)}c.fadeIn("fast",e)}},hideLoadingIndicator:function= (c){this.$el.find("div#loading-indicator").fadeOut("fast",c)},renderPlot:fu= nction(){var c=3Dthis;c.data=3Dnull;c.meta=3Dnull;_.extend(this.chartConfig= ,this.getGraphSettings());this.log("this.chartConfig:",this.chartConfig);th= is.plot.updateConfig(this.chartConfig,false);this.loader.url=3Dthis.dataURL= +"&"+jQuery.param(this.getDataSettings());this.log("this.loader, url:",this= .loader.url,"total:",this.loader.total);$(this.loader).bind("loaded.new",fu= nction(e,d){c.log(c+" loaded.new",d);c.postProcessDataFetchResponse(d);c.lo= g("postprocessed data:",c.data,"meta:",c.meta);c.showLoadingIndicator("Rend= ering...",function(){c.$el.find("ul.nav").find('a[href=3D"#chart-stats"]').= tab("show");c.plot.render(c.data,c.meta);c.renderStats(c.data,c.meta);c.hid= eLoadingIndicator()})});$(this.loader).bind("complete",function(d,e){c.log(= "complete",e);$(c.loader).unbind()});c.showLoadingIndicator("Fetching data.= ..",function(){c.loader.load()})},renderStats:function(){this.$statsPanel.h= tml(b.templates.statsTable({stats:[{name:"Count",xval:this.meta[0].count,yv= al:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].= min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",x= val:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].= mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:t= his.meta[1].median}]}))},changeChartSettings:function(){var c=3Dthis;newGra= phSettings=3Dthis.getGraphSettings();this.log("newGraphSettings:",newGraphS= ettings);_.extend(this.chartConfig,newGraphSettings);this.log("this.chartCo= nfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);if(= c.data&&c.meta){c.showLoadingIndicator("Rendering...",function(){c.plot.ren= der(c.data,c.meta);c.hideLoadingIndicator()})}else{this.renderPlot()}},post= ProcessDataFetchResponse:function(c){this.postProcessData(c.data);this.post= ProcessMeta(c.meta)},postProcessData:function(d){var c=3Dthis;if(c.data){_.= each(d,function(f,e){c.data[e]=3Dc.data[e].concat(f)})}else{c.data=3Dd}},po= stProcessMeta:function(e){var c=3Dthis,d=3Dthis.dataset.metadata_column_typ= es;if(c.meta){_.each(e,function(g,f){var k=3Dc.meta[f],i=3Dd[f];c.log(f+" p= ostprocessing meta:",g);k.count+=3D(g.count)?(g.count):(0);c.log(f,"count:"= ,k.count);if((i=3D=3D=3D"int")||(i=3D=3D=3D"float")){k.min=3DMath.min(g.min= ,k.min);k.max=3DMath.max(g.max,k.max);k.sum=3Dg.sum+k.sum;k.mean=3D(k.count= )?(k.sum/k.count):(null);var h=3Dc.data[f].slice().sort(),j=3DMath.floor(h.= length/2);if(h.length%2=3D=3D=3D0){k.median=3D((h[j]+h[(j+1)])/2)}else{k.me= dian=3Dh[j]}}})}else{c.meta=3De;c.log("initial meta:",c.meta)}},getDataSett= ings:function(){var d=3Dthis.getColumnSelections(),c=3D[];this.log("columnS= elections:",d);c=3D[d.X.colIndex,d.Y.colIndex];if(this.$dataSettingsPanel.f= ind("#include-id-checkbox").attr("checked")){c.push(d.ID.colIndex)}var e=3D= {data_type:"raw_data",columns:"["+c+"]"};this.log("params:",e);return e},ge= tColumnSelections:function(){var c=3D{};this.$dataSettingsPanel.find("div.c= olumn-select select").each(function(){var d=3D$(this),e=3Dd.val();c[d.attr(= "name")]=3D{colIndex:e,colName:d.children('[value=3D"'+e+'"]').text()}});re= turn c},getGraphSettings:function(){var e=3D{},f=3Dthis.getColumnSelections= ();e.datapointSize=3Dthis.$chartSettingsPanel.find("#datapointSize.numeric-= slider-input").find(".slider").slider("value");e.width=3Dthis.$chartSetting= sPanel.find("#width.numeric-slider-input").find(".slider").slider("value");= e.height=3Dthis.$chartSettingsPanel.find("#height.numeric-slider-input").fi= nd(".slider").slider("value");var d=3Dthis.$chartSettingsPanel.find("input#= X-axis-label").val(),c=3Dthis.$chartSettingsPanel.find("input#Y-axis-label"= ).val();e.xLabel=3D(d=3D=3D=3D"X")?(f.X.colName):(d);e.yLabel=3D(c=3D=3D=3D= "Y")?(f.Y.colName):(c);e.animDuration=3D10;if(this.$chartSettingsPanel.find= ("#animDuration.checkbox-input").is(":checked")){e.animDuration=3D500}this.= log("graphSettings:",e);return e},toString:function(){return"ScatterplotCon= trolForm("+this.dataset.id+")"}});b.templates=3D{form:Handlebars.templates[= "template-visualization-scatterplotControlForm"],statsTable:Handlebars.temp= lates["template-visualization-statsTable"],chartSettings:Handlebars.templat= es["template-visualization-chartSettings"]};return{LazyDataLoader:LazyDataL= oader,TwoVarScatterplot:a,ScatterplotControlForm:b}}); \ No newline at end of file

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=3D_.extend;var BEFORE=3D= 1001,CONTAINS=3D1002,OVERLAP_START=3D1003,OVERLAP_END=3D1004,CONTAINED_BY= =3D1005,AFTER=3D1006;var compute_overlap=3Dfunction(first_region,second_reg= ion){var first_start=3Dfirst_region[0],first_end=3Dfirst_region[1],second_s= tart=3Dsecond_region[0],second_end=3Dsecond_region[1],overlap;if(first_star= t<second_start){if(first_end<second_start){overlap=3DBEFORE}else{if(first_e= nd<=3Dsecond_end){overlap=3DOVERLAP_START}else{overlap=3DCONTAINS}}}else{if= (first_start>second_end){overlap=3DAFTER}else{if(first_end<=3Dsecond_end){o= verlap=3DCONTAINED_BY}else{overlap=3DOVERLAP_END}}}return overlap};var is_o= verlap=3Dfunction(first_region,second_region){var overlap=3Dcompute_overlap= (first_region,second_region);return(overlap!=3D=3DBEFORE&&overlap!=3D=3DAFT= ER)};var dashedLine=3Dfunction(ctx,x1,y1,x2,y2,dashLen){if(dashLen=3D=3D=3D= undefined){dashLen=3D4}var dX=3Dx2-x1;var dY=3Dy2-y1;var dashes=3DMath.floo= r(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=3DdX/dashes;var dashY=3DdY/dash= es;var q;for(q=3D0;q<dashes;q++,x1+=3DdashX,y1+=3DdashY){if(q%2!=3D=3D0){co= ntinue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle= =3Dfunction(ctx,down_vertex_x,down_vertex_y,side_len){var x1=3Ddown_vertex_= x-side_len/2,x2=3Ddown_vertex_x+side_len/2,y=3Ddown_vertex_y-Math.sqrt(side= _len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down= _vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=3Dthis.fillStyle;= ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=3Dfunction(default_val)= {this.default_val=3D(default_val?default_val:1)};Scaler.prototype.gen_val= =3Dfunction(input){return this.default_val};var Painter=3Dfunction(data,vie= w_start,view_end,prefs,mode){this.data=3Ddata;this.view_start=3Dview_start;= this.view_end=3Dview_end;this.prefs=3Dextend({},this.default_prefs,prefs);t= his.mode=3Dmode};Painter.prototype.default_prefs=3D{};Painter.prototype.dra= w=3Dfunction(ctx,width,height,w_scale){};var SummaryTreePainter=3Dfunction(= data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view= _end,prefs,mode)};SummaryTreePainter.prototype.default_prefs=3D{show_counts= :false};SummaryTreePainter.prototype.draw=3Dfunction(ctx,width,height,w_sca= le){var view_start=3Dthis.view_start,points=3Dthis.data.data,max=3D(this.pr= efs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=3Dheight;d= elta_x_px=3DMath.ceil(this.data.delta*w_scale);ctx.save();for(var i=3D0,len= =3Dpoints.length;i<len;i++){var x=3DMath.floor((points[i][0]-view_start)*w_= scale);var y=3Dpoints[i][1];if(!y){continue}var y_px=3Dy/max*height;if(y!= =3D=3D0&&y_px<1){y_px=3D1}ctx.fillStyle=3Dthis.prefs.block_color;ctx.fillRe= ct(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=3D4;if(this.prefs.= show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.= fillStyle=3Dthis.prefs.label_color;ctx.textAlign=3D"center";ctx.fillText(y,= x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=3Dfunction(data,view_s= tart,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,= mode);var i,len;if(this.prefs.min_value=3D=3D=3Dundefined){var min_value=3D= Infinity;for(i=3D0,len=3Dthis.data.length;i<len;i++){min_value=3DMath.min(m= in_value,this.data[i][1])}this.prefs.min_value=3Dmin_value}if(this.prefs.ma= x_value=3D=3D=3Dundefined){var max_value=3D-Infinity;for(i=3D0,len=3Dthis.d= ata.length;i<len;i++){max_value=3DMath.max(max_value,this.data[i][1])}this.= prefs.max_value=3Dmax_value}};LinePainter.prototype.default_prefs=3D{min_va= lue:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_co= lor:"#F66"};LinePainter.prototype.draw=3Dfunction(ctx,width,height,w_scale)= {var in_path=3Dfalse,min_value=3Dthis.prefs.min_value,max_value=3Dthis.pref= s.max_value,vertical_range=3Dmax_value-min_value,height_px=3Dheight,view_st= art=3Dthis.view_start,mode=3Dthis.mode,data=3Dthis.data;ctx.save();var y_ze= ro=3DMath.round(height+min_value/vertical_range*height);if(mode!=3D=3D"Inte= nsity"){ctx.fillStyle=3D"#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath= ();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=3DMath.ceil((data= [1][0]-data[0][0])*w_scale)}else{delta_x_px=3D10}var pref_color=3DparseInt(= this.prefs.color.slice(1),16),pref_r=3D(pref_color&16711680)>>16,pref_g=3D(= pref_color&65280)>>8,pref_b=3Dpref_color&255;for(var i=3D0,len=3Ddata.lengt= h;i<len;i++){ctx.fillStyle=3Dctx.strokeStyle=3Dthis.prefs.color;x_scaled=3D= Math.round((data[i][0]-view_start-1)*w_scale);y=3Ddata[i][1];var top_overfl= ow=3Dfalse,bot_overflow=3Dfalse;if(y=3D=3D=3Dnull){if(in_path&&mode=3D=3D= =3D"Filled"){ctx.lineTo(x_scaled,height_px)}in_path=3Dfalse;continue}if(y<m= in_value){bot_overflow=3Dtrue;y=3Dmin_value}else{if(y>max_value){top_overfl= ow=3Dtrue;y=3Dmax_value}}if(mode=3D=3D=3D"Histogram"){y=3DMath.round(y/vert= ical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(m= ode=3D=3D=3D"Intensity"){var saturation=3D(y-min_value)/vertical_range,new_= r=3DMath.round(pref_r+(255-pref_r)*(1-saturation)),new_g=3DMath.round(pref_= g+(255-pref_g)*(1-saturation)),new_b=3DMath.round(pref_b+(255-pref_b)*(1-sa= turation));ctx.fillStyle=3D"rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRec= t(x_scaled,0,delta_x_px,height_px)}else{y=3DMath.round(height_px-(y-min_val= ue)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_pa= th=3Dtrue;if(mode=3D=3D=3D"Filled"){ctx.moveTo(x_scaled,height_px);ctx.line= To(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=3Dthis.prefs.ov= erflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode=3D=3D=3D= "Histogram"||mode=3D=3D=3D"Intensity"){overflow_x=3Ddelta_x_px}else{x_scale= d-=3D2;overflow_x=3D4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3= )}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fil= lStyle=3Dthis.prefs.color}if(mode=3D=3D=3D"Filled"){if(in_path){ctx.lineTo(= x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.rest= ore()};var FeaturePositionMapper=3Dfunction(slot_height){this.feature_posit= ions=3D{};this.slot_height=3Dslot_height;this.translation=3D0;this.y_transl= ation=3D0};FeaturePositionMapper.prototype.map_feature_data=3Dfunction(feat= ure_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature= _positions[slot]=3D[]}this.feature_positions[slot].push({data:feature_data,= x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_= data=3Dfunction(x,y){var slot=3DMath.floor((y-this.y_translation)/this.slot= _height),feature_dict;if(!this.feature_positions[slot]){return null}x+=3Dth= is.translation;for(var i=3D0;i<this.feature_positions[slot].length;i++){fea= ture_dict=3Dthis.feature_positions[slot][i];if(x>=3Dfeature_dict.x_start&&x= <=3Dfeature_dict.x_end){return feature_dict.data}}};var FeaturePainter=3Dfu= nction(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Pain= ter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=3D(alp= ha_scaler?alpha_scaler:new Scaler());this.height_scaler=3D(height_scaler?he= ight_scaler:new Scaler())};FeaturePainter.prototype.default_prefs=3D{block_= color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_r= equired_height:function(rows_required,width){var required_height=3Dthis.get= _row_height(),y_scale=3Drequired_height,mode=3Dthis.mode;if(mode=3D=3D=3D"n= o_detail"||mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Pack"){required_height=3Dro= ws_required*y_scale}return required_height+this.get_top_padding(width)+this= .get_bottom_padding(width)},get_top_padding:function(width){return 0},get_b= ottom_padding:function(width){return Math.max(Math.round(this.get_row_heigh= t()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=3Dthis.da= ta,view_start=3Dthis.view_start,view_end=3Dthis.view_end;ctx.save();ctx.fil= lStyle=3Dthis.prefs.block_color;ctx.textAlign=3D"right";var y_scale=3Dthis.= get_row_height(),feature_mapper=3Dnew FeaturePositionMapper(y_scale),x_draw= _coords;for(var i=3D0,len=3Ddata.length;i<len;i++){var feature=3Ddata[i],fe= ature_uid=3Dfeature[0],feature_start=3Dfeature[1],feature_end=3Dfeature[2],= slot=3D(slots&&slots[feature_uid]!=3D=3Dundefined?slots[feature_uid]:null);= if((feature_start<view_end&&feature_end>view_start)&&(this.mode=3D=3D=3D"De= nse"||slot!=3D=3Dnull)){x_draw_coords=3Dthis.draw_element(ctx,this.mode,fea= ture,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_fea= ture_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();fe= ature_mapper.y_translation=3Dthis.get_top_padding(width);return feature_map= per},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale= ,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]= }});var DENSE_TRACK_HEIGHT=3D10,NO_DETAIL_TRACK_HEIGHT=3D3,SQUISH_TRACK_HEI= GHT=3D5,PACK_TRACK_HEIGHT=3D10,NO_DETAIL_FEATURE_HEIGHT=3D1,DENSE_FEATURE_H= EIGHT=3D9,SQUISH_FEATURE_HEIGHT=3D3,PACK_FEATURE_HEIGHT=3D9,LABEL_SPACING= =3D2,CONNECTOR_COLOR=3D"#ccc";var LinkedFeaturePainter=3Dfunction(data,view= _start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(= this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.d= raw_background_connector=3Dtrue;this.draw_individual_connectors=3Dfalse};ex= tend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_heigh= t:function(){var mode=3Dthis.mode,height;if(mode=3D=3D=3D"Dense"){height=3D= DENSE_TRACK_HEIGHT}else{if(mode=3D=3D=3D"no_detail"){height=3DNO_DETAIL_TRA= CK_HEIGHT}else{if(mode=3D=3D=3D"Squish"){height=3DSQUISH_TRACK_HEIGHT}else{= height=3DPACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,= feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=3Dfe= ature[0],feature_start=3Dfeature[1],feature_end=3Dfeature[2]-1,feature_name= =3Dfeature[3],feature_strand=3Dfeature[4],f_start=3DMath.floor(Math.max(0,(= feature_start-tile_low)*w_scale)),f_end=3DMath.ceil(Math.min(width,Math.max= (0,(feature_end-tile_low)*w_scale))),draw_start=3Df_start,draw_end=3Df_end,= y_center=3D(mode=3D=3D=3D"Dense"?0:(0+slot))*y_scale+this.get_top_padding(w= idth),thickness,y_start,thick_start=3Dnull,thick_end=3Dnull,block_color=3D(= !feature_strand||feature_strand=3D=3D=3D"+"||feature_strand=3D=3D=3D"."?thi= s.prefs.block_color:this.prefs.reverse_strand_color);label_color=3Dthis.pre= fs.label_color;ctx.globalAlpha=3Dthis.alpha_scaler.gen_val(feature);if(mode= =3D=3D=3D"Dense"){slot=3D1}if(mode=3D=3D=3D"no_detail"){ctx.fillStyle=3Dblo= ck_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HE= IGHT)}else{var feature_ts=3Dfeature[5],feature_te=3Dfeature[6],feature_bloc= ks=3Dfeature[7],full_height=3Dtrue;if(feature_ts&&feature_te){thick_start= =3DMath.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=3DMath.c= eil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_hei= ght,thick_height;if(mode=3D=3D=3D"Squish"){thin_height=3D1;thick_height=3DS= QUISH_FEATURE_HEIGHT;full_height=3Dfalse}else{if(mode=3D=3D=3D"Dense"){thin= _height=3D5;thick_height=3DDENSE_FEATURE_HEIGHT}else{thin_height=3D5;thick_= height=3DPACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=3Dblock_col= or;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_s= trand&&full_height){if(feature_strand=3D=3D=3D"+"){ctx.fillStyle=3Dctx.canv= as.manager.get_pattern("right_strand_inv")}else{if(feature_strand=3D=3D=3D"= -"){ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.= fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_cen= ter,cur_height;if(mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Dense"){cur_y_center= =3Dy_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=3D1}else{if(fe= ature_strand){cur_y_center=3Dy_center;cur_height=3Dthick_height}else{cur_y_= center+=3D(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=3D1}}if(this.draw_backgrou= nd_connector){if(mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Dense"){ctx.fillStyle= =3DCONNECTOR_COLOR}else{if(feature_strand){if(feature_strand=3D=3D=3D"+"){c= tx.fillStyle=3Dctx.canvas.manager.get_pattern("right_strand")}else{if(featu= re_strand=3D=3D=3D"-"){ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left= _strand")}}}else{ctx.fillStyle=3DCONNECTOR_COLOR}}ctx.fillRect(f_start,cur_= y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=3D0,k_len= =3Dfeature_blocks.length;k<k_len;k++){var block=3Dfeature_blocks[k],block_s= tart=3DMath.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=3DMath= .ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_s= tart,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=3Dbloc= k_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,bl= ock_end-block_start,thin_height);if(thick_start!=3D=3Dundefined&&feature_te=

feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thi=

ck_start=3DMath.max(block_start,thick_start),block_thick_end=3DMath.min(blo= ck_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end= -block_thick_start,thick_height);if(feature_blocks.length=3D=3D=3D1&&mode= =3D=3D=3D"Pack"){if(feature_strand=3D=3D=3D"+"){ctx.fillStyle=3Dctx.canvas.= manager.get_pattern("right_strand_inv")}else{if(feature_strand=3D=3D=3D"-")= {ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left_strand_inv")}}if(bloc= k_thick_start+14<block_thick_end){block_thick_start+=3D2;block_thick_end-= =3D2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_= start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){= this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_e= nd,y_center)}last_block_start=3Dblock_start;last_block_end=3Dblock_end}if(m= ode=3D=3D=3D"Pack"){ctx.globalAlpha=3D1;ctx.fillStyle=3D"white";var hscale_= factor=3Dthis.height_scaler.gen_val(feature),new_height=3DMath.ceil(thick_h= eight*hscale_factor),ws_height=3DMath.round((thick_height-new_height)/2);if= (hscale_factor!=3D=3D1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,w= s_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-= f_start,ws_height)}}}ctx.globalAlpha=3D1;if(feature_name&&mode=3D=3D=3D"Pac= k"&&feature_start>tile_low){ctx.fillStyle=3Dlabel_color;if(tile_low=3D=3D= =3D0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign=3D"left"= ;ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=3Dctx.= measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign=3D"right";= ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=3Dc= tx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=3D1;retu= rn[draw_start,draw_end]}});var ReadPainter=3Dfunction(data,view_start,view_= end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this= ,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_s= eq=3D(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePaint= er.prototype,{get_row_height:function(){var height,mode=3Dthis.mode;if(mode= =3D=3D=3D"Dense"){height=3DDENSE_TRACK_HEIGHT}else{if(mode=3D=3D=3D"Squish"= ){height=3DSQUISH_TRACK_HEIGHT}else{height=3DPACK_TRACK_HEIGHT;if(this.pref= s.show_insertions){height*=3D2}}}return height},draw_read:function(ctx,mode= ,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,ref_seq){ct= x.textAlign=3D"center";var tile_region=3D[tile_low,tile_high],base_offset= =3D0,seq_offset=3D0,gap=3D0,char_width_px=3Dctx.canvas.manager.char_width_p= x,block_color=3D(strand=3D=3D=3D"+"?this.prefs.block_color:this.prefs.rever= se_strand_color);var draw_last=3D[];if((mode=3D=3D=3D"Pack"||this.mode=3D= =3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w_scale>char_width_px){gap=3DMath.r= ound(w_scale/2)}if(!cigar){cigar=3D[[0,ref_seq.length]]}for(var cig_id=3D0,= len=3Dcigar.length;cig_id<len;cig_id++){var cig=3Dcigar[cig_id],cig_op=3D"M= IDNSHP=3DX"[cig[0]],cig_len=3Dcig[1];if(cig_op=3D=3D=3D"H"||cig_op=3D=3D=3D= "S"){base_offset-=3Dcig_len}var seq_start=3D(feature_start-1)+base_offset,s= _start=3DMath.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=3DMath.= floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start=3D=3D=3D= s_end){s_end+=3D1}switch(cig_op){case"H":break;case"S":case"M":case"=3D":if= (is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=3Dref_seq.s= lice(seq_offset-1,seq_offset+cig_len);if(gap>0){ctx.fillStyle=3Dblock_color= ;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=3DCONNE= CTOR_COLOR;for(var c=3D0,str_len=3Dseq.length;c<str_len;c++){if(this.prefs.= show_differences){if(this.ref_seq){var ref_char=3Dthis.ref_seq[seq_start-ti= le_low+c];if(!ref_char||ref_char.toLowerCase()=3D=3D=3Dseq[c].toLowerCase()= ){continue}}else{continue}}if(seq_start+c>=3Dtile_low&&seq_start+c<=3Dtile_= high){var c_start=3DMath.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));= ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=3Dblock_color;= ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_o= ffset+=3Dcig_len;base_offset+=3Dcig_len;break;case"N":ctx.fillStyle=3DCONNE= CTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset= +=3Dcig_len;break;case"D":ctx.fillStyle=3D"red";ctx.fillRect(s_start-gap,y_= center+4,s_end-s_start,3);base_offset+=3Dcig_len;break;case"P":break;case"I= ":var insert_x_coord=3Ds_start-gap;if(is_overlap([seq_start,seq_start+cig_l= en],tile_region)){var seq=3Dref_seq.slice(seq_offset-1,seq_offset+cig_len);= if(this.prefs.show_insertions){var x_center=3Ds_start-(s_end-s_start)/2;if(= (mode=3D=3D=3D"Pack"||this.mode=3D=3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w= _scale>char_width_px){ctx.fillStyle=3D"yellow";ctx.fillRect(x_center-gap,y_= center-9,s_end-s_start,9);draw_last[draw_last.length]=3D{type:"triangle",da= ta:[insert_x_coord,y_center+4,5]};ctx.fillStyle=3DCONNECTOR_COLOR;switch(co= mpute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_STA= RT):seq=3Dseq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=3Dseq.= slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS= ):seq=3Dseq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c= =3D0,str_len=3Dseq.length;c<str_len;c++){var c_start=3DMath.floor(Math.max(= 0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_sta= rt)/2,y_center)}}else{ctx.fillStyle=3D"yellow";ctx.fillRect(x_center,y_cent= er+(this.mode!=3D=3D"Dense"?2:5),s_end-s_start,(mode!=3D=3D"Dense"?SQUISH_F= EATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode=3D=3D=3D"Pack"||this.mo= de=3D=3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w_scale>char_width_px){draw_la= st.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}= seq_offset+=3Dcig_len;break;case"X":seq_offset+=3Dcig_len;break}}ctx.fillSt= yle=3D"yellow";var item,type,data;for(var i=3D0;i<draw_last.length;i++){ite= m=3Ddraw_last[i];type=3Ditem.type;data=3Ditem.data;if(type=3D=3D=3D"text"){= ctx.save();ctx.font=3D"bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]= );ctx.restore()}else{if(type=3D=3D=3D"triangle"){drawDownwardEquilateralTri= angle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,featu= re,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=3Dfeature= [0],feature_start=3Dfeature[1],feature_end=3Dfeature[2],feature_name=3Dfeat= ure[3],f_start=3DMath.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f= _end=3DMath.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))= ),y_center=3D(mode=3D=3D=3D"Dense"?0:(0+slot))*y_scale,label_color=3Dthis.p= refs.label_color,gap=3D0;if((mode=3D=3D=3D"Pack"||this.mode=3D=3D=3D"Auto")= &&w_scale>ctx.canvas.manager.char_width_px){var gap=3DMath.round(w_scale/2)= }if(feature[5] instanceof Array){var b1_start=3DMath.floor(Math.max(0,(feat= ure[4][0]-tile_low)*w_scale)),b1_end=3DMath.ceil(Math.min(width,Math.max(0,= (feature[4][1]-tile_low)*w_scale))),b2_start=3DMath.floor(Math.max(0,(featu= re[5][0]-tile_low)*w_scale)),b2_end=3DMath.ceil(Math.min(width,Math.max(0,(= feature[5][1]-tile_low)*w_scale))),connector=3Dtrue;if(feature[4][1]>=3Dtil= e_low&&feature[4][0]<=3Dtile_high&&feature[4][2]){this.draw_read(ctx,mode,w= _scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3= ],feature[4][4])}else{connector=3Dfalse}if(feature[5][1]>=3Dtile_low&&featu= re[5][0]<=3Dtile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_cen= ter,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5]= [4])}else{connector=3Dfalse}if(connector&&b2_start>b1_end){ctx.fillStyle=3D= CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+= 5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,featur= e_start,feature[4],feature[5],feature[6])}if(mode=3D=3D=3D"Pack"&&feature_s= tart>tile_low&&feature_name!=3D=3D"."){ctx.fillStyle=3Dthis.prefs.label_col= or;var tile_index=3D1;if(tile_index=3D=3D=3D0&&f_start-ctx.measureText(feat= ure_name).width<0){ctx.textAlign=3D"left";ctx.fillText(feature_name,f_end+L= ABEL_SPACING-gap,y_center+8)}else{ctx.textAlign=3D"right";ctx.fillText(feat= ure_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinke= dFeaturePainter=3Dfunction(data,view_start,view_end,prefs,mode,alpha_scaler= ,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,pre= fs,mode,alpha_scaler,height_scaler);this.longest_feature_length=3Dthis.calc= ulate_longest_feature_length();this.draw_background_connector=3Dfalse;this.= draw_individual_connectors=3Dtrue};extend(ArcLinkedFeaturePainter.prototype= ,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest= _feature_length:function(){var longest_feature_length=3D0;for(var i=3D0,len= =3Dthis.data.length;i<len;i++){var feature=3Dthis.data[i],feature_start=3Df= eature[1],feature_end=3Dfeature[2];longest_feature_length=3DMath.max(longes= t_feature_length,feature_end-feature_start)}return longest_feature_length},= get_top_padding:function(width){var view_range=3Dthis.view_end-this.view_st= art,w_scale=3Dwidth/view_range;return Math.min(128,Math.ceil((this.longest_= feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block= 1_end,block2_start,block2_end,y_center){var x_center=3D(block1_end+block2_s= tart)/2,radius=3Dblock2_start-x_center;var angle1=3DMath.PI,angle2=3D0;if(r= adius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Ma= th.PI,0);ctx.stroke()}}});var Color=3Dfunction(rgb,a){if(Array.isArray(rgb)= ){this.rgb=3Drgb}else{if(rgb.length=3D=3D6){this.rgb=3Drgb.match(/.{2}/g).m= ap(function(c){return parseInt(c,16)})}else{this.rgb=3Drgb.split("").map(fu= nction(c){return parseInt(c+c,16)})}}this.alpha=3Dtypeof(a)=3D=3D=3D"number= "?a:1};Color.prototype=3D{eval:function(){return this},toCSS:function(){if(= this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)})= .concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){= i=3DMath.round(i);i=3D(i>255?255:(i<0?0:i)).toString(16);return i.length=3D= =3D=3D1?"0"+i:i}).join("")}},toHSL:function(){var r=3Dthis.rgb[0]/255,g=3Dt= his.rgb[1]/255,b=3Dthis.rgb[2]/255,a=3Dthis.alpha;var max=3DMath.max(r,g,b)= ,min=3DMath.min(r,g,b);var h,s,l=3D(max+min)/2,d=3Dmax-min;if(max=3D=3D=3Dm= in){h=3Ds=3D0}else{s=3Dl>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h= =3D(g-b)/d+(g<b?6:0);break;case g:h=3D(b-r)/d+2;break;case b:h=3D(r-g)/d+4;= break}h/=3D6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=3D[Mat= h.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i= =3DMath.round(i);i=3D(i>255?255:(i<0?0:i)).toString(16);return i.length=3D= =3D=3D1?"0"+i:i}).join("")},mix:function(color2,weight){color1=3Dthis;var p= =3Dweight;var w=3Dp*2-1;var a=3Dcolor1.toHSL().a-color2.toHSL().a;var w1=3D= (((w*a=3D=3D-1)?w:(w+a)/(1+w*a))+1)/2;var w2=3D1-w1;var rgb=3D[color1.rgb[0= ]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+co= lor2.rgb[2]*w2];var alpha=3Dcolor1.alpha*p+color2.alpha*(1-p);return new Co= lor(rgb,alpha)}};var LinearRamp=3Dfunction(start_color,end_color,start_valu= e,end_value){this.start_color=3Dnew Color(start_color);this.end_color=3Dnew= Color(end_color);this.start_value=3Dstart_value;this.end_value=3Dend_value= ;this.value_range=3Dend_value-start_value};LinearRamp.prototype.map_value= =3Dfunction(value){value=3DMath.max(value,this.start_value);value=3DMath.mi= n(value,this.end_value);value=3D(value-this.start_value)/this.value_range;r= eturn this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp= =3Dfunction(start_color,middle_color,end_color,start_value,end_value){this.= positive_ramp=3Dnew LinearRamp(middle_color,end_color,0,end_value);this.neg= ative_ramp=3Dnew LinearRamp(middle_color,start_color,0,-start_value);this.s= tart_value=3Dstart_value;this.end_value=3Dend_value};SplitRamp.prototype.ma= p_value=3Dfunction(value){value=3DMath.max(value,this.start_value);value=3D= Math.min(value,this.end_value);if(value>=3D0){return this.positive_ramp.map= _value(value)}else{return this.negative_ramp.map_value(-value)}};var Diagon= alHeatmapPainter=3Dfunction(data,view_start,view_end,prefs,mode){Painter.ca= ll(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_va= lue=3D=3D=3Dundefined){var min_value=3DInfinity;for(i=3D0,len=3Dthis.data.l= ength;i<len;i++){min_value=3DMath.min(min_value,this.data[i][5])}this.prefs= .min_value=3Dmin_value}if(this.prefs.max_value=3D=3D=3Dundefined){var max_v= alue=3D-Infinity;for(i=3D0,len=3Dthis.data.length;i<len;i++){max_value=3DMa= th.max(max_value,this.data[i][5])}this.prefs.max_value=3Dmax_value}};Diagon= alHeatmapPainter.prototype.default_prefs=3D{min_value:undefined,max_value:u= ndefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHe= atmapPainter.prototype.draw=3Dfunction(ctx,width,height,w_scale){var min_va= lue=3Dthis.prefs.min_value,max_value=3Dthis.prefs.max_value,value_range=3Dm= ax_value-min_value,height_px=3Dheight,view_start=3Dthis.view_start,mode=3Dt= his.mode,data=3Dthis.data,invsqrt2=3D1/Math.sqrt(2);var ramp=3D(new SplitRa= mp(this.prefs.neg_color,"FFFFFF",this.prefs.pos_color,min_value,max_value))= ;var d,s1,e1,s2,e2,value;var scale=3Dfunction(p){return(p-view_start)*w_sca= le};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for= (var i=3D0,len=3Ddata.length;i<len;i++){d=3Ddata[i];s1=3Dscale(d[1]);e1=3Ds= cale(d[2]);s2=3Dscale(d[4]);e2=3Dscale(d[5]);value=3Dd[6];ctx.fillStyle=3D(= ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};r= eturn{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LineP= ainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,Ar= cLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:Diagon= alHeatmapPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=3D_.extend;var BEFORE=3D= 1001,CONTAINS=3D1002,OVERLAP_START=3D1003,OVERLAP_END=3D1004,CONTAINED_BY= =3D1005,AFTER=3D1006;var compute_overlap=3Dfunction(first_region,second_reg= ion){var first_start=3Dfirst_region[0],first_end=3Dfirst_region[1],second_s= tart=3Dsecond_region[0],second_end=3Dsecond_region[1],overlap;if(first_star= t<second_start){if(first_end<second_start){overlap=3DBEFORE}else{if(first_e= nd<=3Dsecond_end){overlap=3DOVERLAP_START}else{overlap=3DCONTAINS}}}else{if= (first_start>second_end){overlap=3DAFTER}else{if(first_end<=3Dsecond_end){o= verlap=3DCONTAINED_BY}else{overlap=3DOVERLAP_END}}}return overlap};var is_o= verlap=3Dfunction(first_region,second_region){var overlap=3Dcompute_overlap= (first_region,second_region);return(overlap!=3D=3DBEFORE&&overlap!=3D=3DAFT= ER)};var dashedLine=3Dfunction(ctx,x1,y1,x2,y2,dashLen){if(dashLen=3D=3D=3D= undefined){dashLen=3D4}var dX=3Dx2-x1;var dY=3Dy2-y1;var dashes=3DMath.floo= r(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=3DdX/dashes;var dashY=3DdY/dash= es;var q;for(q=3D0;q<dashes;q++,x1+=3DdashX,y1+=3DdashY){if(q%2!=3D=3D0){co= ntinue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle= =3Dfunction(ctx,down_vertex_x,down_vertex_y,side_len){var x1=3Ddown_vertex_= x-side_len/2,x2=3Ddown_vertex_x+side_len/2,y=3Ddown_vertex_y-Math.sqrt(side= _len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down= _vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=3Dthis.fillStyle;= ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=3Dfunction(default_val)= {this.default_val=3D(default_val?default_val:1)};Scaler.prototype.gen_val= =3Dfunction(input){return this.default_val};var Painter=3Dfunction(data,vie= w_start,view_end,prefs,mode){this.data=3Ddata;this.view_start=3Dview_start;= this.view_end=3Dview_end;this.prefs=3Dextend({},this.default_prefs,prefs);t= his.mode=3Dmode};Painter.prototype.default_prefs=3D{};Painter.prototype.dra= w=3Dfunction(ctx,width,height,w_scale){};var SummaryTreePainter=3Dfunction(= data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view= _end,prefs,mode)};SummaryTreePainter.prototype.default_prefs=3D{show_counts= :false};SummaryTreePainter.prototype.draw=3Dfunction(ctx,width,height,w_sca= le){var view_start=3Dthis.view_start,points=3Dthis.data.data,max=3D(this.pr= efs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=3Dheight;d= elta_x_px=3DMath.ceil(this.data.delta*w_scale);ctx.save();for(var i=3D0,len= =3Dpoints.length;i<len;i++){var x=3DMath.floor((points[i][0]-view_start)*w_= scale);var y=3Dpoints[i][1];if(!y){continue}var y_px=3Dy/max*height;if(y!= =3D=3D0&&y_px<1){y_px=3D1}ctx.fillStyle=3Dthis.prefs.block_color;ctx.fillRe= ct(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=3D4;if(this.prefs.= show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.= fillStyle=3Dthis.prefs.label_color;ctx.textAlign=3D"center";ctx.fillText(y,= x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=3Dfunction(data,view_s= tart,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,= mode);var i,len;if(this.prefs.min_value=3D=3D=3Dundefined){var min_value=3D= Infinity;for(i=3D0,len=3Dthis.data.length;i<len;i++){min_value=3DMath.min(m= in_value,this.data[i][1])}this.prefs.min_value=3Dmin_value}if(this.prefs.ma= x_value=3D=3D=3Dundefined){var max_value=3D-Infinity;for(i=3D0,len=3Dthis.d= ata.length;i<len;i++){max_value=3DMath.max(max_value,this.data[i][1])}this.= prefs.max_value=3Dmax_value}};LinePainter.prototype.default_prefs=3D{min_va= lue:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_co= lor:"#F66"};LinePainter.prototype.draw=3Dfunction(ctx,width,height,w_scale)= {var in_path=3Dfalse,min_value=3Dthis.prefs.min_value,max_value=3Dthis.pref= s.max_value,vertical_range=3Dmax_value-min_value,height_px=3Dheight,view_st= art=3Dthis.view_start,mode=3Dthis.mode,data=3Dthis.data;ctx.save();var y_ze= ro=3DMath.round(height+min_value/vertical_range*height);if(mode!=3D=3D"Inte= nsity"){ctx.fillStyle=3D"#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath= ();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=3DMath.ceil((data= [1][0]-data[0][0])*w_scale)}else{delta_x_px=3D10}var pref_color=3DparseInt(= this.prefs.color.slice(1),16),pref_r=3D(pref_color&16711680)>>16,pref_g=3D(= pref_color&65280)>>8,pref_b=3Dpref_color&255;for(var i=3D0,len=3Ddata.lengt= h;i<len;i++){ctx.fillStyle=3Dctx.strokeStyle=3Dthis.prefs.color;x_scaled=3D= Math.round((data[i][0]-view_start-1)*w_scale);y=3Ddata[i][1];var top_overfl= ow=3Dfalse,bot_overflow=3Dfalse;if(y=3D=3D=3Dnull){if(in_path&&mode=3D=3D= =3D"Filled"){ctx.lineTo(x_scaled,height_px)}in_path=3Dfalse;continue}if(y<m= in_value){bot_overflow=3Dtrue;y=3Dmin_value}else{if(y>max_value){top_overfl= ow=3Dtrue;y=3Dmax_value}}if(mode=3D=3D=3D"Histogram"){y=3DMath.round(y/vert= ical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(m= ode=3D=3D=3D"Intensity"){var saturation=3D(y-min_value)/vertical_range,new_= r=3DMath.round(pref_r+(255-pref_r)*(1-saturation)),new_g=3DMath.round(pref_= g+(255-pref_g)*(1-saturation)),new_b=3DMath.round(pref_b+(255-pref_b)*(1-sa= turation));ctx.fillStyle=3D"rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRec= t(x_scaled,0,delta_x_px,height_px)}else{y=3DMath.round(height_px-(y-min_val= ue)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_pa= th=3Dtrue;if(mode=3D=3D=3D"Filled"){ctx.moveTo(x_scaled,height_px);ctx.line= To(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=3Dthis.prefs.ov= erflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode=3D=3D=3D= "Histogram"||mode=3D=3D=3D"Intensity"){overflow_x=3Ddelta_x_px}else{x_scale= d-=3D2;overflow_x=3D4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3= )}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fil= lStyle=3Dthis.prefs.color}if(mode=3D=3D=3D"Filled"){if(in_path){ctx.lineTo(= x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.rest= ore()};var FeaturePositionMapper=3Dfunction(slot_height){this.feature_posit= ions=3D{};this.slot_height=3Dslot_height;this.translation=3D0;this.y_transl= ation=3D0};FeaturePositionMapper.prototype.map_feature_data=3Dfunction(feat= ure_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature= _positions[slot]=3D[]}this.feature_positions[slot].push({data:feature_data,= x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_= data=3Dfunction(x,y){var slot=3DMath.floor((y-this.y_translation)/this.slot= _height),feature_dict;if(!this.feature_positions[slot]){return null}x+=3Dth= is.translation;for(var i=3D0;i<this.feature_positions[slot].length;i++){fea= ture_dict=3Dthis.feature_positions[slot][i];if(x>=3Dfeature_dict.x_start&&x= <=3Dfeature_dict.x_end){return feature_dict.data}}};var FeaturePainter=3Dfu= nction(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Pain= ter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=3D(alp= ha_scaler?alpha_scaler:new Scaler());this.height_scaler=3D(height_scaler?he= ight_scaler:new Scaler())};FeaturePainter.prototype.default_prefs=3D{block_= color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_r= equired_height:function(rows_required,width){var required_height=3Dthis.get= _row_height(),y_scale=3Drequired_height,mode=3Dthis.mode;if(mode=3D=3D=3D"n= o_detail"||mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Pack"){required_height=3Dro= ws_required*y_scale}return required_height+this.get_top_padding(width)+this= .get_bottom_padding(width)},get_top_padding:function(width){return 0},get_b= ottom_padding:function(width){return Math.max(Math.round(this.get_row_heigh= t()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=3Dthis.da= ta,view_start=3Dthis.view_start,view_end=3Dthis.view_end;ctx.save();ctx.fil= lStyle=3Dthis.prefs.block_color;ctx.textAlign=3D"right";var y_scale=3Dthis.= get_row_height(),feature_mapper=3Dnew FeaturePositionMapper(y_scale),x_draw= _coords;for(var i=3D0,len=3Ddata.length;i<len;i++){var feature=3Ddata[i],fe= ature_uid=3Dfeature[0],feature_start=3Dfeature[1],feature_end=3Dfeature[2],= slot=3D(slots&&slots[feature_uid]!=3D=3Dundefined?slots[feature_uid]:null);= if((feature_start<view_end&&feature_end>view_start)&&(this.mode=3D=3D=3D"De= nse"||slot!=3D=3Dnull)){x_draw_coords=3Dthis.draw_element(ctx,this.mode,fea= ture,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_fea= ture_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();fe= ature_mapper.y_translation=3Dthis.get_top_padding(width);return feature_map= per},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale= ,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]= }});var DENSE_TRACK_HEIGHT=3D10,NO_DETAIL_TRACK_HEIGHT=3D3,SQUISH_TRACK_HEI= GHT=3D5,PACK_TRACK_HEIGHT=3D10,NO_DETAIL_FEATURE_HEIGHT=3D1,DENSE_FEATURE_H= EIGHT=3D9,SQUISH_FEATURE_HEIGHT=3D3,PACK_FEATURE_HEIGHT=3D9,LABEL_SPACING= =3D2,CONNECTOR_COLOR=3D"#ccc";var LinkedFeaturePainter=3Dfunction(data,view= _start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(= this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.d= raw_background_connector=3Dtrue;this.draw_individual_connectors=3Dfalse};ex= tend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_heigh= t:function(){var mode=3Dthis.mode,height;if(mode=3D=3D=3D"Dense"){height=3D= DENSE_TRACK_HEIGHT}else{if(mode=3D=3D=3D"no_detail"){height=3DNO_DETAIL_TRA= CK_HEIGHT}else{if(mode=3D=3D=3D"Squish"){height=3DSQUISH_TRACK_HEIGHT}else{= height=3DPACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,= feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=3Dfe= ature[0],feature_start=3Dfeature[1],feature_end=3Dfeature[2]-1,feature_name= =3Dfeature[3],feature_strand=3Dfeature[4],f_start=3DMath.floor(Math.max(0,(= feature_start-tile_low)*w_scale)),f_end=3DMath.ceil(Math.min(width,Math.max= (0,(feature_end-tile_low)*w_scale))),draw_start=3Df_start,draw_end=3Df_end,= y_center=3D(mode=3D=3D=3D"Dense"?0:(0+slot))*y_scale+this.get_top_padding(w= idth),thickness,y_start,thick_start=3Dnull,thick_end=3Dnull,block_color=3D(= !feature_strand||feature_strand=3D=3D=3D"+"||feature_strand=3D=3D=3D"."?thi= s.prefs.block_color:this.prefs.reverse_strand_color);label_color=3Dthis.pre= fs.label_color;ctx.globalAlpha=3Dthis.alpha_scaler.gen_val(feature);if(mode= =3D=3D=3D"Dense"){slot=3D1}if(mode=3D=3D=3D"no_detail"){ctx.fillStyle=3Dblo= ck_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HE= IGHT)}else{var feature_ts=3Dfeature[5],feature_te=3Dfeature[6],feature_bloc= ks=3Dfeature[7],full_height=3Dtrue;if(feature_ts&&feature_te){thick_start= =3DMath.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=3DMath.c= eil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_hei= ght,thick_height;if(mode=3D=3D=3D"Squish"){thin_height=3D1;thick_height=3DS= QUISH_FEATURE_HEIGHT;full_height=3Dfalse}else{if(mode=3D=3D=3D"Dense"){thin= _height=3D5;thick_height=3DDENSE_FEATURE_HEIGHT}else{thin_height=3D5;thick_= height=3DPACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=3Dblock_col= or;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_s= trand&&full_height){if(feature_strand=3D=3D=3D"+"){ctx.fillStyle=3Dctx.canv= as.manager.get_pattern("right_strand_inv")}else{if(feature_strand=3D=3D=3D"= -"){ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.= fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_cen= ter,cur_height;if(mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Dense"){cur_y_center= =3Dy_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=3D1}else{if(fe= ature_strand){cur_y_center=3Dy_center;cur_height=3Dthick_height}else{cur_y_= center+=3D(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=3D1}}if(this.draw_backgrou= nd_connector){if(mode=3D=3D=3D"Squish"||mode=3D=3D=3D"Dense"){ctx.fillStyle= =3DCONNECTOR_COLOR}else{if(feature_strand){if(feature_strand=3D=3D=3D"+"){c= tx.fillStyle=3Dctx.canvas.manager.get_pattern("right_strand")}else{if(featu= re_strand=3D=3D=3D"-"){ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left= _strand")}}}else{ctx.fillStyle=3DCONNECTOR_COLOR}}ctx.fillRect(f_start,cur_= y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=3D0,k_len= =3Dfeature_blocks.length;k<k_len;k++){var block=3Dfeature_blocks[k],block_s= tart=3DMath.floor(Math.max(0,(block[0]-tile_low)*w_scale)),block_end=3DMath= .ceil(Math.min(width,Math.max((block[1]-1-tile_low)*w_scale))),last_block_s= tart,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=3Dbloc= k_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,bl= ock_end-block_start,thin_height);if(thick_start!=3D=3Dundefined&&feature_te=

feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thi=

ck_start=3DMath.max(block_start,thick_start),block_thick_end=3DMath.min(blo= ck_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end= -block_thick_start,thick_height);if(feature_blocks.length=3D=3D=3D1&&mode= =3D=3D=3D"Pack"){if(feature_strand=3D=3D=3D"+"){ctx.fillStyle=3Dctx.canvas.= manager.get_pattern("right_strand_inv")}else{if(feature_strand=3D=3D=3D"-")= {ctx.fillStyle=3Dctx.canvas.manager.get_pattern("left_strand_inv")}}if(bloc= k_thick_start+14<block_thick_end){block_thick_start+=3D2;block_thick_end-= =3D2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_= start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){= this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_e= nd,y_center)}last_block_start=3Dblock_start;last_block_end=3Dblock_end}if(m= ode=3D=3D=3D"Pack"){ctx.globalAlpha=3D1;ctx.fillStyle=3D"white";var hscale_= factor=3Dthis.height_scaler.gen_val(feature),new_height=3DMath.ceil(thick_h= eight*hscale_factor),ws_height=3DMath.round((thick_height-new_height)/2);if= (hscale_factor!=3D=3D1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,w= s_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-= f_start,ws_height)}}}ctx.globalAlpha=3D1;if(feature_name&&mode=3D=3D=3D"Pac= k"&&feature_start>tile_low){ctx.fillStyle=3Dlabel_color;if(tile_low=3D=3D= =3D0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign=3D"left"= ;ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=3Dctx.= measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign=3D"right";= ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=3Dc= tx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=3D1;retu= rn[draw_start,draw_end]}});var ReadPainter=3Dfunction(data,view_start,view_= end,prefs,mode,alpha_scaler,height_scaler,ref_seq){FeaturePainter.call(this= ,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_s= eq=3D(ref_seq?ref_seq.data:null)};extend(ReadPainter.prototype,FeaturePaint= er.prototype,{get_row_height:function(){var height,mode=3Dthis.mode;if(mode= =3D=3D=3D"Dense"){height=3DDENSE_TRACK_HEIGHT}else{if(mode=3D=3D=3D"Squish"= ){height=3DSQUISH_TRACK_HEIGHT}else{height=3DPACK_TRACK_HEIGHT;if(this.pref= s.show_insertions){height*=3D2}}}return height},draw_read:function(ctx,mode= ,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,ref_seq){ct= x.textAlign=3D"center";var tile_region=3D[tile_low,tile_high],base_offset= =3D0,seq_offset=3D0,gap=3D0,char_width_px=3Dctx.canvas.manager.char_width_p= x,block_color=3D(strand=3D=3D=3D"+"?this.prefs.block_color:this.prefs.rever= se_strand_color);var draw_last=3D[];if((mode=3D=3D=3D"Pack"||this.mode=3D= =3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w_scale>char_width_px){gap=3DMath.r= ound(w_scale/2)}if(!cigar){cigar=3D[[0,ref_seq.length]]}for(var cig_id=3D0,= len=3Dcigar.length;cig_id<len;cig_id++){var cig=3Dcigar[cig_id],cig_op=3D"M= IDNSHP=3DX"[cig[0]],cig_len=3Dcig[1];if(cig_op=3D=3D=3D"H"||cig_op=3D=3D=3D= "S"){base_offset-=3Dcig_len}var seq_start=3D(feature_start-1)+base_offset,s= _start=3DMath.floor(Math.max(0,(seq_start-tile_low)*w_scale)),s_end=3DMath.= floor(Math.max(0,(seq_start+cig_len-tile_low)*w_scale));if(s_start=3D=3D=3D= s_end){s_end+=3D1}switch(cig_op){case"H":break;case"S":case"M":case"=3D":if= (is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=3Dref_seq.s= lice(seq_offset-1,seq_offset+cig_len);if(gap>0){ctx.fillStyle=3Dblock_color= ;ctx.fillRect(s_start-gap,y_center+1,s_end-s_start,9);ctx.fillStyle=3DCONNE= CTOR_COLOR;for(var c=3D0,str_len=3Dseq.length;c<str_len;c++){if(this.prefs.= show_differences){if(this.ref_seq){var ref_char=3Dthis.ref_seq[seq_start-ti= le_low+c];if(!ref_char||ref_char.toLowerCase()=3D=3D=3Dseq[c].toLowerCase()= ){continue}}else{continue}}if(seq_start+c>=3Dtile_low&&seq_start+c<=3Dtile_= high){var c_start=3DMath.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));= ctx.fillText(seq[c],c_start,y_center+9)}}}else{ctx.fillStyle=3Dblock_color;= ctx.fillRect(s_start,y_center+4,s_end-s_start,SQUISH_FEATURE_HEIGHT)}}seq_o= ffset+=3Dcig_len;base_offset+=3Dcig_len;break;case"N":ctx.fillStyle=3DCONNE= CTOR_COLOR;ctx.fillRect(s_start-gap,y_center+5,s_end-s_start,1);base_offset= +=3Dcig_len;break;case"D":ctx.fillStyle=3D"red";ctx.fillRect(s_start-gap,y_= center+4,s_end-s_start,3);base_offset+=3Dcig_len;break;case"P":break;case"I= ":var insert_x_coord=3Ds_start-gap;if(is_overlap([seq_start,seq_start+cig_l= en],tile_region)){var seq=3Dref_seq.slice(seq_offset-1,seq_offset+cig_len);= if(this.prefs.show_insertions){var x_center=3Ds_start-(s_end-s_start)/2;if(= (mode=3D=3D=3D"Pack"||this.mode=3D=3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w= _scale>char_width_px){ctx.fillStyle=3D"yellow";ctx.fillRect(x_center-gap,y_= center-9,s_end-s_start,9);draw_last[draw_last.length]=3D{type:"triangle",da= ta:[insert_x_coord,y_center+4,5]};ctx.fillStyle=3DCONNECTOR_COLOR;switch(co= mpute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_STA= RT):seq=3Dseq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=3Dseq.= slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS= ):seq=3Dseq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c= =3D0,str_len=3Dseq.length;c<str_len;c++){var c_start=3DMath.floor(Math.max(= 0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_sta= rt)/2,y_center)}}else{ctx.fillStyle=3D"yellow";ctx.fillRect(x_center,y_cent= er+(this.mode!=3D=3D"Dense"?2:5),s_end-s_start,(mode!=3D=3D"Dense"?SQUISH_F= EATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode=3D=3D=3D"Pack"||this.mo= de=3D=3D=3D"Auto")&&ref_seq!=3D=3Dundefined&&w_scale>char_width_px){draw_la= st.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}= seq_offset+=3Dcig_len;break;case"X":seq_offset+=3Dcig_len;break}}ctx.fillSt= yle=3D"yellow";var item,type,data;for(var i=3D0;i<draw_last.length;i++){ite= m=3Ddraw_last[i];type=3Ditem.type;data=3Ditem.data;if(type=3D=3D=3D"text"){= ctx.save();ctx.font=3D"bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]= );ctx.restore()}else{if(type=3D=3D=3D"triangle"){drawDownwardEquilateralTri= angle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,featu= re,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=3Dfeature= [0],feature_start=3Dfeature[1],feature_end=3Dfeature[2],feature_name=3Dfeat= ure[3],f_start=3DMath.floor(Math.max(0,(feature_start-tile_low)*w_scale)),f= _end=3DMath.ceil(Math.min(width,Math.max(0,(feature_end-tile_low)*w_scale))= ),y_center=3D(mode=3D=3D=3D"Dense"?0:(0+slot))*y_scale,label_color=3Dthis.p= refs.label_color,gap=3D0;if((mode=3D=3D=3D"Pack"||this.mode=3D=3D=3D"Auto")= &&w_scale>ctx.canvas.manager.char_width_px){var gap=3DMath.round(w_scale/2)= }if(feature[5] instanceof Array){var b1_start=3DMath.floor(Math.max(0,(feat= ure[4][0]-tile_low)*w_scale)),b1_end=3DMath.ceil(Math.min(width,Math.max(0,= (feature[4][1]-tile_low)*w_scale))),b2_start=3DMath.floor(Math.max(0,(featu= re[5][0]-tile_low)*w_scale)),b2_end=3DMath.ceil(Math.min(width,Math.max(0,(= feature[5][1]-tile_low)*w_scale))),connector=3Dtrue;if(feature[4][1]>=3Dtil= e_low&&feature[4][0]<=3Dtile_high&&feature[4][2]){this.draw_read(ctx,mode,w= _scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3= ],feature[4][4])}else{connector=3Dfalse}if(feature[5][1]>=3Dtile_low&&featu= re[5][0]<=3Dtile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_cen= ter,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5]= [4])}else{connector=3Dfalse}if(connector&&b2_start>b1_end){ctx.fillStyle=3D= CONNECTOR_COLOR;dashedLine(ctx,b1_end-gap,y_center+5,b2_start-gap,y_center+= 5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,featur= e_start,feature[4],feature[5],feature[6])}if(mode=3D=3D=3D"Pack"&&feature_s= tart>tile_low&&feature_name!=3D=3D"."){ctx.fillStyle=3Dthis.prefs.label_col= or;var tile_index=3D1;if(tile_index=3D=3D=3D0&&f_start-ctx.measureText(feat= ure_name).width<0){ctx.textAlign=3D"left";ctx.fillText(feature_name,f_end+L= ABEL_SPACING-gap,y_center+8)}else{ctx.textAlign=3D"right";ctx.fillText(feat= ure_name,f_start-LABEL_SPACING-gap,y_center+8)}}return[0,0]}});var ArcLinke= dFeaturePainter=3Dfunction(data,view_start,view_end,prefs,mode,alpha_scaler= ,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,pre= fs,mode,alpha_scaler,height_scaler);this.longest_feature_length=3Dthis.calc= ulate_longest_feature_length();this.draw_background_connector=3Dfalse;this.= draw_individual_connectors=3Dtrue};extend(ArcLinkedFeaturePainter.prototype= ,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest= _feature_length:function(){var longest_feature_length=3D0;for(var i=3D0,len= =3Dthis.data.length;i<len;i++){var feature=3Dthis.data[i],feature_start=3Df= eature[1],feature_end=3Dfeature[2];longest_feature_length=3DMath.max(longes= t_feature_length,feature_end-feature_start)}return longest_feature_length},= get_top_padding:function(width){var view_range=3Dthis.view_end-this.view_st= art,w_scale=3Dwidth/view_range;return Math.min(128,Math.ceil((this.longest_= feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block= 1_end,block2_start,block2_end,y_center){var x_center=3D(block1_end+block2_s= tart)/2,radius=3Dblock2_start-x_center;var angle1=3DMath.PI,angle2=3D0;if(r= adius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Ma= th.PI,0);ctx.stroke()}}});var Color=3Dfunction(rgb,a){if(Array.isArray(rgb)= ){this.rgb=3Drgb}else{if(rgb.length=3D=3D6){this.rgb=3Drgb.match(/.{2}/g).m= ap(function(c){return parseInt(c,16)})}else{if(rgb.length=3D=3D7){this.rgb= =3Drgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)}= )}else{this.rgb=3Drgb.split("").map(function(c){return parseInt(c+c,16)})}}= }this.alpha=3Dtypeof(a)=3D=3D=3D"number"?a:1};Color.prototype=3D{eval:funct= ion(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb= .map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}e= lse{return"#"+this.rgb.map(function(i){i=3DMath.round(i);i=3D(i>255?255:(i<= 0?0:i)).toString(16);return i.length=3D=3D=3D1?"0"+i:i}).join("")}},toHSL:f= unction(){var r=3Dthis.rgb[0]/255,g=3Dthis.rgb[1]/255,b=3Dthis.rgb[2]/255,a= =3Dthis.alpha;var max=3DMath.max(r,g,b),min=3DMath.min(r,g,b);var h,s,l=3D(= max+min)/2,d=3Dmax-min;if(max=3D=3D=3Dmin){h=3Ds=3D0}else{s=3Dl>0.5?d/(2-ma= x-min):d/(max+min);switch(max){case r:h=3D(g-b)/d+(g<b?6:0);break;case g:h= =3D(b-r)/d+2;break;case b:h=3D(r-g)/d+4;break}h/=3D6}return{h:h*360,s:s,l:l= ,a:a}},toARGB:function(){var argb=3D[Math.round(this.alpha*255)].concat(thi= s.rgb);return"#"+argb.map(function(i){i=3DMath.round(i);i=3D(i>255?255:(i<0= ?0:i)).toString(16);return i.length=3D=3D=3D1?"0"+i:i}).join("")},mix:funct= ion(color2,weight){color1=3Dthis;var p=3Dweight;var w=3Dp*2-1;var a=3Dcolor= 1.toHSL().a-color2.toHSL().a;var w1=3D(((w*a=3D=3D-1)?w:(w+a)/(1+w*a))+1)/2= ;var w2=3D1-w1;var rgb=3D[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w= 1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=3Dcolor1.al= pha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=3Dfun= ction(start_color,end_color,start_value,end_value){this.start_color=3Dnew C= olor(start_color);this.end_color=3Dnew Color(end_color);this.start_value=3D= start_value;this.end_value=3Dend_value;this.value_range=3Dend_value-start_v= alue};LinearRamp.prototype.map_value=3Dfunction(value){value=3DMath.max(val= ue,this.start_value);value=3DMath.min(value,this.end_value);value=3D(value-= this.start_value)/this.value_range;return this.start_color.mix(this.end_col= or,1-value).toCSS()};var SplitRamp=3Dfunction(start_color,middle_color,end_= color,start_value,end_value){this.positive_ramp=3Dnew LinearRamp(middle_col= or,end_color,0,end_value);this.negative_ramp=3Dnew LinearRamp(middle_color,= start_color,0,-start_value);this.start_value=3Dstart_value;this.end_value= =3Dend_value};SplitRamp.prototype.map_value=3Dfunction(value){value=3DMath.= max(value,this.start_value);value=3DMath.min(value,this.end_value);if(value=

=3D0){return this.positive_ramp.map_value(value)}else{return this.negative=

_ramp.map_value(-value)}};var DiagonalHeatmapPainter=3Dfunction(data,view_s= tart,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,= mode);var i,len;if(this.prefs.min_value=3D=3D=3Dundefined){var min_value=3D= Infinity;for(i=3D0,len=3Dthis.data.length;i<len;i++){min_value=3DMath.min(m= in_value,this.data[i][5])}this.prefs.min_value=3Dmin_value}if(this.prefs.ma= x_value=3D=3D=3Dundefined){var max_value=3D-Infinity;for(i=3D0,len=3Dthis.d= ata.length;i<len;i++){max_value=3DMath.max(max_value,this.data[i][5])}this.= prefs.max_value=3Dmax_value}};DiagonalHeatmapPainter.prototype.default_pref= s=3D{min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8= C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=3Dfunction(= ctx,width,height,w_scale){var min_value=3Dthis.prefs.min_value,max_value=3D= this.prefs.max_value,value_range=3Dmax_value-min_value,height_px=3Dheight,v= iew_start=3Dthis.view_start,mode=3Dthis.mode,data=3Dthis.data,invsqrt2=3D1/= Math.sqrt(2);var ramp=3D(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.= prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=3Df= unction(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/= 180);ctx.scale(invsqrt2,invsqrt2);for(var i=3D0,len=3Ddata.length;i<len;i++= ){d=3Ddata[i];s1=3Dscale(d[1]);e1=3Dscale(d[2]);s2=3Dscale(d[4]);e2=3Dscale= (d[5]);value=3Dd[6];ctx.fillStyle=3D(ramp.map_value(value));ctx.fillRect(s1= ,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter= :SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeat= urePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeature= Painter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/tr= ackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filter= s"],function(ab,x,l,u,L,Z,i){var q=3Dab.extend;var V=3Dfunction(ac){return(= "isResolved" in ac)};var n=3D{};var k=3Dfunction(ac,ad){n[ac.attr("id")]=3D= ad};var m=3Dfunction(ac,ae,ag,af){ag=3D".group";var ad=3D{};n[ac.attr("id")= ]=3Daf;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an= =3D$(this),at=3D$(this).parent(),ak=3Dat.children(),am=3Dn[$(this).attr("id= ")],aj,ai,aq,ah,al;ai=3D$(this).parents(ag);if(ai.length!=3D=3D0){aq=3Dai.p= osition().top;ah=3Daq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefo= re(ai);var ar=3Dn[ai.attr("id")];ar.remove_drawable(am);ar.container.add_dr= awable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);= var ar=3Dn[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(= am);return}}}ai=3Dnull;for(al=3D0;al<ak.length;al++){aj=3D$(ak.get(al));aq= =3Daj.position().top;ah=3Daq+aj.outerHeight();if(aj.is(ag)&&this!=3D=3Daj.g= et(0)&&ap.offsetY>=3Daq&&ap.offsetY<=3Dah){if(ap.offsetY-aq<ah-ap.offsetY){= aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(t= his)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add= _drawable(am);return}}for(al=3D0;al<ak.length;al++){aj=3D$(ak.get(al));if(a= p.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass(= "intro"))){break}}if(al=3D=3D=3Dak.length){if(this!=3D=3Dak.get(al-1)){at.a= ppend(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!=3D=3Dak.ge= t(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(= ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=3Dac= .css("border-top");ad["border-bottom"]=3Dac.css("border-bottom");$(this).cs= s({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind(= "dragend",function(){$(this).css(ad)})};exports.moveable=3Dm;var aa=3D16,G= =3D9,D=3D20,A=3D100,I=3D12000,S=3D400,K=3D5000,w=3D100,o=3D"There was an er= ror in indexing this dataset. ",J=3D"A converter for this dataset is not in= stalled. Please check your datatypes_conf.xml file.",E=3D"No data for this = chrom/contig.",v=3D"Preparing data. This can take a while for a large datas= et. If the visualization is saved and closed, preparation will continue in = the background.",y=3D"Tool cannot be rerun: ",a=3D"Loading data...",U=3D"Re= ady for display",Q=3D10,H=3D20;function W(ad,ac){if(!ac){ac=3D0}var ae=3DMa= th.pow(10,ac);return Math.round(ad*ae)/ae}var r=3Dfunction(ad,ac,af){if(!r.= id_counter){r.id_counter=3D0}this.id=3Dr.id_counter++;this.name=3Daf.name;t= his.view=3Dad;this.container=3Dac;this.config=3Dnew F({track:this,params:[{= key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:= af.prefs,onchange:function(){this.track.set_name(this.track.config.values.n= ame)}});this.prefs=3Dthis.config.values;this.drag_handle_class=3Daf.drag_ha= ndle_class;this.is_overview=3Dfalse;this.action_icons=3D{};this.content_vis= ible=3Dtrue;this.container_div=3Dthis.build_container_div();this.header_div= =3Dthis.build_header_div();if(this.header_div){this.container_div.append(th= is.header_div);this.icons_div=3D$("<div/>").css("float","left").hide().appe= ndTo(this.header_div);this.build_action_icons(this.action_icons_def);this.h= eader_div.append($("<div style=3D'clear: both'/>"));this.header_div.dblclic= k(function(ag){ag.stopPropagation()});var ae=3Dthis;this.container_div.hove= r(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div = style=3D'clear: both'/>").appendTo(this.container_div)}};r.prototype.action= _icons_def=3D[{name:"toggle_icon",title:"Hide/show content",css_class:"togg= le",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_= icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.= content_visible=3Dfalse}else{ac.action_icons.toggle_icon.addClass("toggle")= .removeClass("toggle-expand");ac.content_visible=3Dtrue;ac.show_contents()}= }},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on= _click_fn:function(ad){var af=3Dfunction(){hide_modal();$(window).unbind("k= eypress.check_enter_esc")},ac=3Dfunction(){ad.config.update_from_form($(".d= ialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae= =3Dfunction(ag){if((ag.keyCode||ag.which)=3D=3D=3D27){af()}else{if((ag.keyC= ode||ag.which)=3D=3D=3D13){ac()}}};$(window).bind("keypress.check_enter_esc= ",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{n= ame:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:functi= on(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:functio= n(){},changed:function(){this.view.changed()},can_draw:function(){if(this.e= nabled&&this.content_visible){return true}return false},request_draw:functi= on(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.o= ld_name=3Dthis.name;this.name=3Dac;this.name_div.text(this.name)},revert_na= me:function(){if(this.old_name){this.name=3Dthis.old_name;this.name_div.tex= t(this.name)}},remove:function(){this.changed();this.container.remove_drawa= ble(this);var ac=3Dthis.view;this.container_div.hide(0,function(){$(this).r= emove();ac.update_intro_div()})},build_container_div:function(){},build_hea= der_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=3Dt= his;this.action_icons[ad]=3D$("<a/>").attr("href","javascript:void(0);").at= tr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(functio= n(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}}= ,build_action_icons:function(ac){var ae;for(var ad=3D0;ad<ac.length;ad++){a= e=3Dac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_f= n,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){= },show_contents:function(){},get_drawables:function(){}});var z=3Dfunction(= ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=3Dae.obj_type;this.drawables= =3D[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawab= les=3D[];var ad;for(var ac=3D0;ac<ae.length;ac++){ad=3Dp(ae[ac],this.view,t= his);this.add_drawable(ad)}},init:function(){for(var ac=3D0;ac<this.drawabl= es.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=3D0= ;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:functi= on(){var ad=3D[];for(var ac=3D0;ac<this.drawables.length;ac++){ad.push(this= .drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:t= his.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(a= c);ac.container=3Dthis;this.changed()},add_drawable_before:function(ae,ac){= this.changed();var ad=3Dthis.drawables.indexOf(ac);if(ad!=3D=3D-1){this.dra= wables.splice(ad,0,ae);return true}return false},replace_drawable:function(= ae,ac,ad){var af=3Dthis.drawables.indexOf(ae);if(af!=3D=3D-1){this.drawable= s[af]=3Dac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.chang= ed()}return af},remove_drawable:function(ad){var ac=3Dthis.drawables.indexO= f(ad);if(ac!=3D=3D-1){this.drawables.splice(ac,1);ad.container=3Dnull;this.= changed();return true}return false},move_drawable:function(ad,ae){var ac=3D= this.drawables.indexOf(ad);if(ac!=3D=3D-1){this.drawables.splice(ac,1);this= .drawables.splice(ae,0,ad);this.changed();return true}return false},get_dra= wables:function(){return this.drawables}});var P=3Dfunction(ad,ac,af){q(af,= {obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad= ,ac,af);this.content_div=3D$("<div/>").addClass("content-div").attr("id","g= roup_"+this.id+"_content_div").appendTo(this.container_div);k(this.containe= r_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_= class,".group",this);this.filters_manager=3Dnew i.FiltersManager(this);this= .header_div.after(this.filters_manager.parent_div);this.saved_filters_manag= ers=3D[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filt= ers" in af){var ae=3Dthis.filters_manager;this.filters_manager=3Dnew i.Filt= ersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.= parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P= .prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_ic= ons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Sh= ow composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".b= s-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title= :"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_= manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_ma= nagers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filt= ers_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div= :function(){var ac=3D$("<div/>").addClass("group").attr("id","group_"+this.= id);if(this.container){this.container.content_div.append(ac)}return ac},bui= ld_header_div:function(){var ac=3D$("<div/>").addClass("track-header");ac.a= ppend($("<div/>").addClass(this.drag_handle_class));this.name_div=3D$("<div= />").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_co= ntents:function(){this.tiles_div.hide()},show_contents:function(){this.tile= s_div.show();this.request_draw()},update_icons:function(){var ae=3Dthis.dra= wables.length;if(ae=3D=3D=3D0){this.action_icons.composite_icon.hide();this= .action_icons.filters_icon.hide()}else{if(ae=3D=3D=3D1){if(this.drawables[0= ] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.f= ilters_icon.hide()}else{var al,ak,ai,ao=3Dtrue,ag=3Dthis.drawables[0].get_t= ype(),ac=3D0;for(al=3D0;al<ae;al++){ai=3Dthis.drawables[al];if(ai.get_type(= )!=3D=3Dag){can_composite=3Dfalse;break}if(ai instanceof c){ac++}}if(ao||ac= =3D=3D=3D1){this.action_icons.composite_icon.show()}else{this.action_icons.= composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac=3D=3D=3Dthis.dr= awables.length){var ap=3D{},ad;ai=3Dthis.drawables[0];for(ak=3D0;ak<ai.filt= ers_manager.filters.length;ak++){ad=3Dai.filters_manager.filters[ak];ap[ad.= name]=3D[ad]}for(al=3D1;al<this.drawables.length;al++){ai=3Dthis.drawables[= al];for(ak=3D0;ak<ai.filters_manager.filters.length;ak++){ad=3Dai.filters_m= anager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_ma= nager.remove_all();var af,ah,aj,am;for(var an in ap){af=3Dap[an];if(af.leng= th=3D=3D=3Dac){ah=3Dnew i.NumberFilter({name:af[0].name,index:af[0].index})= ;this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.lengt= h>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_i= con.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_= managers:function(){for(var ac=3D0;ac<this.drawables.length;ac++){this.draw= ables[ac].filters_manager=3Dthis.saved_filters_managers[ac]}this.saved_filt= ers_managers=3D[]},setup_multitrack_filtering:function(){if(this.filters_ma= nager.filters.length>0){this.saved_filters_managers=3D[];for(var ac=3D0;ac<= this.drawables.length;ac++){drawable=3Dthis.drawables[ac];this.saved_filter= s_managers.push(drawable.filters_manager);drawable.filters_manager=3Dthis.f= ilters_manager}}this.filters_manager.init_filters()},show_composite_track:f= unction(){var ag=3D[];for(var ad=3D0;ad<this.drawables.length;ad++){ag.push= (this.drawables[ad].name)}var ae=3D"Composite Track of "+this.drawables.len= gth+" tracks ("+ag.join(", ")+")";var af=3Dnew f(this.view,this.view,{name:= ae,drawables:this.drawables});var ac=3Dthis.container.replace_drawable(this= ,af,true);af.request_draw()},add_drawable:function(ac){z.prototype.add_draw= able.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prot= otype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function()= {if(this.filters_manager.visible()){this._restore_filter_managers()}var ac= =3Dq(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()= });if(this.filters_manager.visible()){this.setup_multitrack_filtering()}ret= urn ac},request_draw:function(ac,ae){for(var ad=3D0;ad<this.drawables.lengt= h;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Y=3Dfunction(ac){q(a= c,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=3Dnull;= this.vis_id=3Dac.vis_id;this.dbkey=3Dac.dbkey;this.label_tracks=3D[];this.t= racks_to_be_redrawn=3D[];this.max_low=3D0;this.max_high=3D0;this.zoom_facto= r=3D3;this.min_separation=3D30;this.has_changes=3Dfalse;this.load_chroms_de= ferred=3Dnull;this.init();this.canvas_manager=3Dnew x.CanvasManager(this.co= ntainer.get(0).ownerDocument);this.reset()};ab.extend(Y.prototype,Backbone.= Events);q(Y.prototype,z.prototype,{init:function(){this.requested_redraw=3D= false;var ae=3Dthis.container,ac=3Dthis;this.top_container=3D$("<div/>").ad= dClass("top-container").appendTo(ae);this.browser_content_div=3D$("<div/>")= .addClass("content").css("position","relative").appendTo(ae);this.bottom_co= ntainer=3D$("<div/>").addClass("bottom-container").appendTo(ae);this.top_la= beltrack=3D$("<div/>").addClass("top-labeltrack").appendTo(this.top_contain= er);this.viewport_container=3D$("<div/>").addClass("viewport-container").at= tr("id","viewport-container").appendTo(this.browser_content_div);this.conte= nt_div=3Dthis.viewport_container;k(this.viewport_container,ac);this.intro_d= iv=3D$("<div/>").addClass("intro").appendTo(this.viewport_container).hide()= ;var af=3D$("<div/>").text("Add Datasets to Visualization").addClass("actio= n-button").appendTo(this.intro_div).click(function(){x.select_datasets(sele= ct_datasets_url,add_track_async_url,ac.dbkey,function(ag){ab.each(ag,functi= on(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=3D$("<div/>")= .addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_contai= ner=3D$("<div/>").addClass("trackster-nav-container").prependTo(this.top_co= ntainer);this.nav=3D$("<div/>").addClass("trackster-nav").appendTo(this.nav= _container);this.overview=3D$("<div/>").addClass("overview").appendTo(this.= bottom_container);this.overview_viewport=3D$("<div/>").addClass("overview-v= iewport").appendTo(this.overview);this.overview_close=3D$("<a/>").attr("hre= f","javascript:void(0);").attr("title","Close overview").addClass("icon-but= ton overview-close tooltip").hide().appendTo(this.overview_viewport);this.o= verview_highlight=3D$("<div/>").addClass("overview-highlight").hide().appen= dTo(this.overview_viewport);this.overview_box_background=3D$("<div/>").addC= lass("overview-boxback").appendTo(this.overview_viewport);this.overview_box= =3D$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);th= is.default_overview_height=3Dthis.overview_box.height();this.nav_controls= =3D$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_selec= t=3D$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option= value=3D''>Loading</option>").appendTo(this.nav_controls);var ad=3Dfunctio= n(ag){if(ag.type=3D=3D=3D"focusout"||(ag.keyCode||ag.which)=3D=3D=3D13||(ag= .keyCode||ag.which)=3D=3D=3D27){if((ag.keyCode||ag.which)!=3D=3D27){ac.go_t= o($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.= chrom_select.show()}};this.nav_input=3D$("<input/>").addClass("nav-input").= hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_= span=3D$("<span/>").addClass("location").attr("original-title","Click to ch= ange location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);t= his.location_span.click(function(){ac.location_span.hide();ac.chrom_select.= hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("= display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_= input.autocomplete({source:function(ai,ag){var aj=3D[],ah=3D$.map(ac.get_dr= awables(),function(ak){return ak.data_manager.search_features(ai.term).succ= ess(function(al){aj=3Daj.concat(al)})});$.when.apply($,ah).done(function(){= ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.= vis_id!=3D=3Dundefined){this.hidden_input=3D$("<input/>").attr("type","hidd= en").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=3D$("<a/>").= attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}= ).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_co= ntrols);this.zi_link=3D$("<a/>").attr("id","zoom-in").attr("title","Zoom in= ").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_r= edraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=3Dthis.load= _chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom= (ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(thi= s).find("input").trigger("blur")});this.browser_content_div.bind("dblclick"= ,function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_= box.bind("dragstart",function(ag,ah){this.current_x=3Dah.offsetX}).bind("dr= ag",function(ag,ai){var aj=3Dai.offsetX-this.current_x;this.current_x=3Dai.= offsetX;var ah=3DMath.round(aj/ac.viewport_container.width()*(ac.max_high-a= c.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.re= set_overview()});this.viewport_container.bind("draginit",function(ag,ah){if= (ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragsta= rt",function(ag,ah){ah.original_low=3Dac.low;ah.current_height=3Dag.clientY= ;ah.current_x=3Dah.offsetX}).bind("drag",function(ai,ak){var ag=3D$(this);v= ar al=3Dak.offsetX-ak.current_x;var ah=3Dag.scrollTop()-(ai.clientY-ak.curr= ent_height);ag.scrollTop(ah);ak.current_height=3Dai.clientY;ak.current_x=3D= ak.offsetX;var aj=3DMath.round(al/ac.viewport_container.width()*(ac.high-ac= .low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){a= h*=3D50;var aj=3DMath.round(-ah/ac.viewport_container.width()*(ac.high-ac.l= ow));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,= ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_= labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolu= te","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this)= )}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.= startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var= ah=3DMath.min(ak.pageX,al.startX)-ac.container.offset().left,ag=3DMath.max= (ak.pageX,al.startX)-ac.container.offset().left,aj=3D(ac.high-ac.low),ai=3D= ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.lo= w,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=3DMa= th.min(al.pageX,am.startX),ag=3DMath.max(al.pageX,am.startX),aj=3D(ac.high-= ac.low),ai=3Dac.viewport_container.width(),ak=3Dac.low;ac.low=3DMath.round(= ah/ai*aj)+ak;ac.high=3DMath.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.requ= est_redraw()});this.add_label_track(new X(this,{content_div:this.top_labelt= rack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}))= ;$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this= .resize_timer)}this.resize_timer=3DsetTimeout(function(){ac.resize_window()= },500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(= window).trigger("resize")},changed:function(){this.has_changes=3Dtrue},upda= te_intro_div:function(){if(this.drawables.length=3D=3D=3D0){this.intro_div.= show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){= if(this.timer){clearTimeout(this.timer)}if(ag){var ae=3Dthis;this.timer=3Ds= etTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{vie= w.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){th= is.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val= (this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=3Dview.chrom_select= .val();if(ad!=3D=3D""){this.trigger_navigate(ad,view.low,view.high,true)}},= load_chroms:function(ae){ae.num=3Dw;var ac=3Dthis,ad=3D$.Deferred();$.ajax(= {url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){= if(ag.chrom_info.length=3D=3D=3D0){return}if(ag.reference){ac.add_label_tra= ck(new B(ac))}ac.chrom_data=3Dag.chrom_info;var aj=3D'<option value=3D"">Se= lect Chrom/Contig</option>';for(var ai=3D0,af=3Dac.chrom_data.length;ai<af;= ai++){var ah=3Dac.chrom_data[ai].chrom;aj+=3D'<option value=3D"'+ah+'">'+ah= +"</option>"}if(ag.prev_chroms){aj+=3D'<option value=3D"previous">Previous = '+w+"</option>"}if(ag.next_chroms){aj+=3D'<option value=3D"next">Next '+w+"= </option>"}ac.chrom_select.html(aj);ac.chrom_start_index=3Dag.start_index;a= d.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey= :",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=3Dthis;if= (!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah= ,ad,aj)});return}if(!ah||ah=3D=3D=3D"None"){return}if(ah=3D=3D=3D"previous"= ){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah=3D=3D=3D"next= "){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=3D$.grep(ae= .chrom_data,function(ak,al){return ak.chrom=3D=3D=3Dah})[0];if(ai=3D=3D=3Du= ndefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});= return}else{if(ah!=3D=3Dae.chrom){ae.chrom=3Dah;ae.chrom_select.val(ae.chro= m);ae.max_high=3Dai.len-1;ae.reset();ae.request_redraw(true);for(var ag=3D0= ,ac=3Dae.drawables.length;ag<ac;ag++){var af=3Dae.drawables[ag];if(af.init)= {af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!=3D=3Du= ndefined&&aj!=3D=3Dundefined){ae.low=3DMath.max(ad,0);ae.high=3DMath.min(aj= ,ae.max_high)}else{ae.low=3D0;ae.high=3Dae.max_high}ae.reset_overview();ae.= request_redraw()}},go_to:function(ag){ag=3Dag.replace(/ |,/g,"");var ak=3Dt= his,ac,af,ad=3Dag.split(":"),ai=3Dad[0],aj=3Dad[1];if(aj!=3D=3Dundefined){t= ry{var ah=3Daj.split("-");ac=3DparseInt(ah[0],10);af=3DparseInt(ah[1],10)}c= atch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae= ){var ac=3Dthis;var ad=3Dac.high-ac.low;this.move_delta(ae*ad)},move_delta:= function(af){var ac=3Dthis;var ae=3Dac.high-ac.low;if(ac.low-af<ac.max_low)= {ac.low=3Dac.max_low;ac.high=3Dac.max_low+ae}else{if(ac.high-af>ac.max_high= ){ac.high=3Dac.max_high;ac.low=3Dac.max_high-ae}else{ac.high-=3Daf;ac.low-= =3Daf}}ac.request_redraw();var ad=3Dac.chrom_select.val();this.trigger_navi= gate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_dra= wable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_l= abel_track:function(ac){ac.view=3Dthis;ac.init();this.label_tracks.push(ac)= },remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae)= ;if(ad){var ac=3Dthis;ae.container_div.hide(0,function(){$(this).remove();a= c.update_intro_div()})}},reset:function(){this.low=3Dthis.max_low;this.high= =3Dthis.max_high;this.viewport_container.find(".yaxislabel").remove()},requ= est_redraw:function(ak,ac,aj,al){var ai=3Dthis,ah=3D(al?[al]:ai.drawables),= ae;var ad;for(var ag=3D0;ag<ah.length;ag++){ad=3Dah[ag];ae=3D-1;for(var af= =3D0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af]= [0]=3D=3D=3Dad){ae=3Daf;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac= ,aj])}else{ai.tracks_to_be_redrawn[ag][1]=3Dac;ai.tracks_to_be_redrawn[ag][= 2]=3Daj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._re= draw(ak)});this.requested_redraw=3Dtrue}},_redraw:function(am){this.request= ed_redraw=3Dfalse;var aj=3Dthis.low,af=3Dthis.high;if(aj<this.max_low){aj= =3Dthis.max_low}if(af>this.max_high){af=3Dthis.max_high}var al=3Dthis.high-= this.low;if(this.high!=3D=3D0&&al<this.min_separation){af=3Daj+this.min_sep= aration}this.low=3DMath.floor(aj);this.high=3DMath.ceil(af);this.update_loc= ation(this.low,this.high);this.resolution_b_px=3D(this.high-this.low)/this.= viewport_container.width();this.resolution_px_b=3Dthis.viewport_container.w= idth()/(this.high-this.low);var ac=3D(this.low/(this.max_high-this.max_low)= *this.overview_viewport.width())||0;var ai=3D((this.high-this.low)/(this.ma= x_high-this.max_low)*this.overview_viewport.width())||0;var an=3D13;this.ov= erview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overv= iew_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_= highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=3D0,ah=3D= this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=3Dthis.tracks_to_be_redrawn= [ag][0];ad=3Dthis.tracks_to_be_redrawn[ag][1];ak=3Dthis.tracks_to_be_redraw= n[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=3D[];for(ag=3D0,= ah=3Dthis.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},= zoom_in:function(ad,ae){if(this.max_high=3D=3D=3D0||this.high-this.low<=3Dt= his.min_separation){return}var af=3Dthis.high-this.low,ag=3Daf/2+this.low,a= c=3D(af/this.zoom_factor)/2;if(ad){ag=3Dad/this.viewport_container.width()*= (this.high-this.low)+this.low}this.low=3DMath.round(ag-ac);this.high=3DMath= .round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(= this.max_high=3D=3D=3D0){return}var ad=3Dthis.high-this.low,ae=3Dad/2+this.= low,ac=3D(ad*this.zoom_factor)/2;this.low=3DMath.round(ae-ac);this.high=3DM= ath.round(ae+ac);this.changed();this.request_redraw()},resize_window:functi= on(){this.viewport_container.height(this.container.height()-this.top_contai= ner.height()-this.bottom_container.height());this.request_redraw()},set_ove= rview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dat= aset_id=3D=3D=3Dae.dataset_id){return}this.overview_viewport.find(".track")= .remove()}var ad=3Dae.copy({content_div:this.overview_viewport}),ac=3Dthis;= ad.header_div.hide();ad.is_overview=3Dtrue;ac.overview_drawable=3Dad;this.o= verview_drawable.postdraw_actions=3Dfunction(){ac.overview_highlight.show()= .height(ac.overview_drawable.content_div.height());ac.overview_viewport.hei= ght(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight()= );ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request= _draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove()= ;this.overview_viewport.find(".track-tile").remove();this.overview_viewport= .height(this.default_overview_height);this.overview_box.height(this.default= _overview_height);this.overview_close.hide();this.overview_highlight.hide()= ;view.resize_window();view.overview_drawable=3Dnull}});var s=3Dfunction(ae,= aj,af){this.track=3Dae;this.name=3Daj.name;this.params=3D[];var aq=3Daj.par= ams;for(var ag=3D0;ag<aq.length;ag++){var al=3Daq[ag],ad=3Dal.name,ap=3Dal.= label,ah=3Dunescape(al.html),ar=3Dal.value,an=3Dal.type;if(an=3D=3D=3D"numb= er"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}e= lse{if(an=3D=3D=3D"select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad= ]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an= )}}}this.parent_div=3D$("<div/>").addClass("dynamic-tool").hide();this.pare= nt_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){a= u.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});v= ar ao=3D$("<div class=3D'tool-name'>").appendTo(this.parent_div).text(this.= name);var am=3Dthis.params;var ak=3Dthis;$.each(this.params,function(av,ay)= {var ax=3D$("<div>").addClass("param-row").appendTo(ak.parent_div);var au= =3D$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=3D= $("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":in= put").val(ay.value);$("<div style=3D'clear: both;'/>").appendTo(ax)});this.= parent_div.find("input").click(function(){$(this).select()});var at=3D$("<d= iv>").addClass("param-row").appendTo(this.parent_div);var ai=3D$("<input ty= pe=3D'submit'>").attr("value","Run on complete dataset").appendTo(at);var a= c=3D$("<input type=3D'submit'>").attr("value","Run on visible region").css(= "margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});= ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){t= his.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac= 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Z.Dataset(aj));ai.tiles_div.text("Running job."= );ai.init()})},run:function(ac,ae,af){ac.inputs=3Dthis.get_param_values_dic= t();var ad=3Dnew l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get= ("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"applicati= on/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=3D= =3D"pending"}});$.when(ad.go()).then(function(ag){if(ag=3D=3D=3D"no convert= er"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.e= rror){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}= else{af(ag)}}})}});var N=3Dfunction(ad,ac,ae,af){this.name=3Dad;this.label= =3Dac;this.html=3D$(ae);this.value=3Daf};q(N.prototype,{update_value:functi= on(){this.value=3D$(this.html).val()}});var e=3Dfunction(ae,ad,ag,ah,af,ac)= {N.call(this,ae,ad,ag,ah);this.min=3Daf;this.max=3Dac};q(e.prototype,N.prot= otype,{update_value:function(){N.prototype.update_value.call(this);this.val= 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arameter space visualization",css_class:"arrow-split",on_click_fn:function(= ac){var af=3D'<strong>Tool</strong>: <%=3D track.tool.name %><br/><strong>D= ataset</strong>: <%=3D track.name %><br/><strong>Region(s)</strong>: <selec= t name=3D"regions"><option value=3D"cur">current viewing area</option><opti= on value=3D"bookmarks">bookmarks</option><option value=3D"both">current vie= wing area and bookmarks</option></select>',ae=3Dab.template(af,{track:ac});= var ah=3Dfunction(){hide_modal();$(window).unbind("keypress.check_enter_esc= ")},ad=3Dfunction(){var aj=3D$('select[name=3D"regions"] option:selected').= val(),al,ai=3Dnew x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.= high}),ak=3Dab.map($(".bookmark"),function(am){return new x.GenomeRegion({f= rom_str:$(am).children(".position").text()})});if(aj=3D=3D=3D"cur"){al=3D[a= i]}else{if(aj=3D=3D=3D"bookmarks"){al=3Dak}else{al=3D[ai].concat(ak)}}hide_= modal();window.location.href=3Dgalaxy_paths.get("sweepster_url")+"?"+$.para= m({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new= Backbone.Collection(al).toJSON())})},ag=3Dfunction(ai){if((ai.keyCode||ai.= which)=3D=3D=3D27){ah()}else{if((ai.keyCode||ai.which)=3D=3D=3D13){ad()}}};= show_modal("Visualize tool parameter space and output from different parame= ter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_dr= aw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return t= rue}return false},build_container_div:function(){return $("<div/>").addClas= s("track").attr("id","track_"+this.id).css("position","relative")},build_he= ader_div:function(){var ac=3D$("<div class=3D'track-header'/>");if(this.vie= w.editor){this.drag_div=3D$("<div/>").addClass(this.drag_handle_class).appe= ndTo(ac)}this.name_div=3D$("<div/>").addClass("track-name").appendTo(ac).te= xt(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9= -]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle= 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ll||af.data.length=3D=3D=3D0))){ad.container_div.addClass("nodata");ad.tile= s_div.text(E)}else{if(af=3D=3D=3D"pending"){ad.container_div.addClass("pend= ing");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_w= ait)}else{if(af=3D=3D=3D"data"||af.status=3D=3D=3D"data"){if(af.valid_chrom= s){ad.valid_chroms=3Daf.valid_chroms;ad.update_icons()}ad.tiles_div.text(U)= ;if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visib= le_height_px+"px");ad.enabled=3Dtrue;$.when(ad.predraw_init()).done(functio= n(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.re= quest_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},pre= draw_init:function(){},get_drawables:function(){return this}});var M=3Dfunc= tion(ae,ad,af){g.call(this,ae,ad,af);var ac=3Dthis;m(ac.container_div,ac.dr= ag_handle_class,".group",ac);this.filters_manager=3Dnew i.FiltersManager(th= is,("filters" in af?af.filters:null));this.data_manager.set("filters_manage= r",this.filters_manager);this.filters_available=3Dfalse;this.tool=3D("tool"= in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=3Dn= ew x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_man= ager);if(this.tool){this.dynamic_tool_div=3Dthis.tool.parent_div;this.heade= r_div.after(this.dynamic_tool_div)}}this.tiles_div=3D$("<div/>").addClass("= tiles").appendTo(this.content_div);this.overlay_div=3D$("<div/>").addClass(= "overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)= }};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.acti= on_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track h= eight, not all feature rows are displayed. Click to display more rows.",css= _class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.= slotters[ac.view.resolution_px_b].max_rows*=3D2;ac.request_draw(true)},hide= :true}]),copy:function(ac){var ad=3Dthis.to_dict();q(ad,{data_manager:this.= data_manager});var ae=3Dnew this.constructor(this.view,ac,ad);ae.change_mod= e(this.mode);ae.enabled=3Dthis.enabled;return ae},set_filters_manager:funct= ion(ac){this.filters_manager=3Dac;this.header_div.after(this.filters_manage= r.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:th= is.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,= mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool= ?this.tool.state_dict():{})}},change_mode:function(ad){var ac=3Dthis;ac.mod= e=3Dad;ac.config.values.mode=3Dad;ac.tile_cache.clear();ac.request_draw();t= his.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+"= )");return ac},update_icons:function(){var ac=3Dthis;if(ac.filters_availabl= e){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hi= de()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_sp= ace_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.= param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return= ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(fa= lse,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.ca= n_draw()){return}var al=3Dthis.view.low,ah=3Dthis.view.high,aj=3Dah-al,ae= =3Dthis.view.container.width(),ap=3Dthis.view.resolution_px_b,ag=3Dthis.vie= w.resolution_b_px;if(this.is_overview){al=3Dthis.view.max_low;ah=3Dthis.vie= w.max_high;ag=3D(view.max_high-view.max_low)/ae;ap=3D1/ag}this.before_draw(= );this.tiles_div.children().addClass("remove");var ac=3DMath.floor(al/(ag*S= )),ak=3Dtrue,ao=3D[],ai=3Dfunction(aq){return(aq&&"track" in aq)};while((ac= *S*ag)<ah){var am=3Dthis.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(a= m)){ao.push(am)}else{ak=3Dfalse}ac+=3D1}if(!an){this.tiles_div.children(".r= emove").removeClass("remove").remove()}var af=3Dthis;if(ak){this.tiles_div.= children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_ac= tions:function(ae,af,ah,ac){var ag=3Dfalse;for(var ad=3D0;ad<ae.length;ad++= ){if(ae[ad].has_icons){ag=3Dtrue;break}}if(ag){for(var ad=3D0;ad<ae.length;= ad++){tile=3Dae[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}= }}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=3Dthis,ax=3Dthis._gen= _tile_cache_key(ao,ai,au),af=3Dthis._get_tile_bounds(au,ar);if(!ap){ap=3D{}= }var aw=3D(ac?undefined:an.tile_cache.get_elt(ax));if(aw){an.show_tile(aw,a= h,ai);return aw}var al=3Dtrue;var at=3Dan.data_manager.get_data(af,an.mode,= ar,an.data_url_extra_params);if(V(at)){al=3Dfalse}var aj;if(view.reference_= track&&ai>view.canvas_manager.char_width_px){aj=3Dview.reference_track.data= _manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params)= ;if(V(aj)){al=3Dfalse}}if(al){q(at,ap.more_tile_data);var ak=3Dan.mode;if(a= k=3D=3D=3D"Auto"){ak=3Dan.get_mode(at);an.update_auto_mode(ak)}var ae=3Dan.= view.canvas_manager.new_canvas(),av=3Daf.get("start"),ad=3Daf.get("end"),ao= =3DMath.ceil((ad-av)*ai)+an.left_offset,am=3Dan.get_canvas_height(at,ak,ai,= ao);ae.width=3Dao;ae.height=3Dam;var aq=3Dae.getContext("2d");aq.translate(= this.left_offset,0);var aw=3Dan.draw_tile(at,aq,ak,ar,af,ai,aj);if(aw!=3D= =3Dundefined){an.tile_cache.set_elt(ax,aw);an.show_tile(aw,ah,ai)}return aw= }var ag=3D$.Deferred();$.when(at,aj).then(function(){view.request_redraw(fa= lse,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac= ,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag= ,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},sh= ow_tile:function(ae,ah,ai){var ad=3Dthis,ac=3Dae.html_elt;ae.predisplay_act= ions();var ag=3D(ae.low-(this.is_overview?this.view.max_low:this.view.low))= *ai;if(this.left_offset){ag-=3Dthis.left_offset}ac.css({position:"absolute"= ,top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah= .append(ac)}ae.html_elt.height("auto");this.max_height_px=3DMath.max(this.m= ax_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("hei= ght",this.max_height_px+"px");var af=3Dthis.max_height_px;if(this.visible_h= eight_px!=3D=3D0){af=3DMath.min(this.max_height_px,this.visible_height_px)}= this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var = af=3DMath.floor(ac*S*ad),ag=3DMath.ceil(S*ad),ae=3D(af+ag<=3Dthis.view.max_= high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.c= hrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae,ac,af){v= ar ad=3Dthis,ag=3D(ae!=3D=3Dundefined&&ac!=3D=3Dundefined&&af!=3D=3Dundefin= ed?ae+":"+ac+"-"+af:"all");return" - region=3D["+ag+"], parameters=3D["+ad.= tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(a= c,ad){return true},can_subset:function(ac){return false},init_for_tool_data= :function(){this.data_manager.set("data_type","raw_data");this.data_query_w= ait=3D1000;this.dataset_check_type=3D"state";this.normal_postdraw_actions= =3Dthis.postdraw_actions;this.postdraw_actions=3Dfunction(ae,af,ah,ac){var = ad=3Dthis;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type=3D"= converted_datasets_state";ad.data_query_wait=3DK;var ag=3Dnew l.ServerState= Deferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda= _ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){retu= rn ai!=3D=3D"pending"}});$.when(ag.go()).then(function(){ad.data_manager.se= t("data_type","data")});ad.postdraw_actions=3Dad.normal_postdraw_actions}}}= );var X=3Dfunction(ad,ac){var ae=3D{resize:false};g.call(this,ad,ac,ae);thi= s.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_h= eader_div:function(){},init:function(){this.enabled=3Dtrue},_draw:function(= ){var ae=3Dthis.view,af=3Dae.high-ae.low,ai=3DMath.floor(Math.pow(10,Math.f= loor(Math.log(af)/Math.log(10)))),ac=3DMath.floor(ae.low/ai)*ai,ag=3Dthis.v= iew.container.width(),ad=3D$("<div style=3D'position: relative; height: 1.3= em;'></div>");while(ac<ae.high){var ah=3D(ac-ae.low)/af*ag;ad.append($("<di= v class=3D'label'>"+commatize(ac)+"</div>").css({position:"absolute",left:a= h-1}));ac+=3Dai}this.content_div.children(":first").remove();this.content_d= iv.append(ad)}});var f=3Dfunction(ad,ac,ag){M.call(this,ad,ac,ag);this.draw= ables=3D[];this.left_offset=3D0;if("drawables" in ag){var af;for(var ae=3D0= ;ae<ag.drawables.length;ae++){af=3Dag.drawables[ae];this.drawables[ae]=3Dp(= af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=3Daf.left_= offset}}this.enabled=3Dtrue}if(this.drawables.length!=3D=3D0){this.set_disp= lay_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.upda= te_icons();this.obj_type=3D"CompositeTrack"};q(f.prototype,M.prototype,{act= ion_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_cl= ass:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.sh= ow_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_d= ict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpa= ck_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac)= ;for(var ad=3D0;ad<this.drawables.length;ad++){this.drawables[ad].change_mo= de(ac)}},init:function(){var ae=3D[];for(var ad=3D0;ad<this.drawables.lengt= h;ad++){ae.push(this.drawables[ad].init())}var ac=3Dthis;$.when.apply($,ae)= .then(function(){ac.enabled=3Dtrue;ac.request_draw()})},update_icons:functi= on(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hid= e();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can= _draw,draw_helper:function(ad,at,az,aw,ak,am,au){var ar=3Dthis,aD=3Dthis._g= en_tile_cache_key(at,am,az),ah=3Dthis._get_tile_bounds(az,aw);if(!au){au=3D= {}}var aC=3D(ad?undefined:ar.tile_cache.get_elt(aD));if(aC){ar.show_tile(aC= ,ak,am);return aC}var al=3D[],ar,ap=3Dtrue,ax,an;for(var ay=3D0;ay<this.dra= wables.length;ay++){ar=3Dthis.drawables[ay];ax=3Dar.data_manager.get_data(a= h,ar.mode,aw,ar.data_url_extra_params);if(V(ax)){ap=3Dfalse}al.push(ax);an= =3Dnull;if(view.reference_track&&am>view.canvas_manager.char_width_px){an= =3Dview.reference_track.data_manager.get_data(ah,ar.mode,aw,view.reference_= track.data_url_extra_params);if(V(an)){ap=3Dfalse}}al.push(an)}if(ap){q(ax,= au.more_tile_data);this.tile_predraw_init();var ag=3Dar.view.canvas_manager= .new_canvas(),ai=3Dar._get_tile_bounds(az,aw),aA=3Dah.get("start"),ae=3Dah.= get("end"),aB=3D0,at=3DMath.ceil((ae-aA)*am)+this.left_offset,aq=3D0,af=3D[= ],ay;var ac=3D0;for(ay=3D0;ay<this.drawables.length;ay++,aB+=3D2){ar=3Dthis= .drawables[ay];ax=3Dal[aB];var ao=3Dar.mode;if(ao=3D=3D=3D"Auto"){ao=3Dar.g= et_mode(ax);ar.update_auto_mode(ao)}af.push(ao);ac=3Dar.get_canvas_height(a= x,ao,am,at);if(ac>aq){aq=3Dac}}ag.width=3Dat;ag.height=3D(au.height?au.heig= ht:aq);aB=3D0;var av=3Dag.getContext("2d");av.translate(this.left_offset,0)= ;av.globalAlpha=3D0.5;av.globalCompositeOperation=3D"source-over";for(ay=3D= 0;ay<this.drawables.length;ay++,aB+=3D2){ar=3Dthis.drawables[ay];ax=3Dal[aB= ];an=3Dal[aB+1];aC=3Dar.draw_tile(ax,av,af[ay],aw,ah,am,an)}this.tile_cache= .set_elt(aD,aC);this.show_tile(aC,ak,am);return aC}var aj=3D$.Deferred(),ar= =3Dthis;$.when.apply($,al).then(function(){view.request_redraw(false,false,= false,ar);aj.resolve()});return aj},show_group:function(){var af=3Dnew P(th= is.view,this.container,{name:this.name}),ac;for(var ae=3D0;ae<this.drawable= s.length;ae++){ac=3Dthis.drawables[ae];ac.update_icons();af.add_drawable(ac= );ac.container=3Daf;af.content_div.append(ac.container_div)}var ad=3Dthis.c= ontainer.replace_drawable(this,af,true);af.request_draw()},tile_predraw_ini= t:function(){var af=3DNumber.MAX_VALUE,ac=3D-af,ad;for(var ae=3D0;ae<this.d= rawables.length;ae++){ad=3Dthis.drawables[ae];if(ad instanceof h){if(ad.pre= fs.min_value<af){af=3Dad.prefs.min_value}if(ad.prefs.max_value>ac){ac=3Dad.= prefs.max_value}}}for(var ae=3D0;ae<this.drawables.length;ae++){ad=3Dthis.d= rawables[ae];ad.prefs.min_value=3Daf;ad.prefs.max_value=3Dac}},postdraw_act= ions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,= ad);var ag=3D-1;for(var af=3D0;af<ae.length;af++){var ac=3Dae[af].html_elt.= find("canvas").height();if(ac>ag){ag=3Dac}}for(var af=3D0;af<ae.length;af++= ){var ai=3Dae[af];if(ai.html_elt.find("canvas").height()!=3D=3Dag){this.dra= w_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag}= );ai.html_elt.remove()}}}});var B=3Dfunction(ac){M.call(this,ac,{content_di= v:ac.top_labeltrack},{resize:false});ac.reference_track=3Dthis;this.left_of= fset=3D200;this.visible_height_px=3D12;this.container_div.addClass("referen= ce-track");this.content_div.css("background","none");this.content_div.css("= min-height","0px");this.content_div.css("border","none");this.data_url=3Dre= ference_url+"/"+this.view.dbkey;this.data_url_extra_params=3D{reference:tru= e};this.data_manager=3Dnew x.ReferenceTrackDataManager({data_url:this.data_= url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_he= ader_div:function(){},init:function(){this.data_manager.clear();this.enable= d=3Dtrue},can_draw:r.prototype.can_draw,draw_helper:function(ag,ae,ac,ad,ah= ,ai,af){if(ai>this.view.canvas_manager.char_width_px){return M.prototype.dr= aw_helper.call(this,ag,ae,ac,ad,ah,ai,af)}else{this.hide_contents();return = null}},draw_tile:function(ak,al,ag,af,ai,am){var ae=3Dthis;if(am>this.view.= canvas_manager.char_width_px){if(ak.data=3D=3D=3Dnull){this.hide_contents()= ;return}var ad=3Dal.canvas;al.font=3Dal.canvas.manager.default_font;al.text= Align=3D"center";ak=3Dak.data;for(var ah=3D0,aj=3Dak.length;ah<aj;ah++){var= ac=3DMath.floor(ah*am);al.fillText(ak[ah],ac,10)}this.show_contents();retu= rn new b(ae,ai,af,ad,ak)}this.hide_contents()}});var h=3Dfunction(ae,ad,af)= {var ac=3Dthis;this.display_modes=3D["Histogram","Line","Filled","Intensity= "];this.mode=3D"Histogram";M.call(this,ae,ad,af);this.hda_ldda=3Daf.hda_ldd= a;this.dataset_id=3Daf.dataset_id;this.original_dataset_id=3Dthis.dataset_i= d;this.left_offset=3D0;this.config=3Dnew F({track:this,params:[{key:"name",= label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color= ",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"= Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Ma= x Value",type:"float",default_value:undefined},{key:"mode",type:"string",de= fault_value:this.mode,hidden:true},{key:"height",type:"int",default_value:3= 2,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.pr= efs.name);ac.vertical_range=3Dac.prefs.max_value-ac.prefs.min_value;ac.set_= min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.= prefs=3Dthis.config.values;this.visible_height_px=3Dthis.config.values.heig= ht;this.vertical_range=3Dthis.config.values.max_value-this.config.values.mi= n_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.r= equest_draw(true)},set_min_value:function(ac){this.prefs.min_value=3Dac;$("= #linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.til= e_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.= max_value=3Dac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.m= ax_value);this.tile_cache.clear();this.request_draw()},predraw_init:functio= n(){var ac=3Dthis;ac.vertical_range=3Dundefined;return $.getJSON(ac.dataset= .url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.= max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line= -track");var ag=3Dad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(p= arseFloat(ac.prefs.max_value))){var ae=3Dag.min,ai=3Dag.max;ae=3DMath.floor= (Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=3DMath.ceil(Math.max(0,Math.m= in(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=3Dae;ac.prefs.max_value=3Dai;$(= "#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.d= ataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=3Dac.prefs.m= ax_value-ac.prefs.min_value;ac.total_frequency=3Dag.total_frequency;ac.cont= ainer_div.find(".yaxislabel").remove();var ah=3D$("<div/>").text(W(ac.prefs= .min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs= -tooltip").remove();var aj=3DparseFloat(aj);if(!isNaN(aj)){ac.set_min_value= (aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id",= "linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=3D$("<= div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_fin= ish:function(aj){$(".bs-tooltip").remove();var aj=3DparseFloat(aj);if(!isNa= N(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxisla= bel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.cont= ainer_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=3Daj.canvas,af= =3Dag.get("start"),ai=3Dag.get("end"),ah=3Dnew L.LinePainter(al.data,af,ai,= this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac= ,al.data)},can_subset:function(ac){return false}});var t=3Dfunction(ae,ad,a= f){var ac=3Dthis;this.display_modes=3D["Heatmap"];this.mode=3D"Heatmap";M.c= all(this,ae,ad,af);this.hda_ldda=3Daf.hda_ldda;this.dataset_id=3Daf.dataset= _id;this.original_dataset_id=3Dthis.dataset_id;this.left_offset=3D0;this.co= nfig=3Dnew F({track:this,params:[{key:"name",label:"Name",type:"text",defau= lt_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",de= fault_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color"= ,default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",d= efault_value:0},{key:"max_value",label:"Max Value",type:"float",default_val= ue:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"= height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,on= change:function(){ac.set_name(ac.prefs.name);ac.vertical_range=3Dac.prefs.m= ax_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max= _value(ac.prefs.max_value)}});this.prefs=3Dthis.config.values;this.visible_= height_px=3Dthis.config.values.height;this.vertical_range=3Dthis.config.val= ues.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.pro= totype,{on_resize:function(){this.request_draw(true)},set_min_value:functio= n(ac){this.prefs.min_value=3Dac;this.tile_cache.clear();this.request_draw()= },set_max_value:function(ac){this.prefs.max_value=3Dac;this.tile_cache.clea= r();this.request_draw()},draw_tile:function(am,ak,ah,af,ad,al){var ae=3Dak.= canvas,ac=3Dthis._get_tile_bounds(ad,af),ag=3Dac[0],aj=3Dac[1],ai=3Dnew L.D= iagonalHeatmapPainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.h= eight,al);return new b(this,ad,af,ae,am.data)}});var c=3Dfunction(af,ae,ah)= {var ad=3Dthis;this.display_modes=3D["Auto","Coverage","Dense","Squish","Pa= ck"];M.call(this,af,ae,ah);var ag=3Dl.get_random_color(),ac=3Dl.get_random_= color([ag,"#ffffff"]);this.config=3Dnew F({track:this,params:[{key:"name",l= abel:"Name",type:"text",default_value:this.name},{key:"block_color",label:"= Block color",type:"color",default_value:ag},{key:"reverse_strand_color",lab= el:"Antisense strand color",type:"color",default_value:ac},{key:"label_colo= r",label:"Label color",type:"color",default_value:"black"},{key:"show_count= s",label:"Show summary counts",type:"bool",default_value:true,help:"Show th= e number of items in each bin when drawing summary histogram"},{key:"histog= ram_max",label:"Histogram maximum",type:"float",default_value:null,help:"cl= ear value to set automatically"},{key:"connector_style",label:"Connector st= yle",type:"select",default_value:"fishbones",options:[{label:"Line with arr= ows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"stri= ng",default_value:this.mode,hidden:true},{key:"height",type:"int",default_v= alue:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:fu= nction(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_fr= om_config();ad.request_draw()}});this.prefs=3Dthis.config.values;this.visib= le_height_px=3Dthis.config.values.height;this.container_div.addClass("featu= re-track");this.hda_ldda=3Dah.hda_ldda;this.dataset_id=3Dah.dataset_id;this= .original_dataset_id=3Dah.dataset_id;this.show_labels_scale=3D0.001;this.sh= owing_details=3Dfalse;this.summary_draw_height=3D30;this.slotters=3D{};this= .start_end_dct=3D{};this.left_offset=3D200;this.set_painter_from_config()};= q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.datase= t_id=3Dac.get("id");this.hda_ldda=3Dac.get("hda_ldda");this.dataset=3Dac;th= is.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(th= is.config.values.connector_style=3D=3D=3D"arcs"){this.painter=3DL.ArcLinked= FeaturePainter}else{this.painter=3DL.LinkedFeaturePainter}},before_draw:fun= ction(){this.max_height_px=3D0},postdraw_actions:function(ar,am,ah,ag){M.pr= ototype.postdraw_actions.call(this,ar,ag);var al=3Dthis,ao;if(al.mode=3D=3D= =3D"Coverage"){var ad=3D-1;for(ao=3D0;ao<ar.length;ao++){var an=3Dar[ao].ma= x_val;if(an>ad){ad=3Dan}}for(ao=3D0;ao<ar.length;ao++){var au=3Dar[ao];if(a= u.max_val!=3D=3Dad){au.html_elt.remove();al.draw_helper(true,am,au.index,au= .resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filt= ers_manager){var ai=3Dal.filters_manager.filters;for(var aq=3D0;aq<ai.lengt= h;aq++){ai[aq].update_ui_elt()}var at=3Dfalse,ac,aj;for(ao=3D0;ao<ar.length= ;ao++){if(ar[ao].data.length){ac=3Dar[ao].data[0];for(var aq=3D0;aq<ai.leng= th;aq++){aj=3Dai[aq];if(aj.applies_to(ac)&&aj.min!=3D=3Daj.max){at=3Dtrue;b= reak}}}}if(al.filters_available!=3D=3Dat){al.filters_available=3Dat;if(!al.= filters_available){al.filters_manager.hide()}al.update_icons()}}this.contai= ner_div.find(".yaxislabel").remove();var af=3Dar[0];if(af instanceof j){var= ak=3D(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=3D$= ("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){= $(".bs-tooltip").remove();var av=3DparseFloat(av);al.prefs.histogram_max=3D= (!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Se= t max value; leave blank to use default"}).addClass("yaxislabel top").css("= color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanc= eof O){var ap=3Dtrue;for(ao=3D0;ao<ar.length;ao++){if(!ar[ao].all_slotted){= ap=3Dfalse;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else= {this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_= more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode= =3D=3D=3D"Auto"){if(ac=3D=3D=3D"no_detail"){ac=3D"feature spans"}else{if(ac= =3D=3D=3D"summary_tree"){ac=3D"coverage histogram"}}this.action_icons.mode_= icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slot= s:function(ag,ac,af){var ad=3Dthis.view.canvas_manager.dummy_context,ae=3Dt= his.slotters[ag];if(!ae||(ae.mode!=3D=3Daf)){ae=3Dnew (u.FeatureSlotter)(ag= ,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=3Dae}retur= n ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type=3D=3D=3D"s= ummary_tree"){mode=3D"summary_tree"}else{if(ac.extra_info=3D=3D=3D"no_detai= l"||this.is_overview){mode=3D"no_detail"}else{if(this.view.high-this.view.l= ow>I){mode=3D"Squish"}else{mode=3D"Pack"}}}return mode},get_canvas_height:f= unction(ac,ag,ah,ad){if(ag=3D=3D=3D"summary_tree"||ag=3D=3D=3D"Coverage"){r= eturn this.summary_draw_height}else{var af=3Dthis.incremental_slots(ah,ac.d= ata,ag);var ae=3Dnew (this.painter)(null,null,null,this.prefs,ag);return Ma= th.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,a= f,aj,ae){var ap=3Dthis,ad=3Daq.canvas,ay=3Daf.get("start"),ac=3Daf.get("end= "),ag=3Dthis.left_offset;if(ao=3D=3D=3D"summary_tree"||ao=3D=3D=3D"Coverage= "){var aA=3Dnew L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.wid= th,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=3D[],an=3D= this.slotters[aj].slots;all_slotted=3Dtrue;if(am.data){var ak=3Dthis.filter= s_manager.filters;for(var at=3D0,av=3Dam.data.length;at<av;at++){var ah=3Da= m.data[at];var au=3Dfalse;var al;for(var ax=3D0,aC=3Dak.length;ax<aC;ax++){= al=3Dak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=3Dtrue;break}}if(!au){a= i.push(ah);if(!(ah[0] in an)){all_slotted=3Dfalse}}}}var aB=3D(this.filters= _manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var az= =3D(this.filters_manager.height_filter?new C(this.filters_manager.height_fi= lter):null);var aA=3Dnew (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae);va= r aw=3Dnull;aq.fillStyle=3Dthis.prefs.block_color;aq.font=3Daq.canvas.manag= er.default_font;aq.textAlign=3D"right";if(am.data){aw=3DaA.draw(aq,ad.width= ,ad.height,aj,an);aw.translation=3D-ag}return new O(ap,af,ar,ad,am.data,aj,= ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(= ad=3D=3D=3D"Auto"){return true}else{if(ad=3D=3D=3D"Coverage"){return ac.dat= aset_type=3D=3D=3D"summary_tree"}else{if(ac.extra_info=3D=3D=3D"no_detail"|= |ac.dataset_type=3D=3D=3D"summary_tree"){return false}else{return true}}}},= can_subset:function(ac){if(ac.dataset_type=3D=3D=3D"summary_tree"||ac.messa= ge||ac.extra_info=3D=3D=3D"no_detail"){return false}return true}});var R=3D= function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=3Dnew F({track:this,pa= rams:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"b= lock_color",label:"Block color",type:"color",default_value:l.get_random_col= or()},{key:"label_color",label:"Label color",type:"color",default_value:"bl= ack"},{key:"show_insertions",label:"Show insertions",type:"bool",default_va= lue:false},{key:"show_counts",label:"Show summary counts",type:"bool",defau= lt_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:tru= e}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.trac= k.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});th= is.prefs=3Dthis.config.values;this.painter=3DL.ReadPainter};q(R.prototype,r= .prototype,M.prototype,c.prototype);var T=3Dfunction(ae,ad,ag){c.call(this,= ae,ad,ag);var af=3Dl.get_random_color(),ac=3Dl.get_random_color([af,"#fffff= f"]);this.config=3Dnew F({track:this,params:[{key:"name",label:"Name",type:= "text",default_value:this.name},{key:"block_color",label:"Block and sense s= trand color",type:"color",default_value:af},{key:"reverse_strand_color",lab= el:"Antisense strand color",type:"color",default_value:ac},{key:"label_colo= r",label:"Label color",type:"color",default_value:"black"},{key:"show_inser= tions",label:"Show insertions",type:"bool",default_value:false},{key:"show_= differences",label:"Show differences only",type:"bool",default_value:true},= {key:"show_counts",label:"Show summary counts",type:"bool",default_value:tr= ue},{key:"histogram_max",label:"Histogram maximum",type:"float",default_val= ue:null,help:"Clear value to set automatically"},{key:"mode",type:"string",= default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:functi= on(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear= ();this.track.request_draw()}});this.prefs=3Dthis.config.values;this.painte= r=3DL.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototyp= e,c.prototype);var d=3D{LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,C= ompositeTrack:f,DrawableGroup:P};var p=3Dfunction(ae,ad,ac){if("copy" in ae= ){return ae.copy(ac)}else{var af=3Dae.obj_type;if(!af){af=3Dae.track_type}r= eturn new d[af](ad,ac,ae)}};return{View:Y,DrawableGroup:P,LineTrack:h,Featu= reTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,ob= ject_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/tr= ackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filter= s"],function(ab,x,l,u,L,Y,i){var q=3Dab.extend;var V=3Dfunction(ac){return(= "isResolved" in ac)};var n=3D{};var k=3Dfunction(ac,ad){n[ac.attr("id")]=3D= ad};var m=3Dfunction(ac,ae,ag,af){ag=3D".group";var ad=3D{};n[ac.attr("id")= ]=3Daf;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an= =3D$(this),at=3D$(this).parent(),ak=3Dat.children(),am=3Dn[$(this).attr("id= ")],aj,ai,aq,ah,al;ai=3D$(this).parents(ag);if(ai.length!=3D=3D0){aq=3Dai.p= osition().top;ah=3Daq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefo= re(ai);var ar=3Dn[ai.attr("id")];ar.remove_drawable(am);ar.container.add_dr= awable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);= var ar=3Dn[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(= am);return}}}ai=3Dnull;for(al=3D0;al<ak.length;al++){aj=3D$(ak.get(al));aq= =3Daj.position().top;ah=3Daq+aj.outerHeight();if(aj.is(ag)&&this!=3D=3Daj.g= et(0)&&ap.offsetY>=3Daq&&ap.offsetY<=3Dah){if(ap.offsetY-aq<ah-ap.offsetY){= aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(t= his)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add= _drawable(am);return}}for(al=3D0;al<ak.length;al++){aj=3D$(ak.get(al));if(a= p.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass(= "intro"))){break}}if(al=3D=3D=3Dak.length){if(this!=3D=3Dak.get(al-1)){at.a= ppend(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!=3D=3Dak.ge= t(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(= ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=3Dac= .css("border-top");ad["border-bottom"]=3Dac.css("border-bottom");$(this).cs= s({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind(= "dragend",function(){$(this).css(ad)})};var aa=3D16,G=3D9,D=3D20,A=3D100,I= =3D12000,S=3D400,K=3D5000,w=3D100,o=3D"There was an error in indexing this = dataset. ",J=3D"A converter for this dataset is not installed. Please check= your datatypes_conf.xml file.",E=3D"No data for this chrom/contig.",v=3D"P= reparing data. This can take a while for a large dataset. If the visualizat= ion is saved and closed, preparation will continue in the background.",y=3D= "Tool cannot be rerun: ",a=3D"Loading data...",U=3D"Ready for display",Q=3D= 10,H=3D20;function W(ad,ac){if(!ac){ac=3D0}var ae=3DMath.pow(10,ac);return = Math.round(ad*ae)/ae}var r=3Dfunction(ad,ac,af){if(!r.id_counter){r.id_coun= ter=3D0}this.id=3Dr.id_counter++;this.name=3Daf.name;this.view=3Dad;this.co= ntainer=3Dac;this.config=3Dnew F({track:this,params:[{key:"name",label:"Nam= e",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:fun= ction(){this.track.set_name(this.track.config.values.name)}});this.prefs=3D= this.config.values;this.drag_handle_class=3Daf.drag_handle_class;this.is_ov= erview=3Dfalse;this.action_icons=3D{};this.content_visible=3Dtrue;this.cont= ainer_div=3Dthis.build_container_div();this.header_div=3Dthis.build_header_= div();if(this.header_div){this.container_div.append(this.header_div);this.i= cons_div=3D$("<div/>").css("float","left").hide().appendTo(this.header_div)= ;this.build_action_icons(this.action_icons_def);this.header_div.append($("<= div style=3D'clear: both'/>"));this.header_div.dblclick(function(ag){ag.sto= pPropagation()});var ae=3Dthis;this.container_div.hover(function(){ae.icons= _div.show()},function(){ae.icons_div.hide()});$("<div style=3D'clear: both'= />").appendTo(this.container_div)}};r.prototype.action_icons_def=3D[{name:"= toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:funct= ion(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle= -expand").removeClass("toggle");ac.hide_contents();ac.content_visible=3Dfal= se}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-= expand");ac.content_visible=3Dtrue;ac.show_contents()}}},{name:"settings_ic= on",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad= ){var af=3Dfunction(){hide_modal();$(window).unbind("keypress.check_enter_e= 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his.view;this.container_div.hide(0,function(){$(this).remove();ac.update_in= tro_div()})},build_container_div:function(){},build_header_div:function(){}= ,add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=3Dthis;this.action_icon= s[ad]=3D$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addCl= ass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendT= o(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:= function(ac){var ae;for(var ad=3D0;ad<ac.length;ad++){ae=3Dac[ad];this.add_= action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide= )}},update_icons:function(){},hide_contents:function(){},show_contents:func= tion(){},get_drawables:function(){}});var z=3Dfunction(ad,ac,ae){r.call(thi= s,ad,ac,ae);this.obj_type=3Dae.obj_type;this.drawables=3D[]};q(z.prototype,= r.prototype,{unpack_drawables:function(ae){this.drawables=3D[];var ad;for(v= ar ac=3D0;ac<ae.length;ac++){ad=3Dp(ae[ac],this.view,this);this.add_drawabl= 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name").text(this.name).appendTo(ac);return ac},hide_contents:function(){thi= s.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.req= uest_draw()},update_icons:function(){var ae=3Dthis.drawables.length;if(ae= =3D=3D=3D0){this.action_icons.composite_icon.hide();this.action_icons.filte= rs_icon.hide()}else{if(ae=3D=3D=3D1){if(this.drawables[0] instanceof f){thi= s.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}= else{var al,ak,ai,ao=3Dtrue,ag=3Dthis.drawables[0].get_type(),ac=3D0;for(al= =3D0;al<ae;al++){ai=3Dthis.drawables[al];if(ai.get_type()!=3D=3Dag){can_com= posite=3Dfalse;break}if(ai instanceof c){ac++}}if(ao||ac=3D=3D=3D1){this.ac= tion_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide= ();$(".bs-tooltip").remove()}if(ac>1&&ac=3D=3D=3Dthis.drawables.length){var= ap=3D{},ad;ai=3Dthis.drawables[0];for(ak=3D0;ak<ai.filters_manager.filters= .length;ak++){ad=3Dai.filters_manager.filters[ak];ap[ad.name]=3D[ad]}for(al= 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is).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input= =3D$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).app= endTo(this.nav_controls);this.location_span=3D$("<span/>").addClass("locati= on").attr("original-title","Click to change location").tooltip({placement:"= bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){a= c.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"= +ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_inpu= t.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(= ai,ag){var aj=3D[],ah=3D$.map(ac.get_drawables(),function(ak){return ak.dat= a_manager.search_features(ai.term).success(function(al){aj=3Daj.concat(al)}= )});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{labe= l:ak[0],value:ak[1]}}))})}})});if(this.vis_id!=3D=3Dundefined){this.hidden_= input=3D$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.= nav_controls)}this.zo_link=3D$("<a/>").attr("id","zoom-out").attr("title","= Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.= request_redraw()}).appendTo(this.nav_controls);this.zi_link=3D$("<a/>").att= r("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).cli= ck(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls= );this.load_chroms_deferred=3Dthis.load_chroms({low:0});this.chrom_select.b= ind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.brows= er_content_div.click(function(ag){$(this).find("input").trigger("blur")});t= his.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,th= is.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah)= {this.current_x=3Dah.offsetX}).bind("drag",function(ag,ai){var aj=3Dai.offs= etX-this.current_x;this.current_x=3Dai.offsetX;var ah=3DMath.round(aj/ac.vi= ewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});thi= s.overview_close.click(function(){ac.reset_overview()});this.viewport_conta= iner.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.wi= dth()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low= =3Dac.low;ah.current_height=3Dag.clientY;ah.current_x=3Dah.offsetX}).bind("= drag",function(ai,ak){var ag=3D$(this);var al=3Dak.offsetX-ak.current_x;var= ah=3Dag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.cur= rent_height=3Dai.clientY;ak.current_x=3Dak.offsetX;var aj=3DMath.round(al/a= c.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mo= usewheel",function(ai,ak,ah,ag){if(ah){ah*=3D50;var aj=3DMath.round(-ah/ac.= viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_= labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height= :ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltra= ck.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opaci= ty:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(a= l.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,= width:Math.abs(ak.pageX-al.startX)});var ah=3DMath.min(ak.pageX,al.startX)-= ac.container.offset().left,ag=3DMath.max(ak.pageX,al.startX)-ac.container.o= ffset().left,aj=3D(ac.high-ac.low),ai=3Dac.viewport_container.width();ac.up= date_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bi= nd("dragend",function(al,am){var ah=3DMath.min(al.pageX,am.startX),ag=3DMat= h.max(al.pageX,am.startX),aj=3D(ac.high-ac.low),ai=3Dac.viewport_container.= width(),ak=3Dac.low;ac.low=3DMath.round(ah/ai*aj)+ak;ac.high=3DMath.round(a= g/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track= (new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(= this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function()= {if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=3D= setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",= function(){ac.redraw()});this.reset();$(window).trigger("resize")}});q(Z.pr= ototype,z.prototype,{changed:function(){this.has_changes=3Dtrue},update_int= ro_div:function(){if(this.drawables.length=3D=3D=3D0){this.intro_div.show()= }else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(thi= s.timer){clearTimeout(this.timer)}if(ag){var ae=3Dthis;this.timer=3DsetTime= out(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trig= ger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.loc= ation_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.= chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=3Dview.chrom_select.val()= ;if(ad!=3D=3D""){this.trigger_navigate(ad,view.low,view.high,true)}},load_c= hroms:function(ae){ae.num=3Dw;var ac=3Dthis,ad=3D$.Deferred();$.ajax({url:c= hrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.= chrom_info.length=3D=3D=3D0){return}if(ag.reference){ac.add_label_track(new= B(ac))}ac.chrom_data=3Dag.chrom_info;var aj=3D'<option value=3D"">Select C= hrom/Contig</option>';for(var ai=3D0,af=3Dac.chrom_data.length;ai<af;ai++){= var ah=3Dac.chrom_data[ai].chrom;aj+=3D'<option value=3D"'+ah+'">'+ah+"</op= tion>"}if(ag.prev_chroms){aj+=3D'<option value=3D"previous">Previous '+w+"<= /option>"}if(ag.next_chroms){aj+=3D'<option value=3D"next">Next '+w+"</opti= on>"}ac.chrom_select.html(aj);ac.chrom_start_index=3Dag.start_index;ad.reso= lve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.= dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=3Dthis;if(!ae.c= hrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj= )});return}if(!ah||ah=3D=3D=3D"None"){return}if(ah=3D=3D=3D"previous"){ae.l= oad_chroms({low:this.chrom_start_index-w});return}if(ah=3D=3D=3D"next"){ae.= load_chroms({low:this.chrom_start_index+w});return}var ai=3D$.grep(ae.chrom= 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on(af){var ac=3Dthis;var ae=3Dac.high-ac.low;if(ac.low-af<ac.max_low){ac.lo= w=3Dac.max_low;ac.high=3Dac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.h= igh=3Dac.max_high;ac.low=3Dac.max_high-ae}else{ac.high-=3Daf;ac.low-=3Daf}}= ac.request_redraw();var ad=3Dac.chrom_select.val();this.trigger_navigate(ad= ,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.c= all(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_tr= ack:function(ac){ac.view=3Dthis;ac.init();this.label_tracks.push(ac)},remov= e_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad)= {var ac=3Dthis;ae.container_div.hide(0,function(){$(this).remove();ac.updat= e_intro_div()})}},reset:function(){this.low=3Dthis.max_low;this.high=3Dthis= .max_high;this.viewport_container.find(".yaxislabel").remove()},request_red= raw:function(ak,ac,aj,al){var ai=3Dthis,ah=3D(al?[al]:ai.drawables),ae;var = ad;for(var ag=3D0;ag<ah.length;ag++){ad=3Dah[ag];ae=3D-1;for(var af=3D0;af<= ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]=3D= =3D=3Dad){ae=3Daf;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}= else{ai.tracks_to_be_redrawn[ag][1]=3Dac;ai.tracks_to_be_redrawn[ag][2]=3Da= j}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(a= k)});this.requested_redraw=3Dtrue}},_redraw:function(am){this.requested_red= raw=3Dfalse;var aj=3Dthis.low,af=3Dthis.high;if(aj<this.max_low){aj=3Dthis.= max_low}if(af>this.max_high){af=3Dthis.max_high}var al=3Dthis.high-this.low= ;if(this.high!=3D=3D0&&al<this.min_separation){af=3Daj+this.min_separation}= this.low=3DMath.floor(aj);this.high=3DMath.ceil(af);this.update_location(th= is.low,this.high);this.resolution_b_px=3D(this.high-this.low)/this.viewport= _container.width();this.resolution_px_b=3Dthis.viewport_container.width()/(= this.high-this.low);var ac=3D(this.low/(this.max_high-this.max_low)*this.ov= erview_viewport.width())||0;var ai=3D((this.high-this.low)/(this.max_high-t= 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ion(){var ac=3Dthis;var af=3Dfalse;var ae=3Dfalse;var ad=3D$("<div class=3D= 'track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visibl= e){af=3Dtrue;ad.show()}},function(){af=3Dfalse;if(!ae){ad.hide()}});ad.hide= ().bind("dragstart",function(ag,ah){ae=3Dtrue;ah.original_height=3D$(ac.con= tent_div).height()}).bind("drag",function(ah,ai){var ag=3DMath.min(Math.max= (ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tile= s_div).css("height",ag);ac.visible_height_px=3D(ac.max_height_px=3D=3D=3Dag= ?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear(= );ae=3Dfalse;if(!af){ad.hide()}ac.config.values.height=3Dac.visible_height_= px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af= ,ai){this.display_modes=3Daf;this.mode=3D(ai?ai:(this.config&&this.config.v= alues.mode?this.config.values.mode:this.display_modes[0]));this.action_icon= s.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=3D= this,ag=3D{};for(var ae=3D0,ac=3Dad.display_modes.length;ae<ac;ae++){var ah= =3Dad.display_modes[ae];ag[ah]=3Dfunction(aj){return function(){ad.change_m= ode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons= _div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_a= ction_icons:function(){r.prototype.build_action_icons.call(this,this.action= _icons_def);if(this.display_modes!=3D=3Dundefined){this.set_display_modes(t= his.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.co= ntainer_div.find(".yaxislabel, .track-resize").hide()},show_contents:functi= on(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-res= ize").show();this.request_draw()},get_type:function(){if(this instanceof X)= {return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{= if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"R= eadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instance= of f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack= "}}}}}}}return""},init:function(){var ad=3Dthis;ad.enabled=3Dfalse;ad.tile_= cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");a= d.tiles_div.children().remove();ad.container_div.removeClass("nodata error = pending");if(!ad.dataset_id){return}var ac=3D$.Deferred(),ae=3D{hda_ldda:ad= .hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom};$.getJSON(= this.dataset.url(),ae,function(af){if(!af||af=3D=3D=3D"error"||af.kind=3D= =3D=3D"error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(a= f.message){var ag=3D$(" <a href=3D'javascript:void(0);'></a>").text("View e= rror").click(function(){show_modal("Trackster Error","<pre>"+af.message+"</= pre>",{Close:hide_modal})});ad.tiles_div.append(ag)}}else{if(af=3D=3D=3D"no= converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{i= f(af=3D=3D=3D"no data"||(af.data!=3D=3Dundefined&&(af.data=3D=3D=3Dnull||af= .data.length=3D=3D=3D0))){ad.container_div.addClass("nodata");ad.tiles_div.= text(E)}else{if(af=3D=3D=3D"pending"){ad.container_div.addClass("pending");= ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}e= lse{if(af=3D=3D=3D"data"||af.status=3D=3D=3D"data"){if(af.valid_chroms){ad.= valid_chroms=3Daf.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad= .view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_hei= ght_px+"px");ad.enabled=3Dtrue;$.when(ad.predraw_init()).done(function(){ac= .resolve();ad.container_div.removeClass("nodata error pending");ad.request_= draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_i= nit:function(){},get_drawables:function(){return this}});var M=3Dfunction(a= e,ad,af){g.call(this,ae,ad,af);var ac=3Dthis;m(ac.container_div,ac.drag_han= dle_class,".group",ac);this.filters_manager=3Dnew i.FiltersManager(this,("f= ilters" in af?af.filters:null));this.data_manager.set("filters_manager",thi= s.filters_manager);this.filters_available=3Dfalse;this.tool=3D("tool" in af= &&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=3Dnew x.C= ache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);= if(this.tool){this.dynamic_tool_div=3Dthis.tool.parent_div;this.header_div.= after(this.dynamic_tool_div)}}this.tiles_div=3D$("<div/>").addClass("tiles"= ).appendTo(this.content_div);this.overlay_div=3D$("<div/>").addClass("overl= ay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M= .prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_ico= ns_def.concat([{name:"show_more_rows_icon",title:"To minimize track height,= not all feature rows are displayed. Click to display more rows.",css_class= :"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotte= rs[ac.view.resolution_px_b].max_rows*=3D2;ac.request_draw(true)},hide:true}= ]),copy:function(ac){var ad=3Dthis.to_dict();q(ad,{data_manager:this.data_m= anager});var ae=3Dnew this.constructor(this.view,ac,ad);ae.change_mode(this= .mode);ae.enabled=3Dthis.enabled;return ae},set_filters_manager:function(ac= ){this.filters_manager=3Dac;this.header_div.after(this.filters_manager.pare= nt_div)},to_dict:function(){return{track_type:this.get_type(),name:this.nam= e,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:t= his.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.= tool.state_dict():{})}},change_mode:function(ad){var ac=3Dthis;ac.mode=3Dad= ;ac.config.values.mode=3Dad;ac.tile_cache.clear();ac.request_draw();this.ac= tion_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");re= turn ac},update_icons:function(){var ac=3Dthis;if(ac.filters_available){ac.= action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}i= f(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_vi= z_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_= space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_= "+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad= ,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw= ()){return}var al=3Dthis.view.low,ah=3Dthis.view.high,aj=3Dah-al,ae=3Dthis.= view.container.width(),ap=3Dthis.view.resolution_px_b,ag=3Dthis.view.resolu= tion_b_px;if(this.is_overview){al=3Dthis.view.max_low;ah=3Dthis.view.max_hi= gh;ag=3D(view.max_high-view.max_low)/ae;ap=3D1/ag}this.before_draw();this.t= iles_div.children().addClass("remove");var ac=3DMath.floor(al/(ag*S)),ak=3D= true,ao=3D[],ai=3Dfunction(aq){return(aq&&"track" in aq)};while((ac*S*ag)<a= h){var am=3Dthis.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.p= ush(am)}else{ak=3Dfalse}ac+=3D1}if(!an){this.tiles_div.children(".remove").= removeClass("remove").remove()}var af=3Dthis;if(ak){this.tiles_div.children= (".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:fu= nction(ae,af,ah,ac){var ag=3Dfalse;for(var ad=3D0;ad<ae.length;ad++){if(ae[= ad].has_icons){ag=3Dtrue;break}}if(ag){for(var ad=3D0;ad<ae.length;ad++){ti= le=3Dae[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",D)}}}},draw= _helper:function(ac,ao,au,ar,ah,ai,ap){var an=3Dthis,ax=3Dthis._gen_tile_ca= che_key(ao,ai,au),af=3Dthis._get_tile_bounds(au,ar);if(!ap){ap=3D{}}var aw= =3D(ac?undefined:an.tile_cache.get_elt(ax));if(aw){an.show_tile(aw,ah,ai);r= eturn aw}var al=3Dtrue;var at=3Dan.data_manager.get_data(af,an.mode,ar,an.d= ata_url_extra_params);if(V(at)){al=3Dfalse}var aj;if(view.reference_track&&= ai>view.canvas_manager.char_width_px){aj=3Dview.reference_track.data_manage= r.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(a= j)){al=3Dfalse}}if(al){q(at,ap.more_tile_data);var ak=3Dan.mode;if(ak=3D=3D= =3D"Auto"){ak=3Dan.get_mode(at);an.update_auto_mode(ak)}var ae=3Dan.view.ca= nvas_manager.new_canvas(),av=3Daf.get("start"),ad=3Daf.get("end"),ao=3DMath= .ceil((ad-av)*ai)+an.left_offset,am=3Dan.get_canvas_height(at,ak,ai,ao);ae.= width=3Dao;ae.height=3Dam;var aq=3Dae.getContext("2d");aq.translate(this.le= ft_offset,0);var aw=3Dan.draw_tile(at,aq,ak,ar,af,ai,aj);if(aw!=3D=3Dundefi= ned){an.tile_cache.set_elt(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag= =3D$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,fal= se,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,= ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae)= {console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile= :function(ae,ah,ai){var ad=3Dthis,ac=3Dae.html_elt;ae.predisplay_actions();= var ag=3D(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(= this.left_offset){ag-=3Dthis.left_offset}ac.css({position:"absolute",top:0,= left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append= (ac)}ae.html_elt.height("auto");this.max_height_px=3DMath.max(this.max_heig= ht_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",th= is.max_height_px+"px");var af=3Dthis.max_height_px;if(this.visible_height_p= x!=3D=3D0){af=3DMath.min(this.max_height_px,this.visible_height_px)}this.ti= les_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=3DMa= th.floor(ac*S*ad),ag=3DMath.ceil(S*ad),ae=3D(af+ag<=3Dthis.view.max_high?af= +ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,st= art:af,end:ae})},tool_region_and_parameters_str:function(ae,ac,af){var ad= =3Dthis,ag=3D(ae!=3D=3Dundefined&&ac!=3D=3Dundefined&&af!=3D=3Dundefined?ae= +":"+ac+"-"+af:"all");return" - region=3D["+ag+"], parameters=3D["+ad.tool.= get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad)= {return true},can_subset:function(ac){return false},init_for_tool_data:func= tion(){this.data_manager.set("data_type","raw_data");this.data_query_wait= =3D1000;this.dataset_check_type=3D"state";this.normal_postdraw_actions=3Dth= is.postdraw_actions;this.postdraw_actions=3Dfunction(ae,af,ah,ac){var ad=3D= this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type=3D"conve= rted_datasets_state";ad.data_query_wait=3DK;var ag=3Dnew l.ServerStateDefer= red({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda= :ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai= !=3D=3D"pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("da= ta_type","data")});ad.postdraw_actions=3Dad.normal_postdraw_actions}}});var= X=3Dfunction(ad,ac){var ae=3D{resize:false};g.call(this,ad,ac,ae);this.con= tainer_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header= _div:function(){},init:function(){this.enabled=3Dtrue},_draw:function(){var= ae=3Dthis.view,af=3Dae.high-ae.low,ai=3DMath.floor(Math.pow(10,Math.floor(= Math.log(af)/Math.log(10)))),ac=3DMath.floor(ae.low/ai)*ai,ag=3Dthis.view.c= ontainer.width(),ad=3D$("<div style=3D'position: relative; height: 1.3em;'>= </div>");while(ac<ae.high){var ah=3D(ac-ae.low)/af*ag;ad.append($("<div cla= ss=3D'label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1})= );ac+=3Dai}this.content_div.children(":first").remove();this.content_div.ap= pend(ad)}});var f=3Dfunction(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables= =3D[];this.left_offset=3D0;if("drawables" in ag){var af;for(var ae=3D0;ae<a= g.drawables.length;ae++){af=3Dag.drawables[ae];this.drawables[ae]=3Dp(af,ad= ,null);if(af.left_offset>this.left_offset){this.left_offset=3Daf.left_offse= t}}this.enabled=3Dtrue}if(this.drawables.length!=3D=3D0){this.set_display_m= odes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_ic= ons();this.obj_type=3D"CompositeTrack"};q(f.prototype,M.prototype,{action_i= cons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"= layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_gr= oup()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,a= dd_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_dr= awables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(= var ad=3D0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac= )}},init:function(){var ae=3D[];for(var ad=3D0;ad<this.drawables.length;ad+= +){ae.push(this.drawables[ad].init())}var ac=3Dthis;$.when.apply($,ae).then= (function(){ac.enabled=3Dtrue;ac.request_draw()})},update_icons:function(){= this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();t= his.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw= ,draw_helper:function(ad,at,az,aw,ak,am,au){var ar=3Dthis,aD=3Dthis._gen_ti= le_cache_key(at,am,az),ah=3Dthis._get_tile_bounds(az,aw);if(!au){au=3D{}}va= r aC=3D(ad?undefined:ar.tile_cache.get_elt(aD));if(aC){ar.show_tile(aC,ak,a= m);return aC}var al=3D[],ar,ap=3Dtrue,ax,an;for(var ay=3D0;ay<this.drawable= s.length;ay++){ar=3Dthis.drawables[ay];ax=3Dar.data_manager.get_data(ah,ar.= mode,aw,ar.data_url_extra_params);if(V(ax)){ap=3Dfalse}al.push(ax);an=3Dnul= l;if(view.reference_track&&am>view.canvas_manager.char_width_px){an=3Dview.= reference_track.data_manager.get_data(ah,ar.mode,aw,view.reference_track.da= ta_url_extra_params);if(V(an)){ap=3Dfalse}}al.push(an)}if(ap){q(ax,au.more_= tile_data);this.tile_predraw_init();var ag=3Dar.view.canvas_manager.new_can= vas(),ai=3Dar._get_tile_bounds(az,aw),aA=3Dah.get("start"),ae=3Dah.get("end= "),aB=3D0,at=3DMath.ceil((ae-aA)*am)+this.left_offset,aq=3D0,af=3D[],ay;var= ac=3D0;for(ay=3D0;ay<this.drawables.length;ay++,aB+=3D2){ar=3Dthis.drawabl= es[ay];ax=3Dal[aB];var ao=3Dar.mode;if(ao=3D=3D=3D"Auto"){ao=3Dar.get_mode(= ax);ar.update_auto_mode(ao)}af.push(ao);ac=3Dar.get_canvas_height(ax,ao,am,= at);if(ac>aq){aq=3Dac}}ag.width=3Dat;ag.height=3D(au.height?au.height:aq);a= B=3D0;var av=3Dag.getContext("2d");av.translate(this.left_offset,0);av.glob= alAlpha=3D0.5;av.globalCompositeOperation=3D"source-over";for(ay=3D0;ay<thi= s.drawables.length;ay++,aB+=3D2){ar=3Dthis.drawables[ay];ax=3Dal[aB];an=3Da= l[aB+1];aC=3Dar.draw_tile(ax,av,af[ay],aw,ah,am,an)}this.tile_cache.set_elt= (aD,aC);this.show_tile(aC,ak,am);return aC}var aj=3D$.Deferred(),ar=3Dthis;= $.when.apply($,al).then(function(){view.request_redraw(false,false,false,ar= );aj.resolve()});return aj},show_group:function(){var af=3Dnew P(this.view,= this.container,{name:this.name}),ac;for(var ae=3D0;ae<this.drawables.length= ;ae++){ac=3Dthis.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.con= tainer=3Daf;af.content_div.append(ac.container_div)}var ad=3Dthis.container= .replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:functi= on(){var af=3DNumber.MAX_VALUE,ac=3D-af,ad;for(var ae=3D0;ae<this.drawables= .length;ae++){ad=3Dthis.drawables[ae];if(ad instanceof h){if(ad.prefs.min_v= alue<af){af=3Dad.prefs.min_value}if(ad.prefs.max_value>ac){ac=3Dad.prefs.ma= x_value}}}for(var ae=3D0;ae<this.drawables.length;ae++){ad=3Dthis.drawables= [ae];ad.prefs.min_value=3Daf;ad.prefs.max_value=3Dac}},postdraw_actions:fun= ction(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var = ag=3D-1;for(var af=3D0;af<ae.length;af++){var ac=3Dae[af].html_elt.find("ca= nvas").height();if(ac>ag){ag=3Dac}}for(var af=3D0;af<ae.length;af++){var ai= =3Dae[af];if(ai.html_elt.find("canvas").height()!=3D=3Dag){this.draw_helper= (true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.htm= l_elt.remove()}}}});var B=3Dfunction(ac){M.call(this,ac,{content_div:ac.top= _labeltrack},{resize:false});ac.reference_track=3Dthis;this.left_offset=3D2= 00;this.visible_height_px=3D12;this.container_div.addClass("reference-track= ");this.content_div.css("background","none");this.content_div.css("min-heig= ht","0px");this.content_div.css("border","none");this.data_url=3Dreference_= url+"/"+this.view.dbkey;this.data_url_extra_params=3D{reference:true};this.= data_manager=3Dnew x.ReferenceTrackDataManager({data_url:this.data_url});th= is.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div= :function(){},init:function(){this.data_manager.clear();this.enabled=3Dtrue= },can_draw:r.prototype.can_draw,draw_helper:function(ag,ae,ac,ad,ah,ai,af){= if(ai>this.view.canvas_manager.char_width_px){return M.prototype.draw_helpe= r.call(this,ag,ae,ac,ad,ah,ai,af)}else{this.hide_contents();return null}},d= raw_tile:function(ak,al,ag,af,ai,am){var ae=3Dthis;if(am>this.view.canvas_m= anager.char_width_px){if(ak.data=3D=3D=3Dnull){this.hide_contents();return}= var ad=3Dal.canvas;al.font=3Dal.canvas.manager.default_font;al.textAlign=3D= "center";ak=3Dak.data;for(var ah=3D0,aj=3Dak.length;ah<aj;ah++){var ac=3DMa= th.floor(ah*am);al.fillText(ak[ah],ac,10)}this.show_contents();return new b= (ae,ai,af,ad,ak)}this.hide_contents()}});var h=3Dfunction(ae,ad,af){var ac= =3Dthis;this.display_modes=3D["Histogram","Line","Filled","Intensity"];this= .mode=3D"Histogram";M.call(this,ae,ad,af);this.hda_ldda=3Daf.hda_ldda;this.= dataset_id=3Daf.dataset_id;this.original_dataset_id=3Dthis.dataset_id;this.= left_offset=3D0;this.config=3Dnew F({track:this,params:[{key:"name",label:"= Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:= "color",default_value:l.get_random_color()},{key:"min_value",label:"Min Val= ue",type:"float",default_value:undefined},{key:"max_value",label:"Max Value= ",type:"float",default_value:undefined},{key:"mode",type:"string",default_v= alue:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidde= n:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.nam= e);ac.vertical_range=3Dac.prefs.max_value-ac.prefs.min_value;ac.set_min_val= ue(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs= =3Dthis.config.values;this.visible_height_px=3Dthis.config.values.height;th= is.vertical_range=3Dthis.config.values.max_value-this.config.values.min_val= ue};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.reques= t_draw(true)},set_min_value:function(ac){this.prefs.min_value=3Dac;$("#line= track_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cac= he.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_v= alue=3Dac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_va= lue);this.tile_cache.clear();this.request_draw()},predraw_init:function(){v= ar ac=3Dthis;ac.vertical_range=3Dundefined;return $.getJSON(ac.dataset.url(= ),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_h= igh,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-trac= k");var ag=3Dad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseF= loat(ac.prefs.max_value))){var ae=3Dag.min,ai=3Dag.max;ae=3DMath.floor(Math= .min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=3DMath.ceil(Math.max(0,Math.min(ai= ,ag.mean+2*ag.sd)));ac.prefs.min_value=3Dae;ac.prefs.max_value=3Dai;$("#tra= ck_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.datase= t_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=3Dac.prefs.max_va= lue-ac.prefs.min_value;ac.total_frequency=3Dag.total_frequency;ac.container= _div.find(".yaxislabel").remove();var ah=3D$("<div/>").text(W(ac.prefs.min_= value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tool= tip").remove();var aj=3DparseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}= },help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","line= track_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=3D$("<div/>= ").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:f= unction(aj){$(".bs-tooltip").remove();var aj=3DparseFloat(aj);if(!isNaN(aj)= ){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel t= op").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container= _div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=3Daj.canvas,af=3Dag.g= et("start"),ai=3Dag.get("end"),ah=3Dnew L.LinePainter(al.data,af,ai,this.pr= efs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.dat= a)},can_subset:function(ac){return false}});var t=3Dfunction(ae,ad,af){var = ac=3Dthis;this.display_modes=3D["Heatmap"];this.mode=3D"Heatmap";M.call(thi= s,ae,ad,af);this.hda_ldda=3Daf.hda_ldda;this.dataset_id=3Daf.dataset_id;thi= s.original_dataset_id=3Dthis.dataset_id;this.left_offset=3D0;this.config=3D= new F({track:this,params:[{key:"name",label:"Name",type:"text",default_valu= e:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_v= alue:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",defaul= t_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_= value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},= {key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height= ",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange= :function(){ac.set_name(ac.prefs.name);ac.vertical_range=3Dac.prefs.max_val= ue-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value= (ac.prefs.max_value)}});this.prefs=3Dthis.config.values;this.visible_height= _px=3Dthis.config.values.height;this.vertical_range=3Dthis.config.values.ma= x_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype= ,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){= this.prefs.min_value=3Dac;this.tile_cache.clear();this.request_draw()},set_= max_value:function(ac){this.prefs.max_value=3Dac;this.tile_cache.clear();th= is.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=3Dae.canvas= ,ad=3Dnew L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),th= is.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,a= c.data)}});var c=3Dfunction(af,ae,ah){var ad=3Dthis;this.display_modes=3D["= Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=3Dl.= get_random_color(),ac=3Dl.get_random_color([ag,"#FFFFFF"]);this.config=3Dne= w F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:= this.name},{key:"block_color",label:"Block color",type:"color",default_valu= e:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"colo= r",default_value:ac},{key:"label_color",label:"Label color",type:"color",de= fault_value:"black"},{key:"show_counts",label:"Show summary counts",type:"b= ool",default_value:true,help:"Show the number of items in each bin when dra= wing summary histogram"},{key:"histogram_max",label:"Histogram maximum",typ= e:"float",default_value:null,help:"clear value to set automatically"},{key:= "connector_style",label:"Connector style",type:"select",default_value:"fish= bones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",v= alue:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:tru= e},{key:"height",type:"int",default_value:this.visible_height_px,hidden:tru= e}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad= .tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.= prefs=3Dthis.config.values;this.visible_height_px=3Dthis.config.values.heig= ht;this.container_div.addClass("feature-track");this.hda_ldda=3Dah.hda_ldda= ;this.dataset_id=3Dah.dataset_id;this.original_dataset_id=3Dah.dataset_id;t= his.show_labels_scale=3D0.001;this.showing_details=3Dfalse;this.summary_dra= w_height=3D30;this.slotters=3D{};this.start_end_dct=3D{};this.left_offset= =3D200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototyp= e,{set_dataset:function(ac){this.dataset_id=3Dac.get("id");this.hda_ldda=3D= ac.get("hda_ldda");this.dataset=3Dac;this.data_manager.set("dataset",ac)},s= et_painter_from_config:function(){if(this.config.values.connector_style=3D= =3D=3D"arcs"){this.painter=3DL.ArcLinkedFeaturePainter}else{this.painter=3D= L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=3D0},pos= tdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,= ar,ag);var al=3Dthis,ao;if(al.mode=3D=3D=3D"Coverage"){var ad=3D-1;for(ao= =3D0;ao<ar.length;ao++){var an=3Dar[ao].max_val;if(an>ad){ad=3Dan}}for(ao= =3D0;ao<ar.length;ao++){var au=3Dar[ao];if(au.max_val!=3D=3Dad){au.html_elt= .remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(= ),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=3Dal.filter= s_manager.filters;for(var aq=3D0;aq<ai.length;aq++){ai[aq].update_ui_elt()}= var at=3Dfalse,ac,aj;for(ao=3D0;ao<ar.length;ao++){if(ar[ao].data.length){a= c=3Dar[ao].data[0];for(var aq=3D0;aq<ai.length;aq++){aj=3Dai[aq];if(aj.appl= ies_to(ac)&&aj.min!=3D=3Daj.max){at=3Dtrue;break}}}}if(al.filters_available= !=3D=3Dat){al.filters_available=3Dat;if(!al.filters_available){al.filters_m= anager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").rem= ove();var af=3Dar[0];if(af instanceof j){var ak=3D(this.prefs.histogram_max= ?this.prefs.histogram_max:af.max_val),ae=3D$("<div/>").text(ak).make_text_e= ditable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var a= v=3DparseFloat(av);al.prefs.histogram_max=3D(!isNaN(av)?av:null);al.tile_ca= che.clear();al.request_draw()},help_text:"Set max value; leave blank to use= default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);= this.container_div.prepend(ae)}if(af instanceof O){var ap=3Dtrue;for(ao=3D0= ;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=3Dfalse;break}}if(!ap){this.= action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_ro= ws_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_= auto_mode:function(ac){var ac;if(this.mode=3D=3D=3D"Auto"){if(ac=3D=3D=3D"n= o_detail"){ac=3D"feature spans"}else{if(ac=3D=3D=3D"summary_tree"){ac=3D"co= verage histogram"}}this.action_icons.mode_icon.attr("title","Set display mo= de (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=3Dthi= s.view.canvas_manager.dummy_context,ae=3Dthis.slotters[ag];if(!ae||(ae.mode= !=3D=3Daf)){ae=3Dnew (u.FeatureSlotter)(ag,af,A,function(ah){return ad.meas= ureText(ah)});this.slotters[ag]=3Dae}return ae.slot_features(ac)},get_mode:= function(ac){if(ac.dataset_type=3D=3D=3D"summary_tree"){mode=3D"summary_tre= e"}else{if(ac.extra_info=3D=3D=3D"no_detail"||this.is_overview){mode=3D"no_= detail"}else{if(this.view.high-this.view.low>I){mode=3D"Squish"}else{mode= =3D"Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag=3D= =3D=3D"summary_tree"||ag=3D=3D=3D"Coverage"){return this.summary_draw_heigh= t}else{var af=3Dthis.incremental_slots(ah,ac.data,ag);var ae=3Dnew (this.pa= inter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_hei= ght(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=3Dthis,ad=3Da= q.canvas,ay=3Daf.get("start"),ac=3Daf.get("end"),ag=3Dthis.left_offset;if(a= o=3D=3D=3D"summary_tree"||ao=3D=3D=3D"Coverage"){var aA=3Dnew L.SummaryTree= Painter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j= (ap,af,ar,ad,am.data,am.max)}var ai=3D[],an=3Dthis.slotters[aj].slots;all_s= lotted=3Dtrue;if(am.data){var ak=3Dthis.filters_manager.filters;for(var at= =3D0,av=3Dam.data.length;at<av;at++){var ah=3Dam.data[at];var au=3Dfalse;va= r al;for(var ax=3D0,aC=3Dak.length;ax<aC;ax++){al=3Dak[ax];al.update_attrs(= ah);if(!al.keep(ah)){au=3Dtrue;break}}if(!au){ai.push(ah);if(!(ah[0] in an)= ){all_slotted=3Dfalse}}}}var aB=3D(this.filters_manager.alpha_filter?new C(= this.filters_manager.alpha_filter):null);var az=3D(this.filters_manager.hei= ght_filter?new C(this.filters_manager.height_filter):null);var aA=3Dnew (th= is.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae);var aw=3Dnull;aq.fillStyle=3Dt= his.prefs.block_color;aq.font=3Daq.canvas.manager.default_font;aq.textAlign= =3D"right";if(am.data){aw=3DaA.draw(aq,ad.width,ad.height,aj,an);aw.transla= tion=3D-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw= )},data_and_mode_compatible:function(ac,ad){if(ad=3D=3D=3D"Auto"){return tr= ue}else{if(ad=3D=3D=3D"Coverage"){return ac.dataset_type=3D=3D=3D"summary_t= ree"}else{if(ac.extra_info=3D=3D=3D"no_detail"||ac.dataset_type=3D=3D=3D"su= mmary_tree"){return false}else{return true}}}},can_subset:function(ac){if(a= c.dataset_type=3D=3D=3D"summary_tree"||ac.message||ac.extra_info=3D=3D=3D"n= o_detail"){return false}return true}});var R=3Dfunction(ad,ac,ae){c.call(th= is,ad,ac,ae);this.config=3Dnew F({track:this,params:[{key:"name",label:"Nam= e",type:"text",default_value:this.name},{key:"block_color",label:"Block col= or",type:"color",default_value:l.get_random_color()},{key:"label_color",lab= el:"Label color",type:"color",default_value:"black"},{key:"show_insertions"= ,label:"Show insertions",type:"bool",default_value:false},{key:"show_counts= ",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",t= ype:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,on= change:function(){this.track.set_name(this.track.prefs.name);this.track.til= e_cache.clear();this.track.request_draw()}});this.prefs=3Dthis.config.value= s;this.painter=3DL.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.pro= totype);var T=3Dfunction(ae,ad,ag){c.call(this,ae,ad,ag);var af=3Dl.get_ran= dom_color(),ac=3Dl.get_random_color([af,"#ffffff"]);this.config=3Dnew F({tr= ack:this,params:[{key:"name",label:"Name",type:"text",default_value:this.na= me},{key:"block_color",label:"Block and sense strand color",type:"color",de= fault_value:af},{key:"reverse_strand_color",label:"Antisense strand color",= type:"color",default_value:ac},{key:"label_color",label:"Label color",type:= "color",default_value:"black"},{key:"show_insertions",label:"Show insertion= s",type:"bool",default_value:false},{key:"show_differences",label:"Show dif= ferences only",type:"bool",default_value:true},{key:"show_counts",label:"Sh= ow summary counts",type:"bool",default_value:true},{key:"histogram_max",lab= el:"Histogram maximum",type:"float",default_value:null,help:"Clear value to= set automatically"},{key:"mode",type:"string",default_value:this.mode,hidd= en:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(thi= s.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()= }});this.prefs=3Dthis.config.values;this.painter=3DL.ReadPainter;this.updat= e_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d=3D{Line= Track:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,Compos= iteTrack:f,DrawableGroup:P};var p=3Dfunction(ae,ad,ac){if("copy" in ae){ret= urn ae.copy(ac)}else{var af=3Dae.obj_type;if(!af){af=3Dae.track_type}return= new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,F= eatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:= f,object_from_template:p}}); \ No newline at end of file

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/p= ainters","viz/trackster/tracks","viz/visualization"],function(g,c,h,e,b,d){= var a=3Db.object_from_template;var f=3Dg.Base.extend({initialize:function(j= ){this.baseURL=3Dj},createButtonMenu:function(){var j=3Dthis,k=3Dcreate_ico= n_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:funct= ion(){d.select_datasets(select_datasets_url,add_track_async_url,view.dbkey,= function(l){c.each(l,function(m){view.add_drawable(a(m,view,view))})})}},{i= con_class:"block--plus",title:"Add group",on_click:function(){view.add_draw= able(new b.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"book= marks",title:"Bookmarks",on_click:function(){parent.force_right_panel(($("d= iv#right").css("right")=3D=3D"0px"?"hide":"show"))}},{icon_class:"globe",ti= tle:"Circster",on_click:function(){window.location=3Dj.baseURL+"visualizati= on/circster?id=3D"+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_= click:function(){show_modal("Saving...","progress");var l=3D[];$(".bookmark= ").each(function(){l.push({position:$(this).children(".position").text(),an= notation:$(this).children(".annotation").text()})});var m=3D(view.overview_= drawable?view.overview_drawable.name:null),n=3D{view:view.to_dict(),viewpor= t:{chrom:view.chrom,start:view.low,end:view.high,overview:m},bookmarks:l};$= .ajax({url:galaxy_paths.get("visualization_url"),type:"POST",dataType:"json= ",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vi= s_json:JSON.stringify(n)}}).success(function(o){hide_modal();view.vis_id=3D= o.vis_id;view.has_changes=3Dfalse;window.history.pushState({},"",o.url+wind= ow.location.hash)}).error(function(){show_modal("Could Not Save","Could not= save visualization. Please try again later.",{Close:hide_modal})})}},{icon= _class:"cross-circle",title:"Close",on_click:function(){window.location=3Dj= .baseURL+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});thi= s.buttonMenu=3Dk;return k},add_bookmarks:function(){var j=3Dthis,k=3Dthis.b= aseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({ur= l:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},= error:function(){alert("Grid failed")},success:function(l){show_modal("Sele= ct dataset for new bookmarks",l,{Cancel:function(){hide_modal()},Insert:fun= ction(){$("input[name=3Did]:checked,input[name=3Dldda_ids]:checked").first(= ).each(function(){var m,n=3D$(this).val();if($(this).attr("name")=3D=3D=3D"= id"){m=3D{hda_id:n}}else{m=3D{ldda_id:n}}$.ajax({url:this.baseURL+"/visuali= zation/bookmarks_from_dataset",data:m,dataType:"json"}).then(function(o){fo= r(i=3D0;i<o.data.length;i++){var p=3Do.data[i];j.add_bookmark(p[0],p[1])}})= });hide_modal()}})}})},add_bookmark:function(n,l,j){var p=3D$("#bookmarks-c= ontainer"),r=3D$("<div/>").addClass("bookmark").appendTo(p);var s=3D$("<div= />").addClass("position").appendTo(r),o=3D$("<a href=3D''/>").text(n).appen= dTo(s).click(function(){view.go_to(n);return false}),m=3D$("<div/>").text(l= ).appendTo(r);if(j){var q=3D$("<div/>").addClass("delete-icon-container").p= rependTo(r).click(function(){r.slideUp("fast");r.remove();view.has_changes= =3Dtrue;return false}),k=3D$("<a href=3D''/>").addClass("icon-button delete= ").appendTo(q);m.make_text_editable({num_rows:3,use_textarea:true,help_text= :"Edit bookmark note"}).addClass("annotation")}view.has_changes=3Dtrue;retu= rn r},create_visualization:function(o,j,n,p,m){var l=3Dthis,k=3Dnew b.View(= o);k.editor=3Dtrue;$.when(k.load_chroms_deferred).then(function(){if(j){var= y=3Dj.chrom,q=3Dj.start,v=3Dj.end,s=3Dj.overview;if(y&&(q!=3D=3Dundefined)= &&v){k.change_chrom(y,q,v)}}if(n){var t,r,u;for(var w=3D0;w<n.length;w++){k= .add_drawable(a(n[w],k,k))}}k.update_intro_div();var z;for(var w=3D0;w<k.dr= awables.length;w++){if(k.drawables[w].name=3D=3D=3Ds){k.set_overview(k.draw= ables[w]);break}}if(p){var x;for(var w=3D0;w<p.length;w++){x=3Dp[w];l.add_b= ookmark(x.position,x.annotation,m)}}k.has_changes=3Dfalse});return k},init_= keyboard_nav:function(j){$(document).keydown(function(k){if($(k.srcElement)= .is(":input")){return}switch(k.which){case 37:j.move_fraction(0.25);break;c= ase 38:var l=3DMath.round(j.viewport_container.height()/15);j.viewport_cont= ainer.scrollTop(j.viewport_container.scrollTop()-20);break;case 39:j.move_f= raction(-0.25);break;case 40:var l=3DMath.round(j.viewport_container.height= ()/15);j.viewport_container.scrollTop(j.viewport_container.scrollTop()+20);= break}})}});return{object_from_template:a,TracksterUI:f}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/p= ainters","viz/trackster/tracks","viz/visualization"],function(g,c,h,e,b,d){= var a=3Db.object_from_template;var f=3Dg.Base.extend({initialize:function(j= ){this.baseURL=3Dj},createButtonMenu:function(){var j=3Dthis,k=3Dcreate_ico= n_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:funct= ion(){d.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":= view.dbkey},function(l){c.each(l,function(m){view.add_drawable(a(m,view,vie= w))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){v= iew.add_drawable(new b.DrawableGroup(view,view,{name:"New Group"}))}},{icon= _class:"bookmarks",title:"Bookmarks",on_click:function(){parent.force_right= _panel(($("div#right").css("right")=3D=3D"0px"?"hide":"show"))}},{icon_clas= s:"globe",title:"Circster",on_click:function(){window.location=3Dj.baseURL+= "visualization/circster?id=3D"+view.vis_id}},{icon_class:"disk--arrow",titl= e:"Save",on_click:function(){show_modal("Saving...","progress");var l=3D[];= $(".bookmark").each(function(){l.push({position:$(this).children(".position= ").text(),annotation:$(this).children(".annotation").text()})});var m=3D(vi= ew.overview_drawable?view.overview_drawable.name:null),n=3D{view:view.to_di= ct(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:m},bo= okmarks:l};$.ajax({url:galaxy_paths.get("visualization_url"),type:"POST",da= taType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"t= rackster",vis_json:JSON.stringify(n)}}).success(function(o){hide_modal();vi= ew.vis_id=3Do.vis_id;view.has_changes=3Dfalse;window.history.pushState({},"= ",o.url+window.location.hash)}).error(function(){show_modal("Could Not Save= ","Could not save visualization. Please try again later.",{Close:hide_modal= })})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.= location=3Dj.baseURL+"visualization/list"}}],{tooltip_config:{placement:"bo= ttom"}});this.buttonMenu=3Dk;return k},add_bookmarks:function(){var j=3Dthi= s,k=3Dthis.baseURL;show_modal("Select dataset for new bookmarks","progress"= );$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":= view.dbkey},error:function(){alert("Grid failed")},success:function(l){show= _modal("Select dataset for new bookmarks",l,{Cancel:function(){hide_modal()= },Insert:function(){$("input[name=3Did]:checked,input[name=3Dldda_ids]:chec= ked").first().each(function(){var m,n=3D$(this).val();if($(this).attr("name= ")=3D=3D=3D"id"){m=3D{hda_id:n}}else{m=3D{ldda_id:n}}$.ajax({url:this.baseU= RL+"/visualization/bookmarks_from_dataset",data:m,dataType:"json"}).then(fu= nction(o){for(i=3D0;i<o.data.length;i++){var p=3Do.data[i];j.add_bookmark(p= [0],p[1])}})});hide_modal()}})}})},add_bookmark:function(n,l,j){var p=3D$("= #bookmarks-container"),r=3D$("<div/>").addClass("bookmark").appendTo(p);var= s=3D$("<div/>").addClass("position").appendTo(r),o=3D$("<a href=3D''/>").t= ext(n).appendTo(s).click(function(){view.go_to(n);return false}),m=3D$("<di= v/>").text(l).appendTo(r);if(j){var q=3D$("<div/>").addClass("delete-icon-c= ontainer").prependTo(r).click(function(){r.slideUp("fast");r.remove();view.= has_changes=3Dtrue;return false}),k=3D$("<a href=3D''/>").addClass("icon-bu= tton delete").appendTo(q);m.make_text_editable({num_rows:3,use_textarea:tru= e,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes= =3Dtrue;return r},create_visualization:function(o,j,n,p,m){var l=3Dthis,k= =3Dnew b.TracksterView(o);k.editor=3Dtrue;$.when(k.load_chroms_deferred).th= en(function(){if(j){var y=3Dj.chrom,q=3Dj.start,v=3Dj.end,s=3Dj.overview;if= (y&&(q!=3D=3Dundefined)&&v){k.change_chrom(y,q,v)}}if(n){var t,r,u;for(var = w=3D0;w<n.length;w++){k.add_drawable(a(n[w],k,k))}}k.update_intro_div();var= z;for(var w=3D0;w<k.drawables.length;w++){if(k.drawables[w].name=3D=3D=3Ds= ){k.set_overview(k.drawables[w]);break}}if(p){var x;for(var w=3D0;w<p.lengt= h;w++){x=3Dp[w];l.add_bookmark(x.position,x.annotation,m)}}k.has_changes=3D= false});return k},init_keyboard_nav:function(j){$(document).keydown(functio= n(k){if($(k.srcElement).is(":input")){return}switch(k.which){case 37:j.move= _fraction(0.25);break;case 38:var l=3DMath.round(j.viewport_container.heigh= t()/15);j.viewport_container.scrollTop(j.viewport_container.scrollTop()-20)= ;break;case 39:j.move_fraction(-0.25);break;case 40:var l=3DMath.round(j.vi= ewport_container.height()/15);j.viewport_container.scrollTop(j.viewport_con= tainer.scrollTop()+20);break}})}});return{object_from_template:a,TracksterU= I:f}}); \ No newline at end of file

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],= function(s,i,l,p){var a=3Dfunction(u,x,v,w){$.ajax({url:u,data:(v?{"f-dbkey= ":v}:{}),error:function(){alert("Grid failed")},success:function(y){show_mo= dal("Select datasets for new tracks",y,{Cancel:function(){hide_modal()},Add= :function(){var z=3D[];$("input[name=3Did]:checked,input[name=3Dldda_ids]:c= hecked").each(function(){var A=3D{data_type:"track_config",hda_ldda:"hda"},= B=3D$(this).val();if($(this).attr("name")!=3D=3D"id"){A.hda_ldda=3D"ldda"}z= [z.length]=3D$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,= z).then(function(){var A=3D(arguments[0] instanceof Array?$.map(arguments,f= unction(B){return B[0]}):[arguments[0]]);w(A)});hide_modal()}})}})};var j= =3Dfunction(u){return("isResolved" in u)};var f=3Dfunction(u){this.default_= font=3Du!=3D=3Dundefined?u:"9px Monaco, Lucida Console, monospace";this.dum= my_canvas=3Dthis.new_canvas();this.dummy_context=3Dthis.dummy_canvas.getCon= text("2d");this.dummy_context.font=3Dthis.default_font;this.char_width_px= =3Dthis.dummy_context.measureText("A").width;this.patterns=3D{};this.load_p= attern("right_strand","/visualization/strand_right.png");this.load_pattern(= "left_strand","/visualization/strand_left.png");this.load_pattern("right_st= rand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_st= rand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load= _pattern:function(u,y){var v=3Dthis.patterns,w=3Dthis.dummy_context,x=3Dnew= Image();x.src=3Dgalaxy_paths.attributes.image_path+y;x.onload=3Dfunction()= {v[u]=3Dw.createPattern(x,"repeat")}},get_pattern:function(u){return this.p= atterns[u]},new_canvas:function(){var u=3D$("<canvas/>")[0];if(window.G_vml= CanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=3Dthis;return u}= });var q=3DBackbone.Model.extend({defaults:{num_elements:20,obj_cache:null,= key_ary:null},initialize:function(u){this.clear()},get_elt:function(v){var = w=3Dthis.attributes.obj_cache,x=3Dthis.attributes.key_ary,u=3Dx.indexOf(v);= if(u!=3D=3D-1){if(w[v].stale){x.splice(u,1);delete w[v]}else{this.move_key_= to_end(v,u)}}return w[v]},set_elt:function(v,x){var y=3Dthis.attributes.obj= _cache,z=3Dthis.attributes.key_ary,w=3Dthis.attributes.num_elements;if(!y[v= ]){if(z.length>=3Dw){var u=3Dz.shift();delete y[u]}z.push(v)}y[v]=3Dx;retur= n x},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this= .attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache=3D{= };this.attributes.key_ary=3D[]},size:function(){return this.attributes.key_= ary.length}});var d=3Dq.extend({defaults:s.extend({},q.prototype.defaults,{= dataset:null,init_data:null,filters_manager:null,data_type:"data",data_mode= _compatible:function(u,v){return true},can_subset:function(u){return false}= }),initialize:function(u){q.prototype.initialize.call(this);var v=3Dthis.ge= t("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("n= um_elements")<u.length){this.set("num_elements",u.length)}var v=3Dthis;s.ea= ch(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x= =3Dthis.get("dataset"),w=3D$.Deferred(),u=3D(this.get("data_type")=3D=3D"ra= w_data"?"state":this.get("data_type")=3D=3D"data"?"converted_datasets_state= ":"error"),v=3Dnew l.ServerStateDeferred({ajax_settings:{url:this.get("data= set").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},= interval:5000,success_fn:function(y){return y!=3D=3D"pending"}});$.when(v.g= o()).then(function(y){w.resolve(y=3D=3D=3D"ok"||y=3D=3D=3D"data")});return = w},search_features:function(u){var v=3Dthis.get("dataset"),w=3D{query:u,hda= 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et_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:fu= nction(C,B,x,A,y){var E=3Dthis._mark_stale(C);if(!(E&&this.get("data_mode_c= ompatible")(E,B))){console.log("ERROR: problem with getting more data: curr= ent data is not compatible");return}var w=3DC.get("start");if(y=3D=3D=3Dthi= s.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y=3D=3D=3D= this.BROAD_DATA_REQ){w=3D(E.max_high?E.max_high:E.data[E.data.length-1][2])= +1}}var D=3DC.copy().set("start",w);var v=3Dthis,z=3Dthis.load_data(D,B,x,A= ),u=3D$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data)= {F.data=3DE.data.concat(F.data);if(F.max_low){F.max_low=3DE.max_low}if(F.me= ssage){F.message=3DF.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,= F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=3D= this.get_elt(v);return(u.dataset_type=3D=3D=3D"bigwig"&&u.data.length<8000)= },get_more_detailed_data:function(x,z,v,y,w){var u=3Dthis._mark_stale(x);if= (!u){console.log("ERROR getting more detailed data: no current data");retur= n}if(!w){w=3D{}}if(u.dataset_type=3D=3D=3D"bigwig"){w.num_samples=3D1000*y}= else{if(u.dataset_type=3D=3D=3D"summary_tree"){w.level=3DMath.min(u.level-1= ,2)}}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=3Dthis.g= et_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("= dataset"),v.toString())}u.stale=3Dtrue;return u},get_genome_wide_data:funct= ion(u){var w=3Dthis,y=3Dtrue,x=3Ds.map(u.get("chroms_info").chrom_info,func= tion(A){var z=3Dw.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){= y=3Dfalse}return z});if(y){return x}var v=3D$.Deferred();$.getJSON(this.get= ("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);= v.resolve(z.data)});return v},get_elt:function(u){return q.prototype.get_el= t.call(this,u.toString())},set_elt:function(v,u){return q.prototype.set_elt= .call(this,v.toString(),u)}});var n=3Dd.extend({initialize:function(u){var = v=3Dnew Backbone.Model();v.urlRoot=3Du.data_url;this.set("dataset",v)},load= _data:function(w,x,u,v){if(u>1){return{data:null}}return d.prototype.load_d= ata.call(this,w,x,u,v)}});var c=3DBackbone.Model.extend({defaults:{name:nul= l,key:null,chroms_info:null},initialize:function(u){this.id=3Du.dbkey},get_= chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_c= hrom_region:function(u){var v=3Ds.find(this.get_chroms_info(),function(w){r= eturn w.chrom=3D=3Du});return new g({chrom:v.chrom,end:v.len})}});var g=3DB= ackbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHRO= MS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTA= INED_BY:1005,AFTER:1006},initialize:function(v){if(v.from_str){var x=3Dv.fr= om_str.split(":"),w=3Dx[0],u=3Dx[1].split("-");this.set({chrom:w,start:pars= eInt(u[0],10),end:parseInt(u[1],10)})}},copy:function(){return new g({chrom= :this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:fu= nction(){return this.get("end")-this.get("start")},toString:function(){retu= rn this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:func= tion(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get(= "end")}},compute_overlap:function(B){var v=3Dthis.get("chrom"),A=3DB.get("c= hrom"),z=3Dthis.get("start"),x=3DB.get("start"),y=3Dthis.get("end"),w=3DB.g= et("end"),u;if(v&&A&&v!=3D=3DA){return this.get("DIF_CHROMS")}if(z<x){if(y<= x){u=3Dthis.get("BEFORE")}else{if(y<=3Dw){u=3Dthis.get("OVERLAP_START")}els= e{u=3Dthis.get("CONTAINS")}}}else{if(z>w){u=3Dthis.get("AFTER")}else{if(y<= =3Dw){u=3Dthis.get("CONTAINED_BY")}else{u=3Dthis.get("OVERLAP_END")}}}retur= n u},contains:function(u){return this.compute_overlap(u)=3D=3D=3Dthis.get("= CONTAINS")},overlaps:function(u){return s.intersection([this.compute_overla= p(u)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length= =3D=3D=3D0}});var m=3DBackbone.Collection.extend({model:g});var e=3DBackbon= e.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:B= ackbone.HasOne,key:"region",relatedModel:g}]});var r=3DBackbone.Collection.= extend({model:e});var t=3Di.Dataset.extend({initialize:function(u){this.set= ("id",u.dataset_id);this.set("config",p.ConfigSettingCollection.from_config= _dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")}= ,{key:"color"}]);var v=3Dthis.get("preloaded_data");if(v){v=3Dv.data}else{v= =3D[]}this.set("data_manager",new d({dataset:this,init_data:v}))}});var o= =3DBackbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_= paths.get("visualization_url"),save:function(){return $.ajax({url:this.url(= ),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var= k=3Do.extend({defaults:s.extend({},o.prototype.defaults,{dbkey:"",tracks:n= ull,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"t= racks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}})= ;var b=3DBackbone.Model.extend({});var h=3DBackbone.Router.extend({initiali= ze:function(v){this.view=3Dv.view;this.route(/([\w]+)$/,"change_location");= this.route(/([\w]+:[\d,]+-[\d,]+)$/,"change_location");var u=3Dthis;u.view= .on("navigate",function(w){u.navigate(w)})},change_location:function(u){thi= s.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmark= Collection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeReg= ion:g,GenomeRegionCollection:m,GenomeVisualization:k,ReferenceTrackDataMana= ger:n,TrackBrowserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}= }); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],= function(s,i,l,p){var a=3Dfunction(u,x,w,v){$.ajax({url:u,data:w,error:func= tion(){alert("Grid failed")},success:function(y){show_modal("Select dataset= s for new tracks",y,{Cancel:function(){hide_modal()},Add:function(){var z= =3D[];$("input[name=3Did]:checked,input[name=3Dldda_ids]:checked").each(fun= ction(){var A=3D{data_type:"track_config",hda_ldda:"hda"},B=3D$(this).val()= ;if($(this).attr("name")!=3D=3D"id"){A.hda_ldda=3D"ldda"}z[z.length]=3D$.aj= ax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(= ){var A=3D(arguments[0] instanceof Array?$.map(arguments,function(B){return= B[0]}):[arguments[0]]);v(A)});hide_modal()}})}})};var j=3Dfunction(u){retu= rn("isResolved" in u)};var f=3Dfunction(u){this.default_font=3Du!=3D=3Dunde= fined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=3Dthis.ne= w_canvas();this.dummy_context=3Dthis.dummy_canvas.getContext("2d");this.dum= my_context.font=3Dthis.default_font;this.char_width_px=3Dthis.dummy_context= .measureText("A").width;this.patterns=3D{};this.load_pattern("right_strand"= ,"/visualization/strand_right.png");this.load_pattern("left_strand","/visua= lization/strand_left.png");this.load_pattern("right_strand_inv","/visualiza= tion/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualiza= tion/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y= ){var v=3Dthis.patterns,w=3Dthis.dummy_context,x=3Dnew Image();x.src=3Dgala= xy_paths.attributes.image_path+y;x.onload=3Dfunction(){v[u]=3Dw.createPatte= rn(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canva= s:function(){var u=3D$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlC= anvasManager.initElement(u)}u.manager=3Dthis;return u}});var q=3DBackbone.M= odel.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initial= ize:function(u){this.clear()},get_elt:function(v){var w=3Dthis.attributes.o= bj_cache,x=3Dthis.attributes.key_ary,u=3Dx.indexOf(v);if(u!=3D=3D-1){if(w[v= ].stale){x.splice(u,1);delete w[v]}else{this.move_key_to_end(v,u)}}return w= [v]},set_elt:function(v,x){var y=3Dthis.attributes.obj_cache,z=3Dthis.attri= butes.key_ary,w=3Dthis.attributes.num_elements;if(!y[v]){if(z.length>=3Dw){= var u=3Dz.shift();delete y[u]}z.push(v)}y[v]=3Dx;return x},move_key_to_end:= function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.p= ush(v)},clear:function(){this.attributes.obj_cache=3D{};this.attributes.key= _ary=3D[]},size:function(){return this.attributes.key_ary.length}});var d= =3Dq.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,init_d= ata:null,filters_manager:null,data_type:"data",data_mode_compatible:functio= n(u,v){return true},can_subset:function(u){return false}}),initialize:funct= ion(u){q.prototype.initialize.call(this);var v=3Dthis.get("init_data");if(v= ){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.len= gth){this.set("num_elements",u.length)}var v=3Dthis;s.each(u,function(w){v.= set_data(w.region,w)})},data_is_ready:function(){var x=3Dthis.get("dataset"= ),w=3D$.Deferred(),u=3D(this.get("data_type")=3D=3D"raw_data"?"state":this.= get("data_type")=3D=3D"data"?"converted_datasets_state":"error"),v=3Dnew l.= ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda= _ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success= _fn:function(y){return y!=3D=3D"pending"}});$.when(v.go()).then(function(y)= {w.resolve(y=3D=3D=3D"ok"||y=3D=3D=3D"data")});return w},search_features:fu= nction(u){var v=3Dthis.get("dataset"),w=3D{query:u,hda_ldda:v.get("hda_ldda= "),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,= B,v,A){var y=3Dthis.get("dataset"),x=3D{data_type:this.get("data_type"),chr= om:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,= hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=3Dthis.get("filters_manager= ");if(E){var F=3D[];var u=3DE.filters;for(var z=3D0;z<u.length;z++){F.push(= u[z].name)}x.filter_cols=3DJSON.stringify(F)}var w=3Dthis,D=3D$.getJSON(y.u= rl(),x,function(G){w.set_data(C,G)});this.set_data(C,D);return D},get_data:= function(A,z,w,y){var B=3Dthis.get_elt(A);if(B&&(j(B)||this.get("data_mode_= compatible")(B,z))){return B}var C=3Dthis.get("key_ary"),v=3Dthis.get("obj_= cache"),D,u;for(var x=3D0;x<C.length;x++){D=3DC[x];u=3Dnew g({from_str:D});= if(u.contains(A)){B=3Dv[D];if(j(B)||(this.get("data_mode_compatible")(B,z)&= &this.get("can_subset")(B))){this.move_key_to_end(D,x);return B}}}return th= is.load_data(A,z,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_= REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E= =3Dthis._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){cons= ole.log("ERROR: problem with getting more data: current data is not compati= ble");return}var w=3DC.get("start");if(y=3D=3D=3Dthis.DEEP_DATA_REQ){$.exte= nd(A,{start_val:E.data.length+1})}else{if(y=3D=3D=3Dthis.BROAD_DATA_REQ){w= =3D(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=3DC.copy().s= et("start",w);var v=3Dthis,z=3Dthis.load_data(D,B,x,A),u=3D$.Deferred();thi= s.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=3DE.data.conca= t(F.data);if(F.max_low){F.max_low=3DE.max_low}if(F.message){F.message=3DF.m= essage.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});retu= rn u},can_get_more_detailed_data:function(v){var u=3Dthis.get_elt(v);return= (u.dataset_type=3D=3D=3D"bigwig"&&u.data.length<8000)},get_more_detailed_da= ta:function(x,z,v,y,w){var u=3Dthis._mark_stale(x);if(!u){console.log("ERRO= R getting more detailed data: no current data");return}if(!w){w=3D{}}if(u.d= ataset_type=3D=3D=3D"bigwig"){w.num_samples=3D1000*y}else{if(u.dataset_type= =3D=3D=3D"summary_tree"){w.level=3DMath.min(u.level-1,2)}}return this.load_= data(x,z,v,w)},_mark_stale:function(v){var u=3Dthis.get_elt(v);if(!u){conso= le.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString()= )}u.stale=3Dtrue;return u},get_genome_wide_data:function(u){var w=3Dthis,y= =3Dtrue,x=3Ds.map(u.get("chroms_info").chrom_info,function(A){var z=3Dw.get= _elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=3Dfalse}return z});= if(y){return x}var v=3D$.Deferred();$.getJSON(this.get("dataset").url(),{da= ta_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});r= eturn v},get_elt:function(u){return q.prototype.get_elt.call(this,u.toStrin= g())},set_elt:function(v,u){return q.prototype.set_elt.call(this,v.toString= (),u)}});var n=3Dd.extend({initialize:function(u){var v=3Dnew Backbone.Mode= l();v.urlRoot=3Du.data_url;this.set("dataset",v)},load_data:function(w,x,u,= v){if(u>1){return{data:null}}return d.prototype.load_data.call(this,w,x,u,v= )}});var c=3DBackbone.Model.extend({defaults:{name:null,key:null,chroms_inf= o:null},initialize:function(u){this.id=3Du.dbkey},get_chroms_info:function(= ){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(= u){var v=3Ds.find(this.get_chroms_info(),function(w){return w.chrom=3D=3Du}= );return new g({chrom:v.chrom,end:v.len})}});var g=3DBackbone.RelationalMod= el.extend({defaults:{chrom:null,start:0,end:0},initialize:function(v){if(v.= from_str){var x=3Dv.from_str.split(":"),w=3Dx[0],u=3Dx[1].split("-");this.s= et({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}},copy:function= (){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.g= et("end")})},length:function(){return this.get("end")-this.get("start")},to= String:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.g= et("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get(= "start"),end:this.get("end")}},compute_overlap:function(B){var v=3Dthis.get= ("chrom"),A=3DB.get("chrom"),z=3Dthis.get("start"),x=3DB.get("start"),y=3Dt= his.get("end"),w=3DB.get("end"),u;if(v&&A&&v!=3D=3DA){return g.overlap_resu= lts.DIF_CHROMS}if(z<x){if(y<x){u=3Dg.overlap_results.BEFORE}else{if(y<=3Dw)= {u=3Dg.overlap_results.OVERLAP_START}else{u=3Dg.overlap_results.CONTAINS}}}= else{if(z>w){u=3Dg.overlap_results.AFTER}else{if(y<=3Dw){u=3Dg.overlap_resu= lts.CONTAINED_BY}else{u=3Dg.overlap_results.OVERLAP_END}}}return u},contain= s:function(u){return this.compute_overlap(u)=3D=3D=3Dg.overlap_results.CONT= AINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],= [g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AF= TER]).length=3D=3D=3D0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONT= AINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}= });var m=3DBackbone.Collection.extend({model:g});var e=3DBackbone.Relationa= lModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.Has= One,key:"region",relatedModel:g}]});var r=3DBackbone.Collection.extend({mod= el:e});var t=3Di.Dataset.extend({initialize:function(u){this.set("id",u.dat= aset_id);this.set("config",p.ConfigSettingCollection.from_config_dict(u.pre= fs));this.get("config").add([{key:"name",value:this.get("name")},{key:"colo= r"}]);var v=3Dthis.get("preloaded_data");if(v){v=3Dv.data}else{v=3D[]}this.= set("data_manager",new d({dataset:this,init_data:v}))}});var o=3DBackbone.R= elationalModel.extend({defaults:{title:"",type:""},url:galaxy_paths.get("vi= sualization_url"),save:function(){return $.ajax({url:this.url(),type:"POST"= ,dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=3Do.extend= ({defaults:s.extend({},o.prototype.defaults,{dbkey:"",tracks:null,bookmarks= :null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relate= dModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=3DBack= bone.Model.extend({});var h=3DBackbone.Router.extend({initialize:function(v= ){this.view=3Dv.view;this.route(/([\w]+)$/,"change_location");this.route(/(= [\w]+:[\d,]+-[\d,]+)$/,"change_location");var u=3Dthis;u.view.on("navigate= ",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(= u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,= Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeR= egionCollection:m,GenomeVisualization:k,ReferenceTrackDataManager:n,TrackBr= owserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -10,7 +10,7 @@ "../libs/d3", =20 "../libs/bootstrap", - "../libs/jquery/jquery-ui-1.8.23.custom.min" + "../libs/jquery/jquery-ui" ], function(){ =20 /* =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/admin/requests/select_datasets_to_transfer.mako --- a/templates/admin/requests/select_datasets_to_transfer.mako +++ b/templates/admin/requests/select_datasets_to_transfer.mako @@ -8,7 +8,7 @@ ${common_javascripts()} </%def> =20 -${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery.coo= kie", "libs/jquery/jquery.dynatree" )} +${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.cookie", "libs/jquery= /jquery.dynatree" )} ${h.css( "dynatree_skin/ui.dynatree" )} =20 <script type=3D"text/javascript">

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/admin/tool_shed_repository/browse_repository.ma= ko --- a/templates/admin/tool_shed_repository/browse_repository.mako +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -9,7 +9,7 @@ =20 <%def name=3D"javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery= .dynatree" )} + ${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.dynatree" )} ${browse_files(repository.name, repository.repo_files_directory(trans.= app))} </%def> =20

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/admin/tool_shed_repository/browse_tool_dependen= cy.mako --- a/templates/admin/tool_shed_repository/browse_tool_dependency.mako +++ b/templates/admin/tool_shed_repository/browse_tool_dependency.mako @@ -9,7 +9,7 @@ =20 <%def name=3D"javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery= .dynatree" )} + ${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.dynatree" )} ${browse_files(tool_dependency.name, tool_dependency.installation_dire= ctory( trans.app ))} </%def> =20

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -23,8 +23,6 @@ <![endif]--> =20 ${render_trackster_js_files()} -${h.js( "libs/jquery/jquery.autocomplete" )} - =20 <script type=3D"text/javascript"> =20 @@ -107,7 +105,12 @@ "Create": function() { $(document).trigger("conver= t_to_values"); continue_fn(); } }); $("#new-title").focus(); - replace_big_select_inputs(); + $("select[name=3D'dbkey']").combobox({ + appendTo: $("#overlay"), + size: 40 + }); + // To support the large number of options for dbkey, e= nable scrolling in overlay. + $("#overlay").css("overflow", "auto"); } }); %endif

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -5,7 +5,7 @@ ${h.css( "base", "autocomplete_tagging", - "jquery-ui/smoothness/jquery-ui-1.8.23.custom" + "jquery-ui/smoothness/jquery-ui" )} =20 <style type=3D"text/css">

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/visualization/sweepster.mako --- a/templates/visualization/sweepster.mako +++ b/templates/visualization/sweepster.mako @@ -107,7 +107,7 @@ ${parent.javascripts()} =20 ${h.templates( "tool_link", "panel_section", "tool_search", "tool_form= " )} - ${h.js( "libs/require", "libs/jquery/jquery-ui-1.8.23.custom.min" )} + ${h.js( "libs/require", "libs/jquery/jquery-ui" )} =20 <script type=3D"text/javascript"> require.config({=20

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/visualization/trackster_common.mako --- a/templates/visualization/trackster_common.mako +++ b/templates/visualization/trackster_common.mako @@ -5,13 +5,14 @@ ## Render needed CSS files. <%def name=3D"render_trackster_css_files()"> ${h.css( "history", "autocomplete_tagging", "trackster", "library",=20 - "jquery-ui/smoothness/jquery-ui-1.8.23.custom" )} + "jquery-ui/smoothness/jquery-ui" )} </%def> =20 =20 ## Render needed JavaScript files. <%def name=3D"render_trackster_js_files()"> - ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.e= vent.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel= ", "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/require", "libs/farbtas= tic" )} + ${h.js( "galaxy.panels", "libs/jquery/jstorage", "libs/jquery/jquery.e= vent.drag", "libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel= ", "libs/jquery/jquery-ui", "libs/jquery/jquery-ui-combobox", + "libs/require", "libs/farbtastic" )} </%def> =20 ## Render a block of JavaScript that contains all necessary variables for = Trackster.

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/webapps/community/repository/browse_repository.= mako --- a/templates/webapps/community/repository/browse_repository.mako +++ b/templates/webapps/community/repository/browse_repository.mako @@ -58,7 +58,7 @@ =20 <%def name=3D"javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery-ui-1.8.23.cus= tom.min", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery-ui", "libs/jq= uery/jquery.cookie", "libs/jquery/jquery.dynatree" )} ${common_javascripts(repository)} </%def> =20

diff -r fa045aad74e90f16995e0cbb670a59e6b9becbed -r 394c3bd89926919b3ff861d= 5bc3daa6c7d10fd12 templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -28,7 +28,7 @@ =20 <%def name=3D"javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/jquery-ui-1.8.23.custom.min", "libs/jquery/jquery= .cookie", "libs/jquery/jquery.dynatree" )} + ${h.js( "libs/jquery/jquery-ui", "libs/jquery/jquery.cookie", "libs/jq= uery/jquery.dynatree" )} ${common_javascripts(repository)} <script type=3D"text/javascript"> $( function() {

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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