1 new changeset in galaxy-central:

http://bitbucket.org/galaxy/galaxy-central/changeset/a98119b07764/ changeset: r5340:a98119b07764 user: jgoecks date: 2011-04-05 17:51:48 summary: Refactor and enhance trackster visual analytics: (a) move all visual analytics code into Tool class for encapsulation; (b) put tool outputs in appropriate history when user is rerunning his own tool; (c) enable users not logged in to run tools; (d) use tool HTML to display inputs rather than sliders. affected #: 9 files (4.7 KB)

--- a/lib/galaxy/visualization/tracks/visual_analytics.py Mon Apr 04 23:27:25 2011 -0400 +++ b/lib/galaxy/visualization/tracks/visual_analytics.py Tue Apr 05 11:51:48 2011 -0400 @@ -1,3 +1,5 @@ +import urllib + from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter, SelectToolParameter from galaxy.tools.parameters.dynamic_options import DynamicOptions

@@ -28,17 +30,19 @@ tool_param_values = dict( [ ( p.name, p.value ) for p in job.parameters ] ) tool_param_values = tool.params_from_strings( tool_param_values, trans.app, ignore_errors=True ) for name, input in tool.inputs.items(): - if type( input ) == IntegerToolParameter: - tool_params.append( { 'name' : name, 'label' : input.label, \ - 'value' : tool_param_values.get( name, input.value ), \ - 'type' : 'int', 'min' : input.min, 'max' : input.max } ) - elif type( input ) == FloatToolParameter: - tool_params.append( { 'name' : name, 'label' : input.label, \ - 'value' : tool_param_values.get( name, input.value ), \ - 'type' : 'float', 'min' : input.min, 'max' : input.max } ) + if type( input ) == IntegerToolParameter or type( input ) == FloatToolParameter: + param_dict = { 'name' : name, 'label' : input.label, \ + 'value' : tool_param_values.get( name, input.value ), \ + 'type' : 'number', 'init_value' : input.value, + 'html' : urllib.quote( input.get_html() ) } + if input.min: + param_dict['min'] = input.min + if input.max: + param_dict['max'] = input.max + tool_params.append( param_dict ) elif type( input ) == SelectToolParameter and type( input.options ) != DynamicOptions: tool_params.append( { 'name' : name, 'label' : input.label, 'type' : 'select', \ - 'options' : [ option[:2] for option in input.get_options( trans, None ) ] } ) + 'html' : urllib.quote( input.get_html() ) } )

# If tool has parameters that can be interactively modified, return tool. # Return empty set otherwise.

--- a/lib/galaxy/web/controllers/tracks.py Mon Apr 04 23:27:25 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Tue Apr 05 11:51:48 2011 -0400 @@ -201,7 +201,6 @@ return trans.fill_template( "tracks/new_browser.mako", dbkeys=self._get_dbkeys( trans ), default_dbkey=kwargs.get("default_dbkey", None) )

@web.json - @web.require_login() def add_track_async(self, trans, hda_id=None, ldda_id=None): if hda_id: hda_ldda = "hda" @@ -707,8 +706,15 @@ # Set input datasets for tool. Input datasets are subsets of full # datasets and are based on chrom, low, high. # - job_history = trans.get_history( create=True ) - hda_permissions = trans.app.security_agent.history_get_default_permissions( job_history ) + + # If user is rerunning own tool, put new data in original dataset's + # history. If another user is running tool, put new data in current + # history. + if original_dataset.history.user == trans.user: + working_history = original_dataset.history + else: + working_history = trans.get_history( create=True ) + hda_permissions = trans.app.security_agent.history_get_default_permissions( working_history ) messages_list = [] for jida in original_job.input_datasets: input_dataset = jida.dataset @@ -730,7 +736,7 @@ name="Subset [%s:%i-%i] of data %i" % \ ( chrom, low, high, input_dataset.hid ), visible=False ) - job_history.add_dataset( new_dataset ) + working_history.add_dataset( new_dataset ) trans.sa_session.add( new_dataset ) trans.app.security_agent.set_all_dataset_permissions( new_dataset.dataset, hda_permissions )

@@ -753,14 +759,14 @@ # Start tool and handle outputs. # try: - subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=job_history ) + subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=working_history ) except Exception, e: # Lots of things can go wrong when trying to execute tool. return to_json_string( { "error" : True, "message" : e.__class__.__name__ + ": " + str(e) } ) for output in subset_job_outputs.values(): output.visible = False trans.sa_session.flush() - + # Return new track that corresponds to the original dataset. output_name = None for joda in original_job.output_datasets:

--- a/static/june_2007_style/blue/trackster.css Mon Apr 04 23:27:25 2011 -0400 +++ b/static/june_2007_style/blue/trackster.css Tue Apr 05 11:51:48 2011 -0400 @@ -38,10 +38,12 @@ .top-labeltrack{position:relative;border-bottom:solid #999 1px;} .nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #333 1px;} input{font:10px verdana;} -.dynamic-tool,.filters{width:400px;margin-left:0.25em;padding-bottom:0.5em;} +.dynamic-tool,.filters{width:410px;margin-left:0.25em;padding-bottom:0.5em;} .slider-row{margin-top:0.4em;margin-left:1em;} .slider-label{float:left;font-weight:bold;} .slider{float:right;width:200px;position:relative;} .tool-name{font-size:110%;font-weight:bold;} +.param-row{margin-top:0.2em;margin-left:1em;} +.param-label{float:left;font-weight:bold;padding-top:0.2em;} .child-track-icon{background:url('../images/fugue/arrow-000-small-bw.png') no-repeat;width:30px;cursor:move;} .track-resize{background:white url('../images/visualization/draggable_vertical.png') no-repeat top center;position:absolute;right:3px;bottom:-4px;width:14px;height:7px;border:solid #999 1px;z-index:100;}

--- a/static/june_2007_style/trackster.css.tmpl Mon Apr 04 23:27:25 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Tue Apr 05 11:51:48 2011 -0400 @@ -229,7 +229,7 @@ font: 10px verdana; } .dynamic-tool, .filters { - width: 400px; + width: 410px; margin-left: 0.25em; padding-bottom:0.5em; } @@ -237,7 +237,7 @@ margin-top: 0.4em; margin-left: 1em; } -.slider-label { +.param-label, .slider-label { float: left; font-weight: bold; } @@ -250,6 +250,15 @@ font-size: 110%; font-weight: bold; } +.param-row { + margin-top: 0.2em; + margin-left: 1em; +} +.param-label{ + float: left; + font-weight: bold; + padding-top: 0.2em; +} .child-track-icon { background:url('../images/fugue/arrow-000-small-bw.png') no-repeat; width: 30px;

--- a/static/scripts/packed/trackster.js Mon Apr 04 23:27:25 2011 -0400 +++ b/static/scripts/packed/trackster.js Tue Apr 05 11:51:48 2011 -0400 @@ -1,1 +1,1 @@ -CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}function get_slider_step(c,a){var b=a-c;return(b<=1?0.01:(b<=1000?1:5))}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!==-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataManager=function(b,a,c){Cache.call(this,b);this.track=a;this.subset=(c!==undefined?c:true)};$.extend(DataManager.prototype,Cache.prototype,{load_data:function(h,j,d,g,a,f){var c={chrom:h,low:j,high:d,mode:g,resolution:a,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(c,f);var k=[];for(var e=0;e<this.track.filters.length;e++){k[k.length]=this.track.filters[e].name}c.filter_cols=JSON.stringify(k);var b=this;return $.getJSON(this.track.data_url,c,function(l){b.set_data(j,d,g,l)})},get_data:function(j,k,c,h,b,f){var l=this.get(this.gen_key(k,c,h));if(l){return l}if(this.subset){var m,g,a,e,h,l;for(var d=0;d<this.key_ary.length;d++){m=this.key_ary[d];g=this.split_key(m);a=g[0];e=g[1];if(k>=a&&c<=e){l=this.obj_cache[m];if(l.dataset_type!=="summary_tree"&&l.extra_info!=="no_detail"){this.move_key_to_end(m,d);return l}}}}return this.load_data(j,k,c,h,b,f)},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.canvas_manager=new CanvasManager(a.get(0).ownerDocument);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown 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Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();$(this).val("");a.location_span.show();a.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup 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/>").click(function(){a.zoom_in();a.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var j=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(j/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return 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"+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.chrom_info.length===0){alert("Invalid chromosome: "+b.chrom);return}if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var k=this,a,d,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}k.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var 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g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(g){this.name=g.name;this.params=[];var a=g.params;for(var e=0;e<a.length;e++){var d=a[e],c=d.name,b=d.label,f=d.type;if(f==="int"||f==="float"){this.params[this.params.length]=new NumberParameter(c,b,d.min,d.max,d.value)}else{if(f=="select"){this.params[this.params.length]=new SelectParameter(c,b,d.options)}else{console.log("WARNING: unrecognized tool parameter type:",c,f)}}}};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=JSON.stringify(c.value)}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var SelectParameter=function(c,b,a){this.name=c;this.label=b;this.options=a;this.value=(a.length!==0?a[0][1]:null)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.min){this.min=Math.floor(b[this.index]);a=true}if(b[this.index]>this.max){this.max=Math.ceil(b[this.index]);a=true}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.min<b||this.max>a){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Tile=function(a,b,c){this.track=a;this.canvas=b;this.histo_max=c};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_url_extra_params={};this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,h,o){var c=this,p=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(h!==undefined&&obj_length(h)>0?new Tool(h):undefined);this.parent_track=o;this.child_tracks=[];if(c.hidden){return}var k=function(r,s,t){r.click(function(){var u=s.text();max=parseFloat(t.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(t.slider("option","values")){input_size=2*input_size+1;multi_value=true}s.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",u).appendTo(s).focus().select().click(function(v){v.stopPropagation()}).blur(function(){$(this).remove();s.text(u)}).keyup(function(z){if(z.keyCode===27){$(this).trigger("blur")}else{if(z.keyCode===13){var x=t.slider("option","min"),v=t.slider("option","max"),y=function(A){return(isNaN(A)||A>v||A<x)},w=$(this).val();if(!multi_value){w=parseFloat(w);if(y(w)){alert("Parameter value must be in the range ["+x+"-"+v+"]");return $(this)}}else{w=w.split("-");w=[parseFloat(w[0]),parseFloat(w[1])];if(y(w[0])||y(w[1])){alert("Parameter value must be in the range ["+x+"-"+v+"]");return $(this)}}t.slider((multi_value?"values":"value"),w)}}})})};if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(r){r.stopPropagation()}).bind("click",function(r){r.stopPropagation()}).bind("dblclick",function(r){r.stopPropagation()});$.each(this.filters,function(x,s){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var r=$("<div/>").addClass("slider-label").appendTo(u);var z=$("<span/>").addClass("slider-name").text(s.name+" ").appendTo(r);var t=$("<span/>");var v=$("<span/>").addClass("slider-value").appendTo(r).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(u);s.control_element=$("<div/>").attr("id",s.name+"-filter-control").appendTo(y);var w=[0,0];s.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(A,B){w=B.values;t.text(B.values[0]+"-"+B.values[1]);setTimeout(function(){if(B.values[0]==w[0]&&B.values[1]==w[1]){var C=B.values;t.text(C[0]+"-"+C[1]);s.low=C[0];s.high=C[1];c.draw(true,true)}},50)},change:function(A,B){s.control_element.slider("option","slide").call(s.control_element,A,B)}});s.slider=s.control_element;s.slider_label=t;k(v,t,s.control_element);$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(r){r.stopPropagation()}).bind("click",function(r){r.stopPropagation()}).bind("dblclick",function(r){r.stopPropagation()});var n=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var m=this.tool.params;var c=this;$.each(this.tool.params,function(A,s){if(s instanceof NumberParameter){var x=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(x);var C=$("<span/>").addClass("slider-name").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var y=$("<span/>").addClass("slider-value").appendTo(u).append("[").append(t).append("]");var B=$("<div/>").addClass("slider").appendTo(x);var r=$("<div id='"+s.name+"-param-control'>").appendTo(B);r.slider({min:s.min,max:s.max,step:get_slider_step(s.min,s.max),value:s.value,slide:function(F,H){var G=H.value;s.value=G;if(0<G&&G<1){G=parseFloat(G).toFixed(2)}t.text(G)},change:function(F,G){r.slider("option","slide").call(r,F,G)}});k(y,t,r);$("<div style='clear: both;'/>").appendTo(x)}else{if(s instanceof SelectParameter){var x=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(x);var C=$("<span/>").addClass("slider-name").text(s.label+" ").appendTo(u);var E=$("<div/>").addClass("slider").appendTo(x);var w=$("<select/>").appendTo(E);w.change(function(){s.value=$(this).val()});var D=w.attr("options");for(var z=0;z<s.options.length;z++){var v=s.options[z];D[D.length]=new Option(v[0],v[1])}$("<div style='clear: both;'/>").appendTo(x)}}});var q=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var l=$("<input type='submit'>").attr("value","Run").appendTo(q);var c=this;l.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(r){c.mode_div.text(r);c.mode=r;c.track_config.values.mode=r;c.tile_cache.clear();c.draw()};var a={};for(var f=0,j=c.display_modes.length;f<j;f++){var g=c.display_modes[f];a[g]=function(r){return function(){d(r)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},draw:function(a,d){var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),f=l/j,m=this.view.resolution,e=$("<div style='position: relative;'></div>");if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}var k=this;var q=setInterval(function(){if(obj_length(c)===0){clearInterval(q);if(d){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var z=$(v[w]);if(u){z.remove()}else{if(z.children().length!==0){u=true}}}}for(var y=0;y<k.filters.length;y++){k.filters[y].update_ui_elt()}var x=false;if(k.example_feature){for(var y=0;y<k.filters.length;y++){if(k.filters[y].applies_to(k.example_feature)){x=true;break}}}if(k.filters_available!==x){k.filters_available=x;if(!k.filters_available){k.filters_div.hide()}k.make_name_popup_menu()}}},50);for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,g,l,c,e,k,m,f){var d=this;var h=function(u,n,p,o,s,t,q){returned_tile=d.draw_tile(n,p,o,s,t,q);var r=$("<div class='track-tile'>").prepend(returned_tile);tile_element=r;d.tile_cache.set(j,tile_element);d.show_tile(tile_element,s,g,t);delete f[u]};var a=setTimeout(function(){if(g<=d.view.high&&l>=d.view.low){var n=(b?undefined:d.tile_cache.get(j));if(n){d.show_tile(n,k,g,m);delete f[a]}else{$.when(d.data_cache.get_data(view.chrom,g,l,d.mode,e,d.data_url_extra_params)).then(function(o){if(view.reference_track&&m>CHAR_WIDTH_PX){$.when(view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params)).then(function(p){h(a,o,e,c,k,m,p)})}else{h(a,o,e,c,k,m)}})}}},50);f[a]=true},show_tile:function(a,f,d,g){var b=this;var c=this.view.high-this.view.low,e=(d-this.view.low)*g;if(this.left_offset){e-=this.left_offset}a.css({position:"absolute",top:0,left:e,height:""});f.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");f.children().css("height",b.max_height+"px")},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:a.dbkey};this.data_cache=new DataManager(CACHED_DATA,this,false);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(m,g,b,j,n){var f=this,d=DENSITY*g;if(n>CHAR_WIDTH_PX){if(m===null){f.content_div.css("height","0px");return}var e=this.view.canvas_manager.new_canvas();var l=e.getContext("2d");e.width=Math.ceil(d*n+f.left_offset);e.height=f.height_px;l.font=DEFAULT_FONT;l.textAlign="center";for(var h=0,k=m.length;h<k;h++){var a=Math.round(h*n);l.fillText(m[h],a+f.left_offset,10)}return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataManager(CACHED_DATA,this);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};$.extend(LineTrack.prototype,TiledTrack.prototype,{add_resize_handle:function(){var a=this;var d=false;var c=false;var b=$("<div class='track-resize'>");$(a.container_div).hover(function(){d=true;b.show()},function(){d=false;if(!c){b.hide()}});b.hide().bind("dragstart",function(f,g){c=true;g.original_height=$(a.content_div).height()}).bind("drag",function(g,h){var f=Math.min(Math.max(h.original_height+h.deltaY,a.min_height_px),a.max_height_px);$(a.content_div).css("height",f);a.height_px=f;a.draw(true)}).bind("dragend",function(f,g){a.tile_cache.clear();c=false;if(!d){b.hide()}a.track_config.values.height=a.height_px}).appendTo(a.container_div)},predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(m,e,b,j,l){if(this.vertical_range===undefined){return}var f=b*DENSITY*e,d=DENSITY*e,a=Math.ceil(d*l),h=this.height_px;var c=this.view.canvas_manager.new_canvas();c.width=a,c.height=h;var k=c.getContext("2d");var g=new LinePainter(m.data,f,f+d,this.prefs.min_value,this.prefs.max_value,this.prefs.color,this.mode);g.draw(k,a,h);return c}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataManager(20,this);this.left_offset=200;this.painter=LinkedFeaturePainter};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(d,b,c){var a=this.inc_slots[d];if(!a||(a.mode!==c)){a=new FeatureSlotter(d,c==="Pack",function(e){return CONTEXT.measureText(e)});a.mode=c;this.inc_slots[d]=a}return a.slot_features(b)},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(o,w,A,k,m,d){var t=this,C=A*DENSITY*w,b=(A+1)*DENSITY*w,q=b-C,u=Math.ceil(q*m),s=this.mode,G=25,e=this.left_offset,p,g;if(s==="Auto"){if(o.dataset_type==="summary_tree"){s=o.dataset_type}else{if(o.extra_info==="no_detail"){s="no_detail"}else{var F=o.data;if((F.length&&F.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){s="Squish"}else{s="Pack"}}}}if(s==="summary_tree"){g=this.summary_draw_height;k.parent().css("height",Math.max(this.height_px,g)+"px");this.container_div.find(".yaxislabel").remove();var a=$("<div />").addClass("yaxislabel");a.text(o.max);a.css({position:"absolute",top:"22px",left:"10px"});a.prependTo(this.container_div);var c=this.view.canvas_manager.new_canvas();c.width=u+e;c.height=g+LABEL_SPACING+CHAR_HEIGHT_PX;var D=new SummaryTreePainter(o.data,o.delta,o.max,C,b,this.prefs.show_counts);var v=c.getContext("2d");v.translate(e,0);D.draw(v,u,g);return c}var p,j=1;if(s==="no_detail"||s==="Squish"||s==="Pack"){j=this.incremental_slots(m,o.data,s);p=this.inc_slots[m].slots}var l=[];if(o.data){for(var x=0,z=o.data.length;x<z;x++){var h=o.data[x];var y=false;var n;for(var B=0,E=this.filters.length;B<E;B++){n=this.filters[B];n.update_attrs(h);if(!n.keep(h)){y=true;break}}if(!y){l.push(h)}}}var D=new (this.painter)(l,C,b,this.prefs,s,d);var g=D.get_required_height(j)+ERROR_PADDING;var c=this.view.canvas_manager.new_canvas();c.width=u+e;c.height=g;k.parent().css("height",Math.max(this.height_px,g)+"px");var v=c.getContext("2d");v.fillStyle=this.prefs.block_color;v.font=this.default_font;v.textAlign="right";this.container_div.find(".yaxislabel").remove();if(o.message){$(c).css({"border-top":"1px solid red"});v.fillStyle="red";v.textAlign="left";var r=v.textBaseline;v.textBaseline="top";v.fillText(o.message,e,0);v.textBaseline=r;if(!o.data){return c}}this.example_feature=(o.data.length?o.data[0]:undefined);v.translate(e,ERROR_PADDING);D.draw(v,u,g,p);return c}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack";this.painter=VariantPainter};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype);var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:c,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=ReadPainter;this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype);var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}});var extend=function(){var c=arguments[0];for(var b=1;b<arguments.length;b++){var a=arguments[b];for(key in a){c[key]=a[key]}}};var CanvasManager=function(a){this.document=a};CanvasManager.prototype.new_canvas=function(){var a=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(a)}return a};var FeatureSlotter=function(c,b,a){this.slots={};this.start_end_dct={};this.w_scale=c;this.include_label=b;this.measureText=a};FeatureSlotter.prototype.slot_features=function(g){var k=this.w_scale,n=this.slots,c=this.start_end_dct,t=[],u=[],h=0;for(var r=0,s=g.length;r<s;r++){var e=g[r],j=e[0];if(n[j]!==undefined){h=Math.max(h,n[j]);u.push(n[j])}else{t.push(r)}}var l=function(A,B){for(var z=0;z<=MAX_FEATURE_DEPTH;z++){var x=false,C=c[z];if(C!==undefined){for(var w=0,y=C.length;w<y;w++){var v=C[w];if(B>v[0]&&A<v[1]){x=true;break}}}if(!x){return z}}return -1};for(var r=0,s=t.length;r<s;r++){var e=g[t[r]],j=e[0],p=e[1],a=e[2],m=e[3],b=Math.floor(p*k),f=Math.ceil(a*k),q=this.measureText(m).width,d;if(m!==undefined&&this.include_label){q+=(LABEL_SPACING+PACK_SPACING);if(b-q>=0){b-=q;d="left"}else{f+=q;d="right"}}var o=l(b,f);if(o>=0){if(c[o]===undefined){c[o]=[]}c[o].push([b,f]);n[j]=o;h=Math.max(h,o)}else{}}return h+1};var SummaryTreePainter=function(d,f,b,e,a,c){this.data=d;this.delta=f;this.max=b;this.view_start=e;this.view_end=a;this.show_counts=c};SummaryTreePainter.prototype.draw=function(o,a,n){var f=this.view_start,q=this.view_end-this.view_start,p=a/q;var l=this.data,k=this.delta,h=this.max,c=n+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(k*p);o.save();for(var d=0,e=l.length;d<e;d++){var j=Math.floor((l[d][0]-f)*p);var g=l[d][1];if(!g){continue}var m=g/h*n;o.fillStyle="black";o.fillRect(j,c-m,delta_x_px,m);var b=4;if(this.show_counts&&(o.measureText(g).width+b)<delta_x_px){o.fillStyle="#666";o.textAlign="center";o.fillText(g,j+(delta_x_px/2),10)}}o.restore()};var LinePainter=function(d,g,a,b,f,c,e){this.data=d;this.view_start=g;this.view_end=a;this.min_value=b;this.max_value=f;this.color=c;this.mode=e};LinePainter.prototype.draw=function(o,n,l){var g=false,h=this.min_value,e=this.max_value,k=e-h,a=l,b=this.view_start,m=this.view_end-this.view_start,c=n/m,j=this.mode,s=this.data;o.save();var t=Math.round(l+h/k*l);if(j!=="Intensity"){o.beginPath();o.moveTo(0,t);o.lineTo(n,t);o.fillStyle="#aaa";o.stroke()}o.beginPath();o.fillStyle=this.color;var r,f,d;if(s.length>1){d=Math.ceil((s[1][0]-s[0][0])*c)}else{d=10}for(var p=0,q=s.length;p<q;p++){r=Math.round((s[p][0]-b)*c);f=s[p][1];if(f===null){if(g&&j==="Filled"){o.lineTo(r,a)}g=false;continue}if(f<h){f=h}else{if(f>e){f=e}}if(j==="Histogram"){f=Math.round(f/k*a);o.fillRect(r,t,d,-f)}else{if(j==="Intensity"){f=255-Math.floor((f-h)/k*255);o.fillStyle="rgb("+f+","+f+","+f+")";o.fillRect(r,0,d,a)}else{f=Math.round(a-(f-h)/k*a);if(g){o.lineTo(r,f)}else{g=true;if(j==="Filled"){o.moveTo(r,a);o.lineTo(r,f)}else{o.moveTo(r,f)}}}}}if(j==="Filled"){if(g){o.lineTo(r,t);o.lineTo(0,t)}o.fill()}else{o.stroke()}o.restore()};var FeaturePainter=function(c,e,a,b,d){this.data=c;this.view_start=e;this.view_end=a;this.prefs=b;this.mode=d};extend(FeaturePainter.prototype,{get_required_height:function(b){var a=y_scale=this.get_row_height(),c=this.mode;if(c==="no_detail"||c==="Squish"||c==="Pack"){a=b*y_scale}return a+Math.round(y_scale/2)},draw:function(n,d,m,j){var g=this.data,k=this.view_start,o=this.view_end;n.save();n.fillStyle=this.prefs.block_color;n.textAlign="right";var r=this.view_end-this.view_start,q=d/r,c=this.get_row_height();for(var f=0,h=g.length;f<h;f++){var p=g[f],e=p[0],a=p[1],b=p[2],l=(j&&j[e]!==undefined?j[e]:null);if(is_overlap([a,b],[k,o])&&(this.mode=="Dense"||l!==null)){this.draw_element(n,this.mode,p,l,k,o,q,c,d)}}n.restore()}});var LinkedFeaturePainter=function(c,e,a,b,d){FeaturePainter.call(this,c,e,a,b,d)};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var b=this.mode,a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_element:function(p,g,x,j,r,H,L,M,a){var u=x[0],J=x[1],B=x[2]-1,s=x[3],C=Math.floor(Math.max(0,(J-r)*L)),q=Math.ceil(Math.min(a,Math.max(0,(B-r)*L))),A=(g==="Dense"?0:(0+j))*M,o,F,t=null,N=null,d=this.prefs.block_color,E=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(C,A,q-C,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(C,A+5,q-C,DENSE_FEATURE_HEIGHT)}else{var n=x[4],z=x[5],D=x[6],e=x[7];if(z&&D){t=Math.floor(Math.max(0,(z-r)*L));N=Math.ceil(Math.min(a,Math.max(0,(D-r)*L)))}var K,v;if(g==="Squish"){K=1;v=SQUISH_FEATURE_HEIGHT}else{K=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(C,A,q-C,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=A+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=A;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(C,m,q-C,w);for(var I=0,c=e.length;I<c;I++){var h=e[I],b=Math.floor(Math.max(0,(h[0]-r)*L)),y=Math.ceil(Math.min(a,Math.max((h[1]-1-r)*L)));if(b>y){continue}p.fillStyle=d;p.fillRect(b,A+(v-K)/2+1,y-b,K);if(t!==undefined&&!(b>N||y<t)){var G=Math.max(b,t),l=Math.min(y,N);p.fillRect(G,A+1,l-G,v)}}}if(g==="Pack"&&J>r){p.fillStyle=E;var f=1;if(f===0&&C-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+LABEL_SPACING,A+8)}else{p.textAlign="right";p.fillText(s,C-LABEL_SPACING,A+8)}p.fillStyle=d}}}}});var VariantPainter=function(c,e,a,b,d){FeaturePainter.call(this,c,e,a,b,d)};extend(VariantPainter.prototype,FeaturePainter.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadPainter=function(d,f,a,c,e,b){FeaturePainter.call(this,d,f,a,c,e);this.ref_seq=b};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var a,b=this.mode;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){a*=2}}}return a},draw_read:function(z,u,p,E,d,y,m,j,h){z.textAlign="center";var x=this,b=[E,d],s=0,A=0,w=0;ref_seq=this.ref_seq;var J=[];if((u==="Pack"||this.mode==="Auto")&&j!==undefined&&p>CHAR_WIDTH_PX){w=Math.round(p/2)}if(!m){m=[[0,j.length]]}for(var q=0,C=m.length;q<C;q++){var n=m[q],e="MIDNSHP=X"[n[0]],r=n[1];if(e==="H"||e==="S"){s-=r}var k=y+s,I=Math.floor(Math.max(0,(k-E)*p)),l=Math.floor(Math.max(0,(k+r-E)*p));switch(e){case"H":break;case"S":case"M":case"=":var t=compute_overlap([k,k+r],b);if(t!==NO_OVERLAP){var v=j.slice(A,A+r);if(w>0){z.fillStyle=this.prefs.block_color;z.fillRect(I-w,h+1,l-I,9);z.fillStyle=CONNECTOR_COLOR;for(var G=0,a=v.length;G<a;G++){if(this.prefs.show_differences&&ref_seq){var o=ref_seq[k-E+G];if(!o||o.toLowerCase()===v[G].toLowerCase()){continue}}if(k+G>=E&&k+G<=d){var H=Math.floor(Math.max(0,(k+G-E)*p));z.fillText(v[G],H,h+9)}}}else{z.fillStyle=this.prefs.block_color;z.fillRect(I,h+(this.mode!=="Dense"?4:5),l-I,(u!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}A+=r;s+=r;break;case"N":z.fillStyle=CONNECTOR_COLOR;z.fillRect(I-w,h+5,l-I,1);s+=r;break;case"D":z.fillStyle="red";z.fillRect(I-w,h+4,l-I,3);s+=r;break;case"P":break;case"I":var t=compute_overlap([k,k+r],b),D=I-w;if(t!==NO_OVERLAP){var v=j.slice(A,A+r);if(this.prefs.show_insertions){var g=I-(l-I)/2;if((u==="Pack"||this.mode==="Auto")&&j!==undefined&&p>CHAR_WIDTH_PX){z.fillStyle="yellow";z.fillRect(g-w,h-9,l-I,9);J[J.length]={type:"triangle",data:[D,h+4,5]};z.fillStyle=CONNECTOR_COLOR;switch(t){case (OVERLAP_START):v=v.slice(E-k);break;case (OVERLAP_END):v=v.slice(0,k-d);break;case (CONTAINED_BY):break;case (CONTAINS):v=v.slice(E-k,k-d);break}for(var G=0,a=v.length;G<a;G++){var H=Math.floor(Math.max(0,(k+G-E)*p));z.fillText(v[G],H-(l-I)/2,h)}}else{z.fillStyle="yellow";z.fillRect(g,h+(this.mode!=="Dense"?2:5),l-I,(u!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((u==="Pack"||this.mode==="Auto")&&j!==undefined&&p>CHAR_WIDTH_PX){J[J.length]={type:"text",data:[v.length,D,h+9]}}else{}}}A+=r;break;case"X":A+=r;break}}z.fillStyle="yellow";var F,f,K;for(var B=0;B<J.length;B++){F=J[B];f=F.type;K=F.data;if(f==="text"){z.font="bold "+DEFAULT_FONT;z.fillText(K[0],K[1],K[2]);z.font=DEFAULT_FONT}else{if(f=="triangle"){z.drawDownwardEquilateralTriangle(K[0],K[1],K[2])}}}},draw_element:function(u,p,g,d,x,b,l,v,s){var k=g[0],t=g[1],c=g[2],m=g[3],f=Math.floor(Math.max(0,(t-x)*l)),h=Math.ceil(Math.min(s,Math.max(0,(c-x)*l))),e=(p==="Dense"?1:(1+d))*v,y=this.prefs.block_color,j=this.prefs.label_color,r=0;if((p==="Pack"||this.mode==="Auto")&&l>CHAR_WIDTH_PX){var r=Math.round(l/2)}u.fillStyle=y;if(g[5] instanceof Array){var q=Math.floor(Math.max(0,(g[4][0]-x)*l)),o=Math.ceil(Math.min(s,Math.max(0,(g[4][1]-x)*l))),n=Math.floor(Math.max(0,(g[5][0]-x)*l)),a=Math.ceil(Math.min(s,Math.max(0,(g[5][1]-x)*l)));if(g[4][1]>=x&&g[4][0]<=b&&g[4][2]){this.draw_read(u,p,l,x,b,g[4][0],g[4][2],g[4][3],e)}if(g[5][1]>=x&&g[5][0]<=b&&g[5][2]){this.draw_read(u,p,l,x,b,g[5][0],g[5][2],g[5][3],e)}if(n>o){u.fillStyle=CONNECTOR_COLOR;u.dashedLine(o-r,e+5,n-r,e+5)}}else{u.fillStyle=y;this.draw_read(u,p,l,x,b,t,g[4],g[5],e)}if(p==="Pack"&&t>x){u.fillStyle=this.prefs.label_color;var w=1;if(w===0&&f-u.measureText(m).width<0){u.textAlign="left";u.fillText(m,h+LABEL_SPACING-r,e+8)}else{u.textAlign="right";u.fillText(m,f-LABEL_SPACING-r,e+8)}u.fillStyle=y}}}); \ No newline at end of file +var extend=function(){var c=arguments[0];for(var b=1;b<arguments.length;b++){var a=arguments[b];for(key in a){c[key]=a[key]}}};var trackster_module=function(f,Q){var o=f("slotting"),G=f("painters");var V=function(W,X){this.document=W;this.default_font=X!==undefined?X:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};extend(V.prototype,{load_pattern:function(W,aa){var X=this.patterns,Y=this.dummy_context,Z=new Image();Z.src=image_path+aa;Z.onload=function(){X[W]=Y.createPattern(Z,"repeat")}},get_pattern:function(W){return this.patterns[W]},new_canvas:function(){var W=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(W)}W.manager=this;return W}});var B=function(W,X){W.bind("drag",{handle:X,relative:true},function(ab,ac){var aa=$(this).parent();var Z=aa.children();var Y;for(Y=0;Y<Z.length;Y++){if(ac.offsetY<$(Z.get(Y)).position().top){break}}if(Y===Z.length){if(this!==Z.get(Y-1)){aa.append(this)}}else{if(this!==Z.get(Y)){$(this).insertBefore(Z.get(Y))}}})};var h=function(Y,W){var X=W-Y;return(X<=2?0.01:(X<=100?1:(X<=1000?5:10)))};var C=9,z=10,L=C+2,w=100,D=12000,J=200,r=10,F=5000,s=100,m="There was an error in indexing this dataset. ",E="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",A="No data for this chrom/contig.",p="Currently indexing... please wait",u="Tool cannot be rerun: ",a="Loading data...",R="Ready for display",d=10,q=5,y=5;function t(W){return Math.round(W*1000)/1000}var c=function(W){this.num_elements=W;this.clear()};extend(c.prototype,{get:function(X){var W=this.key_ary.indexOf(X);if(W!==-1){this.move_key_to_end(X,W)}return this.obj_cache[X]},set:function(X,Y){if(!this.obj_cache[X]){if(this.key_ary.length>=this.num_elements){var W=this.key_ary.shift();delete this.obj_cache[W]}this.key_ary.push(X)}this.obj_cache[X]=Y;return Y},move_key_to_end:function(X,W){this.key_ary.splice(W,1);this.key_ary.push(X)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var K=function(X,W,Y){c.call(this,X);this.track=W;this.subset=(Y!==undefined?Y:true)};extend(K.prototype,c.prototype,{load_data:function(ad,ae,Z,ac,W,ab){var Y={chrom:ad,low:ae,high:Z,mode:ac,resolution:W,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(Y,ab);var af=[];for(var aa=0;aa<this.track.filters.length;aa++){af[af.length]=this.track.filters[aa].name}Y.filter_cols=JSON.stringify(af);var X=this;return $.getJSON(this.track.data_url,Y,function(ag){X.set_data(ae,Z,ac,ag)})},get_data:function(Y,W,ab,ac,X,aa){var Z=this.get(this.gen_key(W,ab,ac));if(Z){return Z}Z=this.load_data(Y,W,ab,ac,X,aa);this.set_data(W,ab,ac,Z);return Z},set_data:function(X,Y,Z,W){return this.set(this.gen_key(X,Y,Z),W)},gen_key:function(W,Y,Z){var X=W+"_"+Y+"_"+Z;return X},split_key:function(W){return W.split("_")}});var U=function(W,Z,Y,X,aa){this.container=W;this.chrom=null;this.vis_id=Y;this.dbkey=X;this.title=Z;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(aa);this.canvas_manager=new V(W.get(0).ownerDocument);this.reset()};extend(U.prototype,{init:function(Z){var Y=this.container,W=this;this.top_container=$("<div/>").addClass("top-container").appendTo(Y);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(Y);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(Y);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var X=function(aa){if(aa.type==="focusout"||(aa.keyCode||aa.which)===13||(aa.keyCode||aa.which)===27){if((aa.keyCode||aa.which)!==27){W.go_to($(this).val())}$(this).hide();$(this).val("");W.location_span.show();W.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",X).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){W.location_span.hide();W.chrom_select.hide();W.nav_input.val(W.chrom+":"+W.low+"-"+W.high);W.nav_input.css("display","inline-block");W.nav_input.select();W.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){W.zoom_out();W.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){W.zoom_in();W.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},Z);this.chrom_select.bind("change",function(){W.change_chrom(W.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(aa){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(aa){W.zoom_in(aa.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aa,ab){this.current_x=ab.offsetX}).bind("drag",function(aa,ac){var ad=ac.offsetX-this.current_x;this.current_x=ac.offsetX;var ab=Math.round(ad/W.viewport_container.width()*(W.max_high-W.max_low));W.move_delta(-ab)});this.overview_close.bind("click",function(){for(var ab=0,aa=W.tracks.length;ab<aa;ab++){W.tracks[ab].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",W.overview_box.height());W.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(aa,ab){if(aa.clientX>W.viewport_container.width()-16){return false}}).bind("dragstart",function(aa,ab){ab.original_low=W.low;ab.current_height=aa.clientY;ab.current_x=ab.offsetX}).bind("drag",function(ac,ae){var aa=$(this);var af=ae.offsetX-ae.current_x;var ab=aa.scrollTop()-(ac.clientY-ae.current_height);aa.scrollTop(ab);ae.current_height=ac.clientY;ae.current_x=ae.offsetX;var ad=Math.round(af/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}).bind("mousewheel",function(ac,ae,ab,aa){if(ab){var ad=Math.round(-ab/W.viewport_container.width()*(W.high-W.low));W.move_delta(ad)}});this.top_labeltrack.bind("dragstart",function(aa,ab){return $("<div />").css({height:W.content_div.height()+W.top_labeltrack.height()+W.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ae,af){$(af.proxy).css({left:Math.min(ae.pageX,af.startX),width:Math.abs(ae.pageX-af.startX)});var ab=Math.min(ae.pageX,af.startX)-W.container.offset().left,aa=Math.max(ae.pageX,af.startX)-W.container.offset().left,ad=(W.high-W.low),ac=W.viewport_container.width();W.update_location(Math.round(ab/ac*ad)+W.low,Math.round(aa/ac*ad)+W.low)}).bind("dragend",function(af,ag){var ab=Math.min(af.pageX,ag.startX),aa=Math.max(af.pageX,ag.startX),ad=(W.high-W.low),ac=W.viewport_container.width(),ae=W.low;W.low=Math.round(ab/ac*ad)+ae;W.high=Math.round(aa/ac*ad)+ae;$(ag.proxy).remove();W.redraw()});this.add_label_track(new T(this,this.top_labeltrack));this.add_label_track(new T(this,this.nav_labeltrack));$(window).bind("resize",function(){W.resize_window()});$(document).bind("redraw",function(){W.redraw()});this.reset();$(window).trigger("resize")},update_location:function(W,X){this.location_span.text(commatize(W)+" - "+commatize(X));this.nav_input.val(this.chrom+":"+commatize(W)+"-"+commatize(X))},load_chroms:function(X,Y){X.num=s;$.extend(X,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var W=this;$.ajax({url:chrom_url,data:X,dataType:"json",success:function(aa){if(aa.chrom_info.length===0){alert("Invalid chromosome: "+X.chrom);return}if(aa.reference){W.add_label_track(new x(W))}W.chrom_data=aa.chrom_info;var ad='<option value="">Select Chrom/Contig</option>';for(var ac=0,Z=W.chrom_data.length;ac<Z;ac++){var ab=W.chrom_data[ac].chrom;ad+='<option value="'+ab+'">'+ab+"</option>"}if(aa.prev_chroms){ad+='<option value="previous">Previous '+s+"</option>"}if(aa.next_chroms){ad+='<option value="next">Next '+s+"</option>"}W.chrom_select.html(ad);if(Y){Y()}W.chrom_start_index=aa.start_index},error:function(){alert("Could not load chroms for this dbkey:",W.dbkey)}})},change_chrom:function(aa,X,ac){if(!aa||aa==="None"){return}var Z=this;if(aa==="previous"){Z.load_chroms({low:this.chrom_start_index-s});return}if(aa==="next"){Z.load_chroms({low:this.chrom_start_index+s});return}var ab=$.grep(Z.chrom_data,function(ae,af){return ae.chrom===aa})[0];if(ab===undefined){Z.load_chroms({chrom:aa},function(){Z.change_chrom(aa,X,ac)});return}else{if(aa!==Z.chrom){Z.chrom=aa;if(!Z.chrom){Z.intro_div.show()}else{Z.intro_div.hide()}Z.chrom_select.val(Z.chrom);Z.max_high=ab.len-1;Z.reset();Z.redraw(true);for(var ad=0,W=Z.tracks.length;ad<W;ad++){var Y=Z.tracks[ad];if(Y.init){Y.init()}}}if(X!==undefined&&ac!==undefined){Z.low=Math.max(X,0);Z.high=Math.min(ac,Z.max_high)}Z.reset_overview();Z.redraw()}},go_to:function(aa){var ae=this,W,Z,X=aa.split(":"),ac=X[0],ad=X[1];if(ad!==undefined){try{var ab=ad.split("-");W=parseInt(ab[0].replace(/,/g,""),10);Z=parseInt(ab[1].replace(/,/g,""),10)}catch(Y){return false}}ae.change_chrom(ac,W,Z)},move_fraction:function(Y){var W=this;var X=W.high-W.low;this.move_delta(Y*X)},move_delta:function(Y){var W=this;var X=W.high-W.low;if(W.low-Y<W.max_low){W.low=W.max_low;W.high=W.max_low+X}else{if(W.high-Y>W.max_high){W.high=W.max_high;W.low=W.max_high-X}else{W.high-=Y;W.low-=Y}}W.redraw()},add_track:function(W){W.view=this;W.track_id=this.track_id_counter;this.tracks.push(W);if(W.init){W.init()}W.container_div.attr("id","track_"+W.track_id);B(W.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(W){W.view=this;this.label_tracks.push(W)},remove_track:function(W){this.has_changes=true;W.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(W)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ad){var ac=this.high-this.low,ab=this.low,X=this.high;if(ab<this.max_low){ab=this.max_low}if(X>this.max_high){X=this.max_high}if(this.high!==0&&ac<this.min_separation){X=ab+this.min_separation}this.low=Math.floor(ab);this.high=Math.ceil(X);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(r,Math.max(0,Math.ceil(Math.log(this.resolution,r)/Math.log(r))));var W=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aa=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=13;this.overview_box.css({left:W,width:Math.max(ae,aa)}).show();if(aa<ae){this.overview_box.css("left",W-(ae-aa)/2)}if(this.overview_highlight){this.overview_highlight.css({left:W,width:aa})}this.update_location(this.low,this.high);if(!ad){for(var Y=0,Z=this.tracks.length;Y<Z;Y++){if(this.tracks[Y]&&this.tracks[Y].enabled){this.tracks[Y].draw()}}for(Y=0,Z=this.label_tracks.length;Y<Z;Y++){this.label_tracks[Y].draw()}}},zoom_in:function(X,Y){if(this.max_high===0||this.high-this.low<this.min_separation){return}var Z=this.high-this.low,aa=Z/2+this.low,W=(Z/this.zoom_factor)/2;if(X){aa=X/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aa-W);this.high=Math.round(aa+W);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var X=this.high-this.low,Y=X/2+this.low,W=(X*this.zoom_factor)/2;this.low=Math.round(Y-W);this.high=Math.round(Y+W);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var n=function(X,aa){this.track=X;this.name=aa.name;this.params=[];var ai=aa.params;for(var Y=0;Y<ai.length;Y++){var ad=ai[Y],W=ad.name,ah=ad.label,Z=unescape(ad.html),af=ad.type;if(af==="number"){this.params[this.params.length]=new g(W,ah,Z,ad.min,ad.max)}else{if(af=="select"){this.params[this.params.length]=new I(W,ah,Z)}else{console.log("WARNING: unrecognized tool parameter type:",W,af)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ak){ak.stopPropagation()}).bind("click",function(ak){ak.stopPropagation()}).bind("dblclick",function(ak){ak.stopPropagation()});var ag=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ae=this.params;var ab=this;$.each(this.params,function(al,ao){var an=$("<div>").addClass("param-row").appendTo(ab.parent_div);var ak=$("<div>").addClass("param-label").text(ao.label).appendTo(an);var am=$("<div/>").addClass("slider").html(ao.html).appendTo(an);$("<div style='clear: both;'/>").appendTo(an)});this.parent_div.find("input").click(function(){$(this).select()});var aj=$("<div>").addClass("slider-row").appendTo(this.parent_div);var ac=$("<input type='submit'>").attr("value","Run").appendTo(aj);var ab=this;ac.click(function(){ab.run()})};extend(n.prototype,{get_param_values_dict:function(){var W={};this.parent_div.find(":input").each(function(){var X=$(this).attr("name"),Y=$(this).val();W[X]=JSON.stringify(Y)});return W},get_param_values:function(){var X=[];var W={};this.parent_div.find(":input").each(function(){var Y=$(this).attr("name"),Z=$(this).val();if(Y){X[X.length]=Z}});return X},run:function(){var X={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name};$.extend(X,this.get_param_values_dict());var Z=this.track,Y=X.tool_id+Z.tool_region_and_parameters_str(X.chrom,X.low,X.high),aa;if(Z.track_type==="FeatureTrack"){aa=new N(Y,view,Z.hda_ldda,undefined,{},{},Z)}this.track.add_track(aa);aa.content_div.text("Starting job.");var W=function(){$.getJSON(run_tool_url,X,function(ab){if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(E)}else{if(ab.error){aa.container_div.addClass("error");aa.content_div.text(u+ab.message)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text("Converting input data so that it can be easily reused.");setTimeout(W,2000)}else{aa.dataset_id=ab.dataset_id;aa.content_div.text("Running job.");aa.init()}}}})};W()}});var I=function(X,W,Y){this.name=X;this.label=W;this.html=Y};var g=function(Y,X,aa,Z,W){I.call(this,Y,X,aa);this.min=Z;this.max=W};var j=function(X,W,Y){this.name=X;this.index=W;this.value=Y};var O=function(X,W){this.name=X;this.index=W;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};extend(O.prototype,{applies_to:function(W){if(W.length>this.index){return true}return false},keep:function(W){if(!this.applies_to(W)){return true}return(W[this.index]>=this.low&&W[this.index]<=this.high)},update_attrs:function(X){var W=false;if(!this.applies_to(X)){return W}if(X[this.index]<this.min){this.min=Math.floor(X[this.index]);W=true}if(X[this.index]>this.max){this.max=Math.ceil(X[this.index]);W=true}return W},update_ui_elt:function(){var X=this.slider.slider("option","min"),W=this.slider.slider("option","max");if(this.min<X||this.max>W){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",h(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var v=function(W){var ac=[];for(var Z=0;Z<W.length;Z++){var ab=W[Z];var Y=ab.name,aa=ab.type,X=ab.index;if(aa==="int"||aa==="float"){ac[Z]=new O(Y,X)}else{ac[Z]=new j(Y,X,aa)}}return ac};var S=function(W){this.track=W.track;this.params=W.params;this.values={};if(W.saved_values){this.restore_values(W.saved_values)}this.onchange=W.onchange};extend(S.prototype,{restore_values:function(W){var X=this;$.each(this.params,function(Y,Z){if(W[Z.key]!==undefined){X.values[Z.key]=W[Z.key]}else{X.values[Z.key]=Z.default_value}})},build_form:function(){var X=this;var W=$("<div />");$.each(this.params,function(ab,Z){if(!Z.hidden){var Y="param_"+ab;var ag=$("<div class='form-row' />").appendTo(W);ag.append($("<label />").attr("for",Y).text(Z.label+":"));if(Z.type==="bool"){ag.append($('<input type="checkbox" />').attr("id",Y).attr("name",Y).attr("checked",X.values[Z.key]))}else{if(Z.type==="color"){var ad=X.values[Z.key];var ac=$("<input />").attr("id",Y).attr("name",Y).val(ad);var ae=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aa=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ae);var af=$("<div/>").appendTo(aa).farbtastic({width:100,height:100,callback:ac,color:ad});$("<div />").append(ac).append(ae).appendTo(ag).bind("click",function(ah){ae.css({left:$(this).position().left+($(ac).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ae.hide();$(document).unbind("click.color-picker")});ah.stopPropagation()})}else{ag.append($("<input />").attr("id",Y).attr("name",Y).val(X.values[Z.key]))}}}});return W},update_from_form:function(W){var Y=this;var X=false;$.each(this.params,function(Z,ab){if(!ab.hidden){var ac="param_"+Z;var aa=W.find("#"+ac).val();if(ab.type==="float"){aa=parseFloat(aa)}else{if(ab.type==="int"){aa=parseInt(aa)}else{if(ab.type==="bool"){aa=W.find("#"+ac).is(":checked")}}}if(aa!==Y.values[ab.key]){Y.values[ab.key]=aa;X=true}}});if(X){this.onchange()}}});var b=function(W,X,Y){this.track=W;this.canvas=X;this.histo_max=Y};var k=function(X,W,aa,Y,Z){this.name=X;this.view=W;this.parent_element=aa;this.data_url=(Y?Y:default_data_url);this.data_url_extra_params={};this.data_query_wait=(Z?Z:F);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};extend(k.prototype,{init:function(){var W=this;W.enabled=false;W.tile_cache.clear();W.data_cache.clear();W.initial_canvas=undefined;W.content_div.css("height","auto");W.container_div.removeClass("nodata error pending");if(!W.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:W.hda_ldda,dataset_id:W.dataset_id,chrom:W.view.chrom},function(X){if(!X||X==="error"||X.kind==="error"){W.container_div.addClass("error");W.content_div.text(m);if(X.message){var Z=W.view.tracks.indexOf(W);var Y=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+X.message+"</pre>",{Close:hide_modal})});W.content_div.append(Y)}}else{if(X==="no converter"){W.container_div.addClass("error");W.content_div.text(E)}else{if(X==="no data"||(X.data!==undefined&&(X.data===null||X.data.length===0))){W.container_div.addClass("nodata");W.content_div.text(A)}else{if(X==="pending"){W.container_div.addClass("pending");W.content_div.text(p);setTimeout(function(){W.init()},W.data_query_wait)}else{if(X.status==="data"){if(X.valid_chroms){W.valid_chroms=X.valid_chroms;W.make_name_popup_menu()}W.content_div.text(R);if(W.view.chrom){W.content_div.text("");W.content_div.css("height",W.height_px+"px");W.enabled=true;$.when(W.predraw_init()).done(function(){W.draw()})}}}}}}})},predraw_init:function(){},update_name:function(W){this.old_name=this.name;this.name=W;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var H=function(X,ad,ag){var Y=this,ah=Y.view;this.filters=(X!==undefined?v(X):[]);this.filters_available=false;this.filters_visible=false;this.tool=(ad!==undefined&&obj_length(ad)>0?new n(this,ad):undefined);this.parent_track=ag;this.child_tracks=[];if(Y.hidden){return}var af=function(ai,aj,ak){ai.click(function(){var al=aj.text();max=parseFloat(ak.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ak.slider("option","values")){input_size=2*input_size+1;multi_value=true}aj.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",al).appendTo(aj).focus().select().click(function(am){am.stopPropagation()}).blur(function(){$(this).remove();aj.text(al)}).keyup(function(aq){if(aq.keyCode===27){$(this).trigger("blur")}else{if(aq.keyCode===13){var ao=ak.slider("option","min"),am=ak.slider("option","max"),ap=function(ar){return(isNaN(ar)||ar>am||ar<ao)},an=$(this).val();if(!multi_value){an=parseFloat(an);if(ap(an)){alert("Parameter value must be in the range ["+ao+"-"+am+"]");return $(this)}}else{an=an.split("-");an=[parseFloat(an[0]),parseFloat(an[1])];if(ap(an[0])||ap(an[1])){alert("Parameter value must be in the range ["+ao+"-"+am+"]");return $(this)}}ak.slider((multi_value?"values":"value"),an)}}})})};if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(ai){ai.stopPropagation()}).bind("click",function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()});$.each(this.filters,function(ao,aj){var al=$("<div/>").addClass("slider-row").appendTo(Y.filters_div);var ai=$("<div/>").addClass("slider-label").appendTo(al);var aq=$("<span/>").addClass("slider-name").text(aj.name+" ").appendTo(ai);var ak=$("<span/>");var am=$("<span/>").addClass("slider-value").appendTo(ai).append("[").append(ak).append("]");var ap=$("<div/>").addClass("slider").appendTo(al);aj.control_element=$("<div/>").attr("id",aj.name+"-filter-control").appendTo(ap);var an=[0,0];aj.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ar,at){an=at.values;ak.text(at.values[0]+"-"+at.values[1]);setTimeout(function(){if(at.values[0]==an[0]&&at.values[1]==an[1]){var au=at.values;ak.text(au[0]+"-"+au[1]);aj.low=au[0];aj.high=au[1];Y.draw(true,true)}},50)},change:function(ar,at){aj.control_element.slider("option","slide").call(aj.control_element,ar,at)}});aj.slider=aj.control_element;aj.slider_label=ak;af(am,ak,aj.control_element);$("<div style='clear: both;'/>").appendTo(al)});if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}Y.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();Y.container_div.append(Y.child_tracks_container);if(Y.display_modes!==undefined){if(Y.mode_div===undefined){Y.mode_div=$("<div class='right-float menubutton popup' />").appendTo(Y.header_div);var aa=(Y.track_config&&Y.track_config.values.mode?Y.track_config.values.mode:Y.display_modes[0]);Y.mode=aa;Y.mode_div.text(aa);var Z=function(ai){Y.mode_div.text(ai);Y.mode=ai;Y.track_config.values.mode=ai;Y.tile_cache.clear();Y.draw()};var W={};for(var ab=0,ae=Y.display_modes.length;ab<ae;ab++){var ac=Y.display_modes[ab];W[ac]=function(ai){return function(){Z(ai)}}(ac)}make_popupmenu(Y.mode_div,W)}else{Y.mode_div.hide()}}this.make_name_popup_menu()};extend(H.prototype,k.prototype,{make_name_popup_menu:function(){var X=this;var W={};W["Edit configuration"]=function(){var ad=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ab=function(){X.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(ae){if((ae.keyCode||ae.which)===27){ad()}else{if((ae.keyCode||ae.which)===13){ab()}}};$(window).bind("keypress.check_enter_esc",ac);show_modal("Configure Track",X.track_config.build_form(),{Cancel:ad,OK:ab})};if(X.filters_available>0){var aa=(X.filters_div.is(":visible")?"Hide filters":"Show filters");W[aa]=function(){X.filters_visible=(X.filters_div.is(":visible"));X.filters_div.toggle();X.make_name_popup_menu()}}if(X.tool){var aa=(X.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");W[aa]=function(){if(!X.dynamic_tool_div.is(":visible")){X.update_name(X.name+X.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";X.revert_name()}X.dynamic_tool_div.toggle();X.make_name_popup_menu()}}if(X.valid_chroms){W["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+X.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var Y=view;var Z=function(){$("#no-tracks").show()};if(this.parent_track){Y=this.parent_track;Z=function(){}}W.Remove=function(){Y.remove_track(X);if(Y.num_tracks===0){Z()}};make_popupmenu(X.name_div,W)},draw:function(W,Z){var an=this.view.low,ac=this.view.high,ae=ac-an,ag=this.view.container.width(),ab=ag/ae,ah=this.view.resolution,aa=$("<div style='position: relative;'></div>");if(!Z){this.content_div.children().remove()}this.content_div.append(aa);this.max_height=0;var aj=Math.floor(an/ah/J);var Y={};while((aj*J*ah)<ac){var am=ag+"_"+ab+"_"+aj;var ad=this.tile_cache.get(am);var ak=aj*J*this.view.resolution;var X=ak+J*this.view.resolution;if(!W&&ad){this.show_tile(ad,aa,ak,ab)}else{this.delayed_draw(W,am,ak,X,aj,ah,aa,ab,Y)}aj+=1}var af=this;var al=setInterval(function(){if(obj_length(Y)===0){clearInterval(al);if(Z){var aq=af.content_div.children();var ap=false;for(var ar=aq.length-1,ao=0;ar>=ao;ar--){var av=$(aq[ar]);if(ap){av.remove()}else{if(av.children().length!==0){ap=true}}}}for(var au=0;au<af.filters.length;au++){af.filters[au].update_ui_elt()}var at=false;if(af.example_feature){for(var au=0;au<af.filters.length;au++){if(af.filters[au].applies_to(af.example_feature)){at=true;break}}}if(af.filters_available!==at){af.filters_available=at;if(!af.filters_available){af.filters_div.hide()}af.make_name_popup_menu()}}},50);for(var ai=0;ai<this.child_tracks.length;ai++){this.child_tracks[ai].draw(W,Z)}},delayed_draw:function(X,ae,ac,ag,Y,aa,af,ah,ab){var Z=this;var ad=function(ap,ai,ak,aj,an,ao,al){returned_tile=Z.draw_tile(ai,ak,aj,an,ao,al);var am=$("<div class='track-tile'>").prepend(returned_tile);tile_element=am;Z.tile_cache.set(ae,tile_element);Z.show_tile(tile_element,an,ac,ao);delete ab[ap]};var W=setTimeout(function(){if(ac<=Z.view.high&&ag>=Z.view.low){var ai=(X?undefined:Z.tile_cache.get(ae));if(ai){Z.show_tile(ai,af,ac,ah);delete ab[W]}else{$.when(Z.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,Z.data_url_extra_params)).then(function(aj){if(view.reference_track&&ah>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ac,ag,Z.mode,aa,view.reference_track.data_url_extra_params)).then(function(ak){ad(W,aj,aa,Y,af,ah,ak)})}else{ad(W,aj,aa,Y,af,ah)}})}}},50);ab[W]=true},show_tile:function(W,ab,Z,ac){var X=this;var Y=this.view.high-this.view.low,aa=(Z-this.view.low)*ac;if(this.left_offset){aa-=this.left_offset}W.css({position:"absolute",top:0,left:aa,height:""});ab.append(W);X.max_height=Math.max(X.max_height,W.height());X.content_div.css("height",X.max_height+"px");ab.children().css("height",X.max_height+"px")},set_overview:function(){var W=this.view;if(this.initial_canvas&&this.is_overview){W.overview_close.show();W.overview_viewport.append(this.initial_canvas);W.overview_highlight.show().height(this.initial_canvas.height());W.overview_viewport.height(this.initial_canvas.height()+W.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(Y,W,Z){var X=this,aa=(Y!==undefined&&W!==undefined&&Z!==undefined?Y+":"+W+"-"+Z:"all");return" - region=["+aa+"], parameters=["+X.tool.get_param_values().join(", ")+"]"},add_track:function(W){W.track_id=this.track_id+"_"+this.child_tracks.length;W.container_div.attr("id","track_"+W.track_id);this.child_tracks_container.append(W.container_div);B(W.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(W);this.view.has_changes=true},remove_track:function(W){W.container_div.fadeOut("slow",function(){$(this).remove()})}});var T=function(W,X){this.track_type="LabelTrack";this.hidden=true;k.call(this,null,W,X);this.container_div.addClass("label-track")};extend(T.prototype,k.prototype,{draw:function(){var Y=this.view,Z=Y.high-Y.low,ac=Math.floor(Math.pow(10,Math.floor(Math.log(Z)/Math.log(10)))),W=Math.floor(Y.low/ac)*ac,aa=this.view.container.width(),X=$("<div style='position: relative; height: 1.3em;'></div>");while(W<Y.high){var ab=(W-Y.low)/Z*aa;X.append($("<div class='label'>"+commatize(W)+"</div>").css({position:"absolute",left:ab-1}));W+=ac}this.content_div.children(":first").remove();this.content_div.append(X)}});var x=function(W){this.track_type="ReferenceTrack";this.hidden=true;k.call(this,null,W,W.top_labeltrack);H.call(this);W.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:W.dbkey};this.data_cache=new K(y,this,false);this.tile_cache=new c(q)};extend(x.prototype,H.prototype,{draw_tile:function(ag,ab,X,ad,ah){var aa=this,Y=J*ab;if(ah>this.view.canvas_manager.char_width_px){if(ag===null){aa.content_div.css("height","0px");return}var Z=this.view.canvas_manager.new_canvas();var af=Z.getContext("2d");Z.width=Math.ceil(Y*ah+aa.left_offset);Z.height=aa.height_px;af.font=af.canvas.manager.default_font;af.textAlign="center";for(var ac=0,ae=ag.length;ac<ae;ac++){var W=Math.round(ac*ah);af.fillText(ag[ac],W+aa.left_offset,10)}return Z}this.content_div.css("height","0px")}});var l=function(aa,Y,ab,W,Z){var X=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";k.call(this,aa,Y,Y.viewport_container);H.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ab;this.dataset_id=W;this.original_dataset_id=W;this.data_cache=new K(y,this);this.tile_cache=new c(q);this.track_config=new S({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:Z,onchange:function(){X.vertical_range=X.prefs.max_value-X.prefs.min_value;$("#linetrack_"+X.track_id+"_minval").text(X.prefs.min_value);$("#linetrack_"+X.track_id+"_maxval").text(X.prefs.max_value);X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};extend(l.prototype,H.prototype,{add_resize_handle:function(){var W=this;var Z=false;var Y=false;var X=$("<div class='track-resize'>");$(W.container_div).hover(function(){Z=true;X.show()},function(){Z=false;if(!Y){X.hide()}});X.hide().bind("dragstart",function(aa,ab){Y=true;ab.original_height=$(W.content_div).height()}).bind("drag",function(ab,ac){var aa=Math.min(Math.max(ac.original_height+ac.deltaY,W.min_height_px),W.max_height_px);$(W.content_div).css("height",aa);W.height_px=aa;W.draw(true)}).bind("dragend",function(aa,ab){W.tile_cache.clear();Y=false;if(!Z){X.hide()}W.track_config.values.height=W.height_px}).appendTo(W.container_div)},predraw_init:function(){var W=this,X=W.view.tracks.indexOf(W);W.vertical_range=undefined;return $.getJSON(W.data_url,{stats:true,chrom:W.view.chrom,low:null,high:null,hda_ldda:W.hda_ldda,dataset_id:W.dataset_id},function(Y){W.container_div.addClass("line-track");var aa=Y.data;if(isNaN(parseFloat(W.prefs.min_value))||isNaN(parseFloat(W.prefs.max_value))){W.prefs.min_value=aa.min;W.prefs.max_value=aa.max;$("#track_"+X+"_minval").val(W.prefs.min_value);$("#track_"+X+"_maxval").val(W.prefs.max_value)}W.vertical_range=W.prefs.max_value-W.prefs.min_value;W.total_frequency=aa.total_frequency;W.container_div.find(".yaxislabel").remove();var ab=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_minval").text(t(W.prefs.min_value));var Z=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+X+"_maxval").text(t(W.prefs.max_value));Z.css({position:"absolute",top:"24px",left:"10px"});Z.prependTo(W.container_div);ab.css({position:"absolute",bottom:"2px",left:"10px"});ab.prependTo(W.container_div)})},draw_tile:function(ah,aa,X,ae,ag){if(this.vertical_range===undefined){return}var ab=X*J*aa,Z=J*aa,W=Math.ceil(Z*ag),ad=this.height_px;var Y=this.view.canvas_manager.new_canvas();Y.width=W,Y.height=ad;var af=Y.getContext("2d");var ac=new G.LinePainter(ah.data,ab,ab+Z,this.prefs.min_value,this.prefs.max_value,this.prefs.color,this.mode);ac.draw(af,W,ad);return Y}});var e=function(W,ab,aa,ae,ad,Y,Z,ac){var X=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new S({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ad,onchange:function(){X.tile_cache.clear();X.draw()}});this.prefs=this.track_config.values;k.call(this,W,ab,ab.viewport_container);H.call(this,Y,Z,ac);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=aa;this.dataset_id=ae;this.original_dataset_id=ae;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new K(20,this);this.left_offset=200;this.painter=G.LinkedFeaturePainter};extend(e.prototype,H.prototype,{update_auto_mode:function(W){if(this.mode=="Auto"){if(W=="no_detail"){W="reduced to feature spans"}else{if(W=="summary_tree"){W="reduced to coverage histogram"}}this.mode_div.text("Auto ("+W+")")}},incremental_slots:function(aa,X,Z){var Y=this.view.canvas_manager.dummy_context,W=this.inc_slots[aa];if(!W||(W.mode!==Z)){W=new (o.FeatureSlotter)(aa,Z==="Pack",w,function(ab){return Y.measureText(ab)});W.mode=Z;this.inc_slots[aa]=W}return W.slot_features(X)},draw_tile:function(ai,aq,av,ae,ag,Z){var an=this,ax=av*J*aq,X=(av+1)*J*aq,ak=X-ax,ao=Math.ceil(ak*ag),am=this.mode,aB=25,aa=this.left_offset,aj,ab;if(am==="Auto"){if(ai.dataset_type==="summary_tree"){am=ai.dataset_type}else{if(ai.extra_info==="no_detail"){am="no_detail"}else{var aA=ai.data;if((aA.length&&aA.length<4)||(this.view.high-this.view.low>D)){am="Squish"}else{am="Pack"}}}this.update_auto_mode(am)}if(am==="summary_tree"){ab=this.summary_draw_height;ae.parent().css("height",Math.max(this.height_px,ab)+"px");this.container_div.find(".yaxislabel").remove();var W=$("<div />").addClass("yaxislabel");W.text(ai.max);W.css({position:"absolute",top:"22px",left:"10px"});W.prependTo(this.container_div);var Y=this.view.canvas_manager.new_canvas();Y.width=ao+aa;Y.height=ab+L;var ay=new G.SummaryTreePainter(ai.data,ai.delta,ai.max,ax,X,this.prefs.show_counts);var ap=Y.getContext("2d");ap.translate(aa,L);ay.draw(ap,ao,ab);return Y}var aj,ad=1;if(am==="no_detail"||am==="Squish"||am==="Pack"){ad=this.incremental_slots(ag,ai.data,am);aj=this.inc_slots[ag].slots}var af=[];if(ai.data){for(var ar=0,au=ai.data.length;ar<au;ar++){var ac=ai.data[ar];var at=false;var ah;for(var aw=0,az=this.filters.length;aw<az;aw++){ah=this.filters[aw];ah.update_attrs(ac);if(!ah.keep(ac)){at=true;break}}if(!at){af.push(ac)}}}var ay=new (this.painter)(af,ax,X,this.prefs,am,Z);var ab=ay.get_required_height(ad)+z;var Y=this.view.canvas_manager.new_canvas();Y.width=ao+aa;Y.height=ab;ae.parent().css("height",Math.max(this.height_px,ab)+"px");var ap=Y.getContext("2d");ap.fillStyle=this.prefs.block_color;ap.font=ap.canvas.manager.default_font;ap.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ai.message){$(Y).css({"border-top":"1px solid red"});ap.fillStyle="red";ap.textAlign="left";var al=ap.textBaseline;ap.textBaseline="top";ap.fillText(ai.message,aa,0);ap.textBaseline=al;if(!ai.data){return Y}}this.example_feature=(ai.data.length?ai.data[0]:undefined);ap.translate(aa,z);ay.draw(ap,ao,ab,aj);return Y}});var M=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_type="VcfTrack";this.painter=G.VariantPainter};extend(M.prototype,H.prototype,e.prototype);var P=function(Z,X,ab,W,Y,aa){e.call(this,Z,X,ab,W,Y,aa);this.track_config=new S({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:Y,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=G.ReadPainter;this.make_name_popup_menu()};extend(P.prototype,H.prototype,e.prototype);var N=function(aa,Y,ac,W,Z,ab,X){e.call(this,aa,Y,ac,W,Z,ab,{},X);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};extend(N.prototype,H.prototype,e.prototype,{predraw_init:function(){var X=this;var W=function(){if(X.data_cache.size()===0){setTimeout(W,300)}else{X.data_url=default_data_url;X.data_query_wait=F;X.dataset_state_url=converted_datasets_state_url;$.getJSON(X.dataset_state_url,{dataset_id:X.dataset_id,hda_ldda:X.hda_ldda},function(Y){})}};W()}});Q.View=U;Q.LineTrack=l;Q.FeatureTrack=e;Q.ReadTrack=P};var slotting_module=function(c,b){var d=2,a=5;b.FeatureSlotter=function(h,g,e,f){this.slots={};this.start_end_dct={};this.w_scale=h;this.include_label=g;this.max_rows=e;this.measureText=f};extend(b.FeatureSlotter.prototype,{slot_features:function(l){var o=this.w_scale,r=this.slots,g=this.start_end_dct,x=[],z=[],m=0,y=this.max_rows;for(var v=0,w=l.length;v<w;v++){var k=l[v],n=k[0];if(r[n]!==undefined){m=Math.max(m,r[n]);z.push(r[n])}else{x.push(v)}}var p=function(F,G){for(var E=0;E<=y;E++){var C=false,H=g[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var A=H[B];if(G>A[0]&&F<A[1]){C=true;break}}}if(!C){return E}}return -1};for(var v=0,w=x.length;v<w;v++){var k=l[x[v]],n=k[0],t=k[1],e=k[2],q=k[3],f=Math.floor(t*o),j=Math.ceil(e*o),u=this.measureText(q).width,h;if(q!==undefined&&this.include_label){u+=(d+a);if(f-u>=0){f-=u;h="left"}else{j+=u;h="right"}}var s=p(f,j);if(s>=0){if(g[s]===undefined){g[s]=[]}g[s].push([f,j]);r[n]=s;m=Math.max(m,s)}else{}}return m+1}})};var painters_module=function(k,A){var q=function(L,D,J,C,I,G){if(G===undefined){G=4}var F=C-D;var E=I-J;var H=Math.floor(Math.sqrt(F*F+E*E)/G);var M=F/H;var K=E/H;var B;for(B=0;B<H;B++,D+=M,J+=K){if(B%2!==0){continue}L.fillRect(D,J,G,1)}};var r=function(D,C,B,G){var F=C-G/2,E=C+G/2,H=B-Math.sqrt(G*3/2);D.beginPath();D.moveTo(F,H);D.lineTo(E,H);D.lineTo(C,B);D.lineTo(F,H);D.strokeStyle=this.fillStyle;D.fill();D.stroke();D.closePath()};var v=function(E,G,C,F,B,D){this.data=E;this.delta=G;this.max=C;this.view_start=F;this.view_end=B;this.show_counts=D};v.prototype.draw=function(O,B,N){var G=this.view_start,Q=this.view_end-this.view_start,P=B/Q;var L=this.data,K=this.delta,I=this.max,D=N;delta_x_px=Math.ceil(K*P);O.save();for(var E=0,F=L.length;E<F;E++){var J=Math.floor((L[E][0]-G)*P);var H=L[E][1];if(!H){continue}var M=H/I*N;O.fillStyle="black";O.fillRect(J,D-M,delta_x_px,M);var C=4;if(this.show_counts&&(O.measureText(H).width+C)<delta_x_px){O.fillStyle="#666";O.textAlign="center";O.fillText(H,J+(delta_x_px/2),10)}}O.restore()};var c=function(E,H,B,C,G,D,F){this.data=E;this.view_start=H;this.view_end=B;this.min_value=C;this.max_value=G;this.color=D;this.mode=F;this.overflow_color="#F66"};c.prototype.draw=function(Q,P,N){var I=false,J=this.min_value,G=this.max_value,M=G-J,C=N,D=this.view_start,O=this.view_end-this.view_start,E=P/O,K=this.mode,U=this.data;Q.save();var V=Math.round(N+J/M*N);if(K!=="Intensity"){Q.fillStyle="#aaa";Q.fillRect(0,V,P,1)}Q.beginPath();Q.fillStyle=this.color;var T,H,F;if(U.length>1){F=Math.ceil((U[1][0]-U[0][0])*E)}else{F=10}for(var R=0,S=U.length;R<S;R++){T=Math.round((U[R][0]-D)*E);H=U[R][1];if(H===null){if(I&&K==="Filled"){Q.lineTo(T,C)}I=false;continue}if(H<J){H=J}else{if(H>G){H=G}}if(K==="Histogram"){H=Math.round(H/M*C);Q.fillRect(T,V,F,-H)}else{if(K==="Intensity"){H=255-Math.floor((H-J)/M*255);Q.fillStyle="rgb("+H+","+H+","+H+")";Q.fillRect(T,0,F,C)}else{H=Math.round(C-(H-J)/M*C);if(I){Q.lineTo(T,H)}else{I=true;if(K==="Filled"){Q.moveTo(T,C);Q.lineTo(T,H)}else{Q.moveTo(T,H)}}}}}if(K==="Filled"){if(I){Q.lineTo(T,V);Q.lineTo(0,V)}Q.fill()}else{Q.stroke()}var B=-1,L=-1;Q.fillStyle=this.overflow_color;for(var R=0,S=U.length;R<S;R++){H=U[R][1];T=Math.round((U[R][0]-D)*E);x_minus_scaled=Math.round((U[R][0]-1-D)*E);if(L>=0&&(H===null||H<G)){Q.fillRect(L,0,x_minus_scaled-L+1,2);L=-1}else{if(B>=0&&(H===null||H>J)){Q.fillRect(B,N-2,x_minus_scaled-B+1,2);B=-1}}if(H!==null&&H>G&&L<0){L=T}else{if(H!==null&&H<J&&B<0){B=T}}}Q.restore()};var p=function(D,F,B,C,E){this.data=D;this.view_start=F;this.view_end=B;this.prefs=C;this.mode=E};extend(p.prototype,{get_required_height:function(C){var B=y_scale=this.get_row_height(),D=this.mode;if(D==="no_detail"||D==="Squish"||D==="Pack"){B=C*y_scale}return B+Math.max(Math.round(y_scale/2),5)},draw:function(N,E,M,J){var H=this.data,K=this.view_start,O=this.view_end;N.save();N.fillStyle=this.prefs.block_color;N.textAlign="right";var R=this.view_end-this.view_start,Q=E/R,D=this.get_row_height();for(var G=0,I=H.length;G<I;G++){var P=H[G],F=P[0],B=P[1],C=P[2],L=(J&&J[F]!==undefined?J[F]:null);if((B<O&&C>K)&&(this.mode=="Dense"||L!==null)){this.draw_element(N,this.mode,P,L,K,O,Q,D,E)}}N.restore()}});var d=10,j=3,n=5,z=10,g=1,t=3,f=3,a=9,o=2,h="#ccc";var s=function(D,F,B,C,E){p.call(this,D,F,B,C,E)};extend(s.prototype,p.prototype,{get_row_height:function(){var C=this.mode,B;if(C==="Dense"){B=d}else{if(C==="no_detail"){B=j}else{if(C==="Squish"){B=n}else{B=z}}}return B},draw_element:function(N,G,V,I,P,af,aj,ak,B){var S=V[0],ah=V[1],Z=V[2]-1,Q=V[3],aa=Math.floor(Math.max(0,(ah-P)*aj)),O=Math.ceil(Math.min(B,Math.max(0,(Z-P)*aj))),Y=(G==="Dense"?0:(0+I))*ak,M,ad,R=null,al=null,E=this.prefs.block_color,ac=this.prefs.label_color;if(G=="Dense"){I=1}if(G==="no_detail"){N.fillStyle=E;N.fillRect(aa,Y+5,O-aa,g)}else{var L=V[4],X=V[5],ab=V[6],F=V[7];if(X&&ab){R=Math.floor(Math.max(0,(X-P)*aj));al=Math.ceil(Math.min(B,Math.max(0,(ab-P)*aj)))}var ai,T;if(G==="Squish"||G==="Dense"){ai=1;T=f}else{ai=5;T=a}if(!F){if(V.strand){if(V.strand==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(V.strand==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}}else{N.fillStyle=E}N.fillRect(aa,Y,O-aa,T)}else{var K,U;if(G==="Squish"||G==="Dense"){N.fillStyle=h;K=Y+Math.floor(f/2)+1;U=1}else{if(L){var K=Y;var U=T;if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand")}}}else{N.fillStyle=h;K+=(f/2)+1;U=1}}N.fillRect(aa,K,O-aa,U);for(var ag=0,D=F.length;ag<D;ag++){var H=F[ag],C=Math.floor(Math.max(0,(H[0]-P)*aj)),W=Math.ceil(Math.min(B,Math.max((H[1]-1-P)*aj)));if(C>W){continue}N.fillStyle=E;N.fillRect(C,Y+(T-ai)/2+1,W-C,ai);if(R!==undefined&&ab>X&&!(C>al||W<R)){var ae=Math.max(C,R),J=Math.min(W,al);N.fillRect(ae,Y+1,J-ae,T);if(F.length==1&&G=="Pack"){if(L==="+"){N.fillStyle=N.canvas.manager.get_pattern("right_strand_inv")}else{if(L==="-"){N.fillStyle=N.canvas.manager.get_pattern("left_strand_inv")}}if(ae+14<J){ae+=2;J-=2}N.fillRect(ae,Y+1,J-ae,T)}}}}if(G==="Pack"&&ah>P){N.fillStyle=ac;if(P===0&&aa-N.measureText(Q).width<0){N.textAlign="left";N.fillText(Q,O+o,Y+8)}else{N.textAlign="right";N.fillText(Q,aa-o,Y+8)}N.fillStyle=E}}}});var b=function(D,F,B,C,E){p.call(this,D,F,B,C,E)};extend(b.prototype,p.prototype,{draw_element:function(U,P,J,F,X,D,M,V,S){var J=data[i],L=J[0],T=J[1],E=J[2]-1,O=J[3],H=Math.floor(Math.max(0,(T-X)*M)),K=Math.ceil(Math.min(S,Math.max(0,(E-X)*M))),G=(P==="Dense"?0:(0+F))*V,B,Y,C=null,N=null;if(no_label){U.fillStyle=block_color;U.fillRect(H+left_offset,G+5,K-H,1)}else{var W=J[4],R=J[5],I=J[6];B=9;Y=1;U.fillRect(H+left_offset,G,K-H,B);if(P!=="Dense"&&O!==undefined&&T>X){U.fillStyle=label_color;if(X===0&&H-U.measureText(O).width<0){U.textAlign="left";U.fillText(O,K+2+left_offset,G+8)}else{U.textAlign="right";U.fillText(O,H-2+left_offset,G+8)}U.fillStyle=block_color}var Q=W+" / "+R;if(T>X&&U.measureText(Q).width<(K-H)){U.fillStyle="white";U.textAlign="center";U.fillText(Q,left_offset+H+(K-H)/2,G+8);U.fillStyle=block_color}}}});var y=1001,m=1002,e=1003,x=1004,l=1005;var w=function(F,C){var H=F[0],G=F[1],E=C[0],D=C[1],B;if(H<E){if(G<E){B=y}else{if(G<=D){B=e}else{B=m}}}else{if(H>D){B=y}else{if(G<=D){B=l}else{B=x}}}return B};var u=function(E,G,B,D,F,C){p.call(this,E,G,B,D,F);this.ref_seq=C};extend(u.prototype,p.prototype,{get_row_height:function(){var B,C=this.mode;if(C==="Dense"){B=d}else{if(C==="Squish"){B=n}else{B=z;if(this.prefs.show_insertions){B*=2}}}return B},draw_read:function(Y,T,O,ad,D,X,L,I,H){Y.textAlign="center";var W=this,C=[ad,D],R=0,Z=0,V=0;ref_seq=this.ref_seq,char_width_px=Y.canvas.manager.char_width_px;var ai=[];if((T==="Pack"||this.mode==="Auto")&&I!==undefined&&O>char_width_px){V=Math.round(O/2)}if(!L){L=[[0,I.length]]}for(var P=0,ab=L.length;P<ab;P++){var M=L[P],E="MIDNSHP=X"[M[0]],Q=M[1];if(E==="H"||E==="S"){R-=Q}var J=X+R,ah=Math.floor(Math.max(0,(J-ad)*O)),K=Math.floor(Math.max(0,(J+Q-ad)*O));switch(E){case"H":break;case"S":case"M":case"=":var S=w([J,J+Q],C);if(S!==y){var U=I.slice(Z,Z+Q);if(V>0){Y.fillStyle=this.prefs.block_color;Y.fillRect(ah-V,H+1,K-ah,9);Y.fillStyle=h;for(var af=0,B=U.length;af<B;af++){if(this.prefs.show_differences&&ref_seq){var N=ref_seq[J-ad+af];if(!N||N.toLowerCase()===U[af].toLowerCase()){continue}}if(J+af>=ad&&J+af<=D){var ag=Math.floor(Math.max(0,(J+af-ad)*O));Y.fillText(U[af],ag,H+9)}}}else{Y.fillStyle=this.prefs.block_color;Y.fillRect(ah,H+4,K-ah,f)}}Z+=Q;R+=Q;break;case"N":Y.fillStyle=h;Y.fillRect(ah-V,H+5,K-ah,1);R+=Q;break;case"D":Y.fillStyle="red";Y.fillRect(ah-V,H+4,K-ah,3);R+=Q;break;case"P":break;case"I":var S=w([J,J+Q],C),ac=ah-V;if(S!==y){var U=I.slice(Z,Z+Q);if(this.prefs.show_insertions){var G=ah-(K-ah)/2;if((T==="Pack"||this.mode==="Auto")&&I!==undefined&&O>char_width_px){Y.fillStyle="yellow";Y.fillRect(G-V,H-9,K-ah,9);ai[ai.length]={type:"triangle",data:[ac,H+4,5]};Y.fillStyle=h;switch(S){case (e):U=U.slice(ad-J);break;case (x):U=U.slice(0,J-D);break;case (l):break;case (m):U=U.slice(ad-J,J-D);break}for(var af=0,B=U.length;af<B;af++){var ag=Math.floor(Math.max(0,(J+af-ad)*O));Y.fillText(U[af],ag-(K-ah)/2,H)}}else{Y.fillStyle="yellow";Y.fillRect(G,H+(this.mode!=="Dense"?2:5),K-ah,(T!=="Dense"?f:t))}}else{if((T==="Pack"||this.mode==="Auto")&&I!==undefined&&O>char_width_px){ai[ai.length]={type:"text",data:[U.length,ac,H+9]}}else{}}}Z+=Q;break;case"X":Z+=Q;break}}Y.fillStyle="yellow";var ae,F,aj;for(var aa=0;aa<ai.length;aa++){ae=ai[aa];F=ae.type;aj=ae.data;if(F==="text"){Y.save();Y.font="bold "+Y.font;Y.fillText(aj[0],aj[1],aj[2]);Y.restore()}else{if(F=="triangle"){r(Y,aj[0],aj[1],aj[2])}}}},draw_element:function(U,P,H,E,X,C,L,V,S){var K=H[0],T=H[1],D=H[2],M=H[3],G=Math.floor(Math.max(0,(T-X)*L)),I=Math.ceil(Math.min(S,Math.max(0,(D-X)*L))),F=(P==="Dense"?0:(0+E))*V,Y=this.prefs.block_color,J=this.prefs.label_color,R=0;if((P==="Pack"||this.mode==="Auto")&&L>U.canvas.manager.char_width_px){var R=Math.round(L/2)}U.fillStyle=Y;if(H[5] instanceof Array){var Q=Math.floor(Math.max(0,(H[4][0]-X)*L)),O=Math.ceil(Math.min(S,Math.max(0,(H[4][1]-X)*L))),N=Math.floor(Math.max(0,(H[5][0]-X)*L)),B=Math.ceil(Math.min(S,Math.max(0,(H[5][1]-X)*L)));if(H[4][1]>=X&&H[4][0]<=C&&H[4][2]){this.draw_read(U,P,L,X,C,H[4][0],H[4][2],H[4][3],F)}if(H[5][1]>=X&&H[5][0]<=C&&H[5][2]){this.draw_read(U,P,L,X,C,H[5][0],H[5][2],H[5][3],F)}if(N>O){U.fillStyle=h;q(U,O-R,F+5,N-R,F+5)}}else{U.fillStyle=Y;this.draw_read(U,P,L,X,C,T,H[4],H[5],F)}if(P==="Pack"&&T>X){U.fillStyle=this.prefs.label_color;var W=1;if(W===0&&G-U.measureText(M).width<0){U.textAlign="left";U.fillText(M,I+o-R,F+8)}else{U.textAlign="right";U.fillText(M,G-o-R,F+8)}U.fillStyle=Y}}});A.SummaryTreePainter=v;A.LinePainter=c;A.LinkedFeaturePainter=s;A.ReadPainter=u;A.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file

--- a/static/scripts/trackster.js Mon Apr 04 23:27:25 2011 -0400 +++ b/static/scripts/trackster.js Tue Apr 05 11:51:48 2011 -0400 @@ -104,7 +104,7 @@ */ var get_slider_step = function(min, max) { var range = max - min; - return (range <= 1 ? 0.01 : (range <= 1000 ? 1 : 5)); + return (range <= 2 ? 0.01 : (range <= 100 ? 1 : (range <= 1000 ? 5 : 10))); }

/** @@ -756,10 +756,13 @@ });

/** - * Encapsulation of tools that users can apply to tracks/datasets. + * Encapsulation of a tool that users can apply to tracks/datasets. */ -var Tool = function(tool_dict) { - // Unpack tool from dictionary. +var Tool = function(track, tool_dict) { + // + // Unpack tool information from dictionary. + // + this.track = track; this.name = tool_dict.name; this.params = []; var params_dict = tool_dict.params; @@ -767,56 +770,161 @@ var param_dict = params_dict[i], name = param_dict.name, label = param_dict.label, + html = unescape(param_dict.html), type = param_dict.type; - if (type === "int" || type === "float") { + if (type === "number") { this.params[this.params.length] = - new NumberParameter(name, label, param_dict.min, param_dict.max, param_dict.value); + new NumberParameter(name, label, html, param_dict.min, param_dict.max); } else if (type == "select") { - this.params[this.params.length] = new SelectParameter(name, label, param_dict.options); + this.params[this.params.length] = new ToolParameter(name, label, html); } else { console.log("WARNING: unrecognized tool parameter type:", name, type); } } + + // + // Create div elt for tool UI. + // + this.parent_div = $("<div/>").addClass("dynamic-tool").hide(); + // Disable dragging, clicking, double clicking on div so that actions on slider do not impact viz. + this.parent_div.bind("drag", function(e) { + e.stopPropagation(); + }).bind("click", function(e) { + e.stopPropagation(); + }).bind("dblclick", function(e) { + e.stopPropagation(); + }); + var name_div = $("<div class='tool-name'>").appendTo(this.parent_div).text(this.name); + var tool_params = this.params; + var tool = this; + $.each(this.params, function(index, param) { + var param_div = $("<div>").addClass("param-row").appendTo(tool.parent_div); + // Param label. + var label_div = $("<div>").addClass("param-label").text(param.label).appendTo(param_div); + // Param HTML. + // TODO: either generalize .slider CSS attributes or create new rule for tool input div. + var html_div = $("<div/>").addClass("slider").html(param.html).appendTo(param_div); + + // Add to clear floating layout. + $("<div style='clear: both;'/>").appendTo(param_div); + }); + + // Highlight value for inputs for easy replacement. + this.parent_div.find("input").click(function() { $(this).select() }); + + // Add 'Go' button. + var run_tool_row = $("<div>").addClass("slider-row").appendTo(this.parent_div); + var run_tool_button = $("<input type='submit'>").attr("value", "Run").appendTo(run_tool_row); + var tool = this; + run_tool_button.click( function() { + tool.run(); + }); }; extend(Tool.prototype, { - // Returns a dictionary of parameter values; key is parameter name, value - // is parameter value. + /** + * Returns dictionary of parameter name-values. + */ get_param_values_dict: function() { var param_dict = {}; - for (var i = 0; i < this.params.length; i++) { - var param = this.params[i]; - param_dict[param.name] = JSON.stringify(param.value); - } + this.parent_div.find(":input").each(function() { + var name = $(this).attr("name"), value = $(this).val(); + param_dict[name] = JSON.stringify(value); + }); return param_dict; }, - // Returns an array of parameter values. + /** + * Returns array of parameter values. + */ get_param_values: function() { var param_values = []; - for (var i = 0; i < this.params.length; i++) { - param_values[i] = this.params[i].value; + var param_dict = {}; + this.parent_div.find(":input").each(function() { + // Only include inputs with names; this excludes Run button. + var name = $(this).attr("name"), value = $(this).val(); + if (name) { + param_values[param_values.length] = value; + } + }); + return param_values; + }, + /** + * Run tool. This creates a new child track, runs tool, and places tool's output in the new track. + */ + run: function() { + // Put together params for running tool. + var url_params = { + dataset_id: this.track.original_dataset_id, + chrom: this.track.view.chrom, + low: this.track.view.low, + high: this.track.view.high, + tool_id: this.name + }; + $.extend(url_params, this.get_param_values_dict()); + + // + // Create track for tool's output immediately to provide user feedback. + // + var + current_track = this.track, + // Set name of track to include tool name, parameters, and region used. + track_name = url_params.tool_id + + current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high), + new_track; + + // TODO: add support for other kinds of tool data tracks. + if (current_track.track_type === 'FeatureTrack') { + new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); } - return param_values; + + this.track.add_track(new_track); + new_track.content_div.text("Starting job."); + + // Run tool. + var json_run_tool = function() { + $.getJSON(run_tool_url, url_params, function(track_data) { + if (track_data === "no converter") { + // No converter available for input datasets, so cannot run tool. + new_track.container_div.addClass("error"); + new_track.content_div.text(DATA_NOCONVERTER); + } + else if (track_data.error) { + // General error. + new_track.container_div.addClass("error"); + new_track.content_div.text(DATA_CANNOT_RUN_TOOL + track_data.message); + } + else if (track_data === "pending") { + // Converting/indexing input datasets; show message and try again. + new_track.container_div.addClass("pending"); + new_track.content_div.text("Converting input data so that it can be easily reused."); + setTimeout(json_run_tool, 2000); + } + else { + // Job submitted and running. + new_track.dataset_id = track_data.dataset_id; + new_track.content_div.text("Running job."); + new_track.init(); + } + }); + }; + json_run_tool(); } });

/** * Tool parameters. */ -var NumberParameter = function(name, label, min, max, init_value) { +var ToolParameter = function(name, label, html) { this.name = name; this.label = label; + this.html = html; +}; + +var NumberParameter = function(name, label, html, min, max) { + ToolParameter.call(this, name, label, html) this.min = min; this.max = max; - this.value = init_value; -}; - -var SelectParameter = function(name, label, options) { - this.name = name; - this.label = label; - this.options = options; - this.value = (options.length !== 0 ? options[0][1] : null); };

/** @@ -1157,7 +1265,7 @@ // filters_available is determined by data, filters_visible is set by user. this.filters_available = false; this.filters_visible = false; - this.tool = (tool_dict !== undefined && obj_length(tool_dict) > 0 ? new Tool(tool_dict) : undefined); + this.tool = (tool_dict !== undefined && obj_length(tool_dict) > 0 ? new Tool(this, tool_dict) : undefined);

// // TODO: Right now there is only the notion of a parent track and multiple child tracks. However, @@ -1250,7 +1358,7 @@ // Disable dragging, double clicking on div so that actions on slider do not impact viz. this.filters_div.bind("drag", function(e) { e.stopPropagation(); - }).bind("click", function( e ) { + }).bind("click", function(e) { e.stopPropagation(); }).bind("dblclick", function(e) { e.stopPropagation(); @@ -1311,89 +1419,8 @@ // Create dynamic tool div. // if (this.tool) { - // Create div elt for tool UI. - this.dynamic_tool_div = $("<div/>").addClass("dynamic-tool").hide(); + this.dynamic_tool_div = this.tool.parent_div; this.header_div.after(this.dynamic_tool_div); - // Disable dragging, clicking, double clicking on div so that actions on slider do not impact viz. - this.dynamic_tool_div.bind( "drag", function(e) { - e.stopPropagation(); - }).bind("click", function( e ) { - e.stopPropagation(); - }).bind("dblclick", function( e ) { - e.stopPropagation(); - }); - var name_div = $("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name); - var tool_params = this.tool.params; - var track = this; - $.each(this.tool.params, function(index, param) { - - if (param instanceof NumberParameter) { - var param_div = $("<div>").addClass("slider-row").appendTo(track.dynamic_tool_div); - - // Slider label. - var label_div = $("<div>").addClass("slider-label").appendTo(param_div); - var name_span = $("<span/>").addClass("slider-name").text(param.label + " ").appendTo(label_div); - var values_span = $("<span/>").text(param.value); - var values_span_container = $("<span/>").addClass("slider-value").appendTo(label_div).append("[").append(values_span).append("]"); - - // Slider. - var slider_div = $("<div/>").addClass("slider").appendTo(param_div); - var slider = $("<div id='" + param.name + "-param-control'>").appendTo(slider_div); - // Step must have a value so that (max-min)%step == 0. - slider.slider({ - min: param.min, - max: param.max, - step: get_slider_step(param.min, param.max), - value: param.value, - slide: function(event, ui) { - var value = ui.value; - param.value = value; - // Set new value in UI. - if (0 < value && value < 1) { - value = parseFloat(value).toFixed(2); - } - values_span.text(value); - }, - change: function(event, ui) { - slider.slider("option", "slide").call(slider, event, ui); - } - }); - - // Enable users to edit parameter's value via text box. - edit_slider_values(values_span_container, values_span, slider); - - // Add to clear floating layout. - $("<div style='clear: both;'/>").appendTo(param_div); - } - else if (param instanceof SelectParameter) { - var param_div = $("<div>").addClass("slider-row").appendTo(track.dynamic_tool_div); - - // Param label. - var label_div = $("<div>").addClass("slider-label").appendTo(param_div); - var name_span = $("<span/>").addClass("slider-name").text(param.label + " ").appendTo(label_div); - - // Param selector. - var select_div = $("<div/>").addClass("slider").appendTo(param_div); - var select_obj = $("<select/>").appendTo(select_div); - select_obj.change(function() {param.value = $(this).val();} ); - var options = select_obj.attr("options"); - for (var i = 0; i < param.options.length; i++) { - var option_data = param.options[i] - options[options.length] = new Option(option_data[0], option_data[1]); - } - - // Add to clear floating layout. - $("<div style='clear: both;'/>").appendTo(param_div); - } - }); - - // Add 'Go' button. - var run_tool_row = $("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div); - var run_tool_button = $("<input type='submit'>").attr("value", "Run").appendTo(run_tool_row); - var track = this; - run_tool_button.click( function() { - track.run_tool(); - }); }

// @@ -1767,66 +1794,6 @@ } $(window).trigger("resize"); }, - // Run track's tool. - run_tool: function() { - // Put together params for running tool. - var url_params = { - dataset_id: this.original_dataset_id, - chrom: this.view.chrom, - low: this.view.low, - high: this.view.high, - tool_id: this.tool.name - }; - $.extend(url_params, this.tool.get_param_values_dict()); - - // - // Create track for tool's output immediately to provide user feedback. - // - var - current_track = this, - // Set name of track to include tool name, parameters, and region used. - track_name = url_params.tool_id + - current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high), - new_track; - - // TODO: add support for other kinds of tool data tracks. - if (current_track.track_type === 'FeatureTrack') { - new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); - } - - this.add_track(new_track); - new_track.content_div.text("Starting job."); - view.has_changes = true; - - // Run tool. - var json_run_tool = function() { - $.getJSON(run_tool_url, url_params, function(track_data) { - if (track_data === "no converter") { - // No converter available for input datasets, so cannot run tool. - new_track.container_div.addClass("error"); - new_track.content_div.text(DATA_NOCONVERTER); - } - else if (track_data.error) { - // General error. - new_track.container_div.addClass("error"); - new_track.content_div.text(DATA_CANNOT_RUN_TOOL + track_data.message); - } - else if (track_data === "pending") { - // Converting/indexing input datasets; show message and try again. - new_track.container_div.addClass("pending"); - new_track.content_div.text("Converting input data so that it can be easily reused."); - setTimeout(json_run_tool, 2000); - } - else { - // Job submitted and running. - new_track.dataset_id = track_data.dataset_id; - new_track.content_div.text("Running job."); - new_track.init(); - } - }); - }; - json_run_tool(); - }, /** * Utility function that creates a label string describing the region and parameters of a track's tool. */ @@ -1850,6 +1817,7 @@ this.child_tracks_container.show(); } this.child_tracks.push(child_track); + this.view.has_changes = true; }, /** * Remove a child track from this track.

--- a/tools/new_operations/intersect.xml Mon Apr 04 23:27:25 2011 -0400 +++ b/tools/new_operations/intersect.xml Tue Apr 05 11:51:48 2011 -0400 @@ -28,7 +28,7 @@ <param format="interval,gff" name="input2" type="data" help="Second dataset"><label>that intersect</label></param> - <param name="min" size="4" type="integer" value="1" min="0" max="600000" help="(bp)"> + <param name="min" size="4" type="integer" value="1" min="1" help="(bp)"><label>for at least</label></param></inputs>

--- a/tools/new_operations/subtract.xml Mon Apr 04 23:27:25 2011 -0400 +++ b/tools/new_operations/subtract.xml Tue Apr 05 11:51:48 2011 -0400 @@ -31,7 +31,7 @@ <option value="-p">Non-overlapping pieces of intervals</option></param>

- <param name="min" size="4" type="integer" value="1" min="0" max="600000" help="(bp)"> + <param name="min" size="4" type="integer" value="1" min="1" help="(bp)"><label>where minimal overlap is</label></param></inputs>

--- a/tools/ngs_rna/cufflinks_wrapper.xml Mon Apr 04 23:27:25 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Tue Apr 05 11:51:48 2011 -0400 @@ -42,7 +42,7 @@ </command><inputs><param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> - <param name="max_intron_len" type="integer" value="300000" min="0" max="600000" label="Max Intron Length" help=""/> + <param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help=""/><param name="min_isoform_fraction" type="float" value="0.05" min="0" max="1" label="Min Isoform Fraction" help=""/><param name="pre_mrna_fraction" type="float" value="0.05" min="0" max="1" label="Pre MRNA Fraction" help=""/><param name="min_map_quality" type="integer" value="0" min="0" max="255" label="Min SAM Map Quality" help=""/>

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