- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Implement a data manager for trackster. Convert DataCache into a DataManager and use jQuery Deferred objects to move data management from the tile level to the track level. Implications of these changes include (a) callbacks are no longer needed when drawing tiles; (a) data is fetched before a tile is drawn; and (c) tile drawing is completely tracked so that actions can be taken after a track has been drawn.
by Bitbucket 24 Mar '11

24 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e37ad896e5fd/ changeset: r5269:e37ad896e5fd user: jgoecks date: 2011-03-24 20:05:28 summary: Implement a data manager for trackster. Convert DataCache into a DataManager and use jQuery Deferred objects to move data management from the tile level to the track level. Implications of these changes include (a) callbacks are no longer needed when drawing tiles; (a) data is fetched before a tile is drawn; and (c) tile drawing is completely tracked so that actions can be taken after a track has been drawn. affected #: 4 files (1.4 KB) --- a/lib/galaxy/web/controllers/tracks.py Thu Mar 24 15:03:12 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Thu Mar 24 15:05:28 2011 -0400 @@ -741,9 +741,9 @@ # try: subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=original_dataset.history ) - except e: + except Exception, e: # Lots of things can go wrong when trying to execute tool. - return to_json_string( { "error" : True, "message" : e.str() } ) + 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() @@ -760,12 +760,6 @@ return self.add_track_async( trans, output_dataset.id ) - @web.expose - def woot( self, trans, ldda_id, target_type ): - ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) - converted_dataset = ldda.get_converted_dataset( trans, target_type ) - raise converted_dataset - # # Helper methods. # --- a/static/scripts/packed/jquery.event.drag.js Thu Mar 24 15:03:12 2011 -0400 +++ b/static/scripts/packed/jquery.event.drag.js Thu Mar 24 15:05:28 2011 -0400 @@ -1,6 +1,6 @@ /* - * jquery.event.drag - v 2.0.0 + * jquery.event.drag - v 2.1.0 * Copyright (c) 2010 Three Dub Media - http://threedubmedia.com * Open Source MIT License - http://threedubmedia.com/code/license */ -(function(d){d.fn.drag=function(i,e,h){var g=typeof i=="string"?i:"",f=d.isFunction(i)?i:d.isFunction(e)?e:null;if(g.indexOf("drag")!==0){g="drag"+g}h=(i==f?e:h)||{};return f?this.bind(g,h,f):this.trigger(g)};var b=d.event,a=b.special,c=a.drag={defaults:{which:1,distance:0,not:":input",handle:null,relative:false,drop:true,click:false},datakey:"dragdata",livekey:"livedrag",add:function(g){var f=d.data(this,c.datakey),e=g.data||{};f.related+=1;if(!f.live&&g.selector){f.live=true;b.add(this,"draginit."+c.livekey,c.delegate)}d.each(c.defaults,function(h,i){if(e[h]!==undefined){f[h]=e[h]}})},remove:function(){d.data(this,c.datakey).related-=1},setup:function(){if(d.data(this,c.datakey)){return}var e=d.extend({related:0},c.defaults);d.data(this,c.datakey,e);b.add(this,"mousedown",c.init,e);if(this.attachEvent){this.attachEvent("ondragstart",c.dontstart)}},teardown:function(){if(d.data(this,c.datakey).related){return}d.removeData(this,c.datakey);b.remove(this,"mousedown",c.init);b.remove(this,"draginit",c.delegate);c.textselect(true);if(this.detachEvent){this.detachEvent("ondragstart",c.dontstart)}},init:function(g){var 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false},callback:function(){}};c.callback.prototype={update:function(){if(a.drop&&this.available.length){d.each(this.available,function(f){a.drop.locate(this,f)})}}};var e=b.handle;b.handle=function(f){if(d.data(this,"suppress."+f.type)-new Date().getTime()>0){d.removeData(this,"suppress."+f.type);return}return e.apply(this,arguments)};a.draginit=a.dragstart=a.dragend=c})(jQuery); \ No newline at end of file --- a/static/scripts/packed/trackster.js Thu Mar 24 15:03:12 2011 -0400 +++ b/static/scripts/packed/trackster.js Thu Mar 24 15:05:28 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 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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 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DataCache=function(a){Cache.call(this,a)};$.extend(DataCache.prototype,Cache.prototype,{get_data:function(g,b,e){var h=this.get(this.gen_key(g,b,e));if(h){return h}var j,f,a,d,e,h;for(var c=0;c<this.key_ary.length;c++){j=this.key_ary[c];f=this.split_key(j);a=f[0];d=f[1];if(g>=a&&b<=d){h=this.obj_cache[j];if(h.dataset_type!=="summary_tree"&&h.extra_info!=="no_detail"){this.move_key_to_end(j,c);return h}}}return undefined},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown 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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())}$(this).hide();a.location_span.show();a.chrom_select.show();return false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",b).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var j=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(j/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,k){var f=$(this);var l=k.offsetX-k.current_x;var g=f.scrollTop()-(h.clientY-k.current_height);f.scrollTop(g);k.current_height=h.clientY;k.current_x=k.offsetX;var j=Math.round(l/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}).bind("mousewheel",function(h,k,g,f){if(g){var j=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(k,l){$(l.proxy).css({left:Math.min(k.pageX,l.startX),width:Math.abs(k.pageX-l.startX)});var g=Math.min(k.pageX,l.startX)-a.container.offset().left,f=Math.max(k.pageX,l.startX)-a.container.offset().left,j=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*j)+a.low,Math.round(f/h*j)+a.low)}).bind("dragend",function(l,m){var g=Math.min(l.pageX,m.startX),f=Math.max(l.pageX,m.startX),j=(a.high-a.low),h=a.viewport_container.width(),k=a.low;a.low=Math.round(g/h*j)+k;a.high=Math.round(f/h*j)+k;$(m.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){d.load_chroms({chrom:e},function(){d.change_chrom(e,b,g)});return}else{if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len-1;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()}},go_to:function(f){var k=this,a,d,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}k.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};$.extend(Track.prototype,{init:function(){var a=this;a.enabled=false;a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:a.hda_ldda,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(!b||b==="error"||b.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(b.message){var d=a.view.tracks.indexOf(a);var c=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+b.message+"</pre>",{Close:hide_modal})});a.content_div.append(c)}}else{if(b==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(b==="no data"||(b.data!==undefined&&(b.data===null||b.data.length===0))){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(b==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{if(b.status==="data"){if(b.valid_chroms){a.valid_chroms=b.valid_chroms;a.make_name_popup_menu()}a.content_div.text(DATA_OK);if(a.view.chrom){a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;$.when(a.predraw_init()).done(function(){a.draw()})}}}}}}})},predraw_init:function(){},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(b,j,n){var c=this,o=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=n;this.child_tracks=[];if(c.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});$.each(this.filters,function(t,w){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var v=$("<div/>").addClass("slider-label").appendTo(u);var s=$("<span/>").addClass("name").appendTo(v);s.text(w.name+" ");var r=$("<span/>").addClass("values").appendTo(v);var q=$("<div/>").addClass("slider").appendTo(u);w.control_element=$("<div/>").attr("id",w.name+"-filter-control").appendTo(q);w.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(y,z){var x=z.values;r.text("["+x[0]+"-"+x[1]+"]");w.low=x[0];w.high=x[1];c.draw(true,true)},change:function(x,y){w.control_element.slider("option","slide").call(w.control_element,x,y)}});w.slider=w.control_element;w.slider_label=r;$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(q){q.stopPropagation()}).bind("click",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});var m=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var l=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span class='param-name'>").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span class='param-value'>").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var q=$("<div id='"+s.name+"-param-control'>").appendTo(y);var r=(s.max<=1?0.01:(s.max<=1000?1:5));q.slider({min:s.min,max:s.max,step:r,value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){s.value=B.value}});w.click(function(){var C=t,B=C.text(),A=(s.max<=1?4:s.max.length);C.text("");$("<input type='text'/>").attr("size",A).attr("maxlength",A).attr("value",B).appendTo(C).focus().select().click(function(D){D.stopPropagation()}).blur(function(){$(this).remove();C.text(B)}).keyup(function(F){if(F.keyCode===27){$(this).trigger("blur")}else{if(F.keyCode===13){var D=$(this),E=parseFloat(D.val());if(isNaN(E)||E>s.max||E<s.min){alert("Parameter value must be in the range ["+s.min+"-"+s.max+"]");return $(this)}C.text(E);q.slider("value",E);s.value=E}}})});$("<div style='clear: both;'/>").appendTo(v)});var p=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var k=$("<input type='submit'>").attr("value","Run").appendTo(p);var c=this;k.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(q){c.mode_div.text(q);c.mode=q;c.track_config.values.mode=q;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(q){return function(){d(q)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide Tool":"Show Tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.track_type=="ReadTrack"){var e=(b.show_insertions?"Hide Insertions":"Show Insertions");a[e]=function(){b.show_insertions=!b.show_insertions;b.draw(true);b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},tile_data:function(d,a,g,k,j){var b=this,h=a*DENSITY*d,f=(a+1)*DENSITY*d,e={chrom:this.view.chrom,low:h,high:f,dbkey:this.view.dbkey};if(j===undefined){j=d+"_"+a}var c=b.data_cache.get(j);if(c){return k(c)}$.extend(e,g);$.ajax({url:this.data_url,dataType:"json",data:e,success:function(l){b.data_cache.set(j,l);return k(l)},error:function(m,l,n){console.log(m,l,n)}})},draw:function(a,d){var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}if(d){var k=this;var q=setInterval(function(){if(obj_length(c)===0){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var x=$(v[w]);if(u){x.remove()}else{if(x.children().length!==0){u=true}}}clearInterval(q)}},50)}for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,h,l,c,e,k,m,f){var d=this;var g=function(n){d.tile_cache.set(j,n);d.show_tile(n,k,h,m)};var a=setTimeout(function(){if(h<=d.view.high&&l>=d.view.low){var n;if(!b){n=d.tile_cache.get(j)}if(!n){d.draw_tile(e,c,k,m,function(p){if(p){var o=$("<div class='track-tile'>").prepend(p);n=o}g(n)})}if(n){g(n)}}delete f[a]},50);f[a]=true},show_tile:function(h,j,e,k){var a=this;var c=this.view.high-this.view.low,b=(e-this.view.low)*k;if(this.left_offset){b-=this.left_offset}h.css({position:"absolute",top:0,left:b,height:""});j.append(h);a.max_height=Math.max(a.max_height,h.height());a.content_div.css("height",a.max_height+"px");j.children().css("height",a.max_height+"px");if(a.hidden){return}for(var g=0;g<a.filters.length;g++){a.filters[g].update_ui_elt()}var d=false;if(a.example_feature){for(var g=0;g<a.filters.length;g++){if(a.filters[g].applies_to(a.example_feature)){d=true;break}}}if(a.filters_available!==d){a.filters_available=d;if(!a.filters_available){a.filters_div.hide()}a.make_name_popup_menu()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{draw_tile:function(c,b,e,g,f){var a=this,d=DENSITY*c;if(g>CHAR_WIDTH_PX){a.tile_data(c,b,{},function(j){if(j===null){a.content_div.css("height","0px");return}var k=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(k)}k=$(k);var h=k.get(0).getContext("2d");k.get(0).width=Math.ceil(d*g+a.left_offset);k.get(0).height=a.height_px;h.font=DEFAULT_FONT;h.textAlign="center";for(var n=0,l=j.length;n<l;n++){var m=Math.round(n*g);h.fillText(j[n],m+a.left_offset,10)}return f(k)})}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataCache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(d,a,j,k,h){if(this.vertical_range===undefined){return}var c=this,f=a*DENSITY*d,b=DENSITY*d,g=d+"_"+a,e={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};this.tile_data(d,a,e,function(C){var l=document.createElement("canvas"),q=C.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(l)}l=$(l);l.get(0).width=Math.ceil(b*k);l.get(0).height=c.height_px;var z=l.get(0).getContext("2d"),n=false,B=c.prefs.min_value,v=c.prefs.max_value,A=c.vertical_range,m=c.total_frequency,u=c.height_px,s=c.mode;var r=Math.round(u+B/A*u);z.beginPath();z.moveTo(0,r);z.lineTo(b*k,r);z.fillStyle="#aaa";z.stroke();z.beginPath();z.fillStyle=c.prefs.color;var p,w,x;if(q.length>1){x=Math.ceil((q[1][0]-q[0][0])*k)}else{x=10}for(var o=0,t=q.length;o<t;o++){p=Math.round((q[o][0]-f)*k);w=q[o][1];if(w===null){if(n&&s==="Filled"){z.lineTo(p,u)}n=false;continue}if(w<B){w=B}else{if(w>v){w=v}}if(s==="Histogram"){w=Math.round(w/A*u);z.fillRect(p,r,x,-w)}else{if(s==="Intensity"){w=255-Math.floor((w-B)/A*255);z.fillStyle="rgb("+w+","+w+","+w+")";z.fillRect(p,0,x,u)}else{w=Math.round(u-(w-B)/A*u);if(n){z.lineTo(p,w)}else{n=true;if(s==="Filled"){z.moveTo(p,u);z.lineTo(p,w)}else{z.moveTo(p,w)}}}}}if(s==="Filled"){if(n){z.lineTo(p,r);z.lineTo(0,r)}z.fill()}else{z.stroke()}h(l)})}});var FeatureTrack=function(a,f,e,j,h,c,d,g){var b=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];this.track_config=new TrackConfig({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:h,onchange:function(){b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;Track.call(this,a,f,f.viewport_container);TiledTrack.call(this,c,d,g);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=e;this.dataset_id=j;this.original_dataset_id=j;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.default_font=DEFAULT_FONT;this.inc_slots={};this.start_end_dct={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new DataCache(20);this.left_offset=200};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2],s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[5],z=x[6],E=x[7],e=x[8];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O-1);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(z,E,l,n,j,d,p){var v=this;if(v.view.reference_track&&n>CHAR_WIDTH_PX&&d===undefined){return v.view.reference_track.tile_data(z,E,{},function(f){v.draw_tile(z,E,l,n,j,f)})}var G=E*DENSITY*z,a=(E+1)*DENSITY*z,s=a-G,H={hda_ldda:v.hda_ldda,dataset_id:v.dataset_id,resolution:this.view.resolution,mode:this.mode};if(p===undefined){var q=this.data_cache.get_data(G,a,this.mode),J=z+"_"+E+"_"+this.mode;if(q===undefined){return v.tile_data(z,E,H,function(f){v.data_cache.set_data(G,a,this.mode,f);v.draw_tile(z,E,l,n,j,d,f)},J)}p=q}var x=Math.ceil(s*n),u=this.mode,K=25,g=this.left_offset,r,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(u==="Auto"){if(p.dataset_type==="summary_tree"){u=p.dataset_type}else{if(p.extra_info==="no_detail"){u="no_detail"}else{var I=p.data;if((I.length&&I.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){u="Squish"}else{u="Pack"}}}}var A=this.get_y_scale(u);if(u==="summary_tree"){h=this.summary_draw_height}if(u==="Dense"){h=K}else{if(u==="no_detail"||u==="Squish"||u==="Pack"){h=this.incremental_slots(n,p.data,u)*A+K;r=this.inc_slots[n]}}c.get(0).width=x+g;c.get(0).height=h;if(p.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}l.parent().css("height",Math.max(this.height_px,h)+"px");var y=c.get(0).getContext("2d");y.fillStyle=this.prefs.block_color;y.font=this.default_font;y.textAlign="right";this.container_div.find(".yaxislabel").remove();if(u==="summary_tree"){this.draw_summary_tree(c,p.data,p.delta,p.max,n,h,G,g);return j(c)}if(p.message){c.css({"border-top":"1px solid red"});y.fillStyle="red";y.textAlign="left";var t=y.textBaseline;y.textBaseline="top";y.fillText(p.message,g,0);y.textBaseline=t;if(!p.data){return j(c)}}this.example_feature=(p.data.length?p.data[0]:undefined);var I=p.data;for(var B=0,D=I.length;B<D;B++){var k=I[B],m=k[0],w=k[1],b=k[2],e=(r&&r[m]!==undefined?r[m]:null);var C=false;var o;for(var F=0;F<this.filters.length;F++){o=this.filters[F];o.update_attrs(k);if(!o.keep(k)){C=true;break}}if(C){continue}if(is_overlap([w,b],[G,a])&&(u=="Dense"||e!==null)){this.draw_element(y,E,u,k,e,G,a,n,A,x,g,d)}}j(c)}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.difference_mode=true;this.show_insertions=false;this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.round(J/2)}if(!e){e=[[0,o.length]]}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.difference_mode&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file +CanvasRenderingContext2D.prototype.dashedLine=function(c,j,b,h,f){if(f===undefined){f=4}var e=b-c;var d=h-j;var g=Math.floor(Math.sqrt(e*e+d*d)/f);var l=e/g;var k=d/g;var a;for(a=0;a<g;a++,c+=l,j+=k){if(a%2!==0){continue}this.fillRect(c,j,f,1)}};CanvasRenderingContext2D.prototype.drawDownwardEquilateralTriangle=function(b,a,e){var d=b-e/2,c=b+e/2,f=a-Math.sqrt(e*3/2);this.beginPath();this.moveTo(d,f);this.lineTo(c,f);this.lineTo(b,a);this.lineTo(d,f);this.strokeStyle=this.fillStyle;this.fill();this.stroke();this.closePath()};function sortable(a,b){a.bind("drag",{handle:b,relative:true},function(h,j){var g=$(this).parent();var f=g.children();var c;for(c=0;c<f.length;c++){if(j.offsetY<$(f.get(c)).position().top){break}}if(c===f.length){if(this!==f.get(c-1)){g.append(this)}}else{if(this!==f.get(c)){$(this).insertBefore(f.get(c))}}})}var NO_OVERLAP=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005;function compute_overlap(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=NO_OVERLAP}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=NO_OVERLAP}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a}function is_overlap(b,a){return(compute_overlap(b,a)!==NO_OVERLAP)}var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=1,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,ERROR_PADDING=10,LABEL_SPACING=2,PACK_SPACING=5,MIN_SQUISH_VIEW_WIDTH=12000,DEFAULT_FONT="9px Monaco, Lucida Console, monospace",DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,MAX_CHROMS_SELECTABLE=100,CONNECTOR_COLOR="#ccc",DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_CANNOT_RUN_TOOL="Tool cannot be rerun: ",DATA_LOADING="Loading data...",DATA_OK="Ready for display",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=5,CACHED_DATA=5,DUMMY_CANVAS=document.createElement("canvas"),RIGHT_STRAND,LEFT_STRAND;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(DUMMY_CANVAS)}var CONTEXT=DUMMY_CANVAS.getContext("2d");CONTEXT.font=DEFAULT_FONT;var CHAR_WIDTH_PX=CONTEXT.measureText("A").width,CHAR_HEIGHT_PX=9;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!==-1){this.move_key_to_end(b,a)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},move_key_to_end:function(b,a){this.key_ary.splice(a,1);this.key_ary.push(b)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var DataManager=function(b,a){Cache.call(this,b);this.track=a};$.extend(DataManager.prototype,Cache.prototype,{load_data:function(d,a,f,h,b,e){var g={chrom:d,low:a,high:f,mode:h,resolution:b,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(g,e);var c=this;return $.getJSON(this.track.data_url,g,function(j){c.set_data(a,f,h,j)})},get_data:function(j,k,c,h,b,f){var l=this.get(this.gen_key(k,c,h));if(l){return l}var m,g,a,e,h,l;for(var d=0;d<this.key_ary.length;d++){m=this.key_ary[d];g=this.split_key(m);a=g[0];e=g[1];if(k>=a&&c<=e){l=this.obj_cache[m];if(l.dataset_type!=="summary_tree"&&l.extra_info!=="no_detail"){this.move_key_to_end(m,d);return l}}}return this.load_data(j,k,c,h,b,f)},set_data:function(b,c,d,a){return this.set(this.gen_key(b,c,d),a)},gen_key:function(a,c,d){var b=a+"_"+c+"_"+d;return b},split_key:function(a){return a.split("_")}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.extend(View.prototype,{init:function(d){var c=this.container,a=this;this.top_container=$("<div/>").addClass("top-container").appendTo(c);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(c);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(c);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var b=function(f){if(f.type==="focusout"||(f.keyCode||f.which)===13||(f.keyCode||f.which)===27){if((f.keyCode||f.which)!==27){a.go_to($(this).val())}$(this).hide();$(this).val("");a.location_span.show();a.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",b).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.val(a.chrom+":"+a.low+"-"+a.high);a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},d);this.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f,g){this.current_x=g.offsetX}).bind("drag",function(f,h){var j=h.offsetX-this.current_x;this.current_x=h.offsetX;var g=Math.round(j/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(f,g){if(f.clientX>a.viewport_container.width()-16){return false}}).bind("dragstart",function(f,g){g.original_low=a.low;g.current_height=f.clientY;g.current_x=g.offsetX}).bind("drag",function(h,k){var f=$(this);var l=k.offsetX-k.current_x;var g=f.scrollTop()-(h.clientY-k.current_height);f.scrollTop(g);k.current_height=h.clientY;k.current_x=k.offsetX;var j=Math.round(l/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}).bind("mousewheel",function(h,k,g,f){if(g){var j=Math.round(-g/a.viewport_container.width()*(a.high-a.low));a.move_delta(j)}});this.top_labeltrack.bind("dragstart",function(f,g){return $("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(k,l){$(l.proxy).css({left:Math.min(k.pageX,l.startX),width:Math.abs(k.pageX-l.startX)});var g=Math.min(k.pageX,l.startX)-a.container.offset().left,f=Math.max(k.pageX,l.startX)-a.container.offset().left,j=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*j)+a.low,Math.round(f/h*j)+a.low)}).bind("dragend",function(l,m){var g=Math.min(l.pageX,m.startX),f=Math.max(l.pageX,m.startX),j=(a.high-a.low),h=a.viewport_container.width(),k=a.low;a.low=Math.round(g/h*j)+k;a.high=Math.round(f/h*j)+k;$(m.proxy).remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(window).bind("resize",function(){a.resize_window()});$(document).bind("redraw",function(){a.redraw()});this.reset();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},load_chroms:function(b,c){b.num=MAX_CHROMS_SELECTABLE;$.extend(b,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var a=this;$.ajax({url:chrom_url,data:b,dataType:"json",success:function(e){if(e.chrom_info.length===0){alert("Invalid chromosome: "+b.chrom);return}if(e.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=e.chrom_info;var h='<option value="">Select Chrom/Contig</option>';for(var g=0,d=a.chrom_data.length;g<d;g++){var f=a.chrom_data[g].chrom;h+='<option value="'+f+'">'+f+"</option>"}if(e.prev_chroms){h+='<option value="previous">Previous '+MAX_CHROMS_SELECTABLE+"</option>"}if(e.next_chroms){h+='<option value="next">Next '+MAX_CHROMS_SELECTABLE+"</option>"}a.chrom_select.html(h);if(c){c()}a.chrom_start_index=e.start_index},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}})},change_chrom:function(e,b,g){if(!e||e==="None"){return}var d=this;if(e==="previous"){d.load_chroms({low:this.chrom_start_index-MAX_CHROMS_SELECTABLE});return}if(e==="next"){d.load_chroms({low:this.chrom_start_index+MAX_CHROMS_SELECTABLE});return}var f=$.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 b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);sortable(a.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(h){var g=this.high-this.low,f=this.low,b=this.high;if(f<this.max_low){f=this.max_low}if(b>this.max_high){b=this.max_high}if(this.high!==0&&g<this.min_separation){b=f+this.min_separation}this.low=Math.floor(f);this.high=Math.ceil(b);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));var a=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var e=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var j=13;this.overview_box.css({left:a,width:Math.max(j,e)}).show();if(e<j){this.overview_box.css("left",a-(j-e)/2)}if(this.overview_highlight){this.overview_highlight.css({left:a,width:e})}this.update_location(this.low,this.high);if(!h){for(var c=0,d=this.tracks.length;c<d;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(c=0,d=this.label_tracks.length;c<d;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide()}});var Tool=function(a,b){this.name=a;this.params=b};$.extend(Tool.prototype,{get_param_values_dict:function(){var b={};for(var a=0;a<this.params.length;a++){var c=this.params[a];b[c.name]=c.value}return b},get_param_values:function(){var b=[];for(var a=0;a<this.params.length;a++){b[a]=this.params[a].value}return b}});var NumberToolParameter=function(c,b,e,a,d){this.name=c;this.label=b;this.min=e;this.max=a;this.value=d};var get_tool_from_dict=function(f){if(obj_length(f)===0){return undefined}var b=f.name;var l=f.params;var c=Array();for(var e=0;e<l.length;e++){var g=l[e];var a=g.name,k=g.label,h=g.type,d=g.min,j=g.max,m=g.value;c[c.length]=new NumberToolParameter(a,k,d,j,m)}return new Tool(b,c)};var Filter=function(b,a,c){this.name=b;this.index=a;this.value=c};var NumberFilter=function(b,a){this.name=b;this.index=a;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.slider_min=Number.MAX_VALUE;this.slider_max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e==="int"||e==="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var TrackConfig=function(a){this.track=a.track;this.params=a.params;this.values={};if(a.saved_values){this.restore_values(a.saved_values)}this.onchange=a.onchange};$.extend(TrackConfig.prototype,{restore_values:function(a){var b=this;$.each(this.params,function(c,d){if(a[d.key]!==undefined){b.values[d.key]=a[d.key]}else{b.values[d.key]=d.default_value}})},build_form:function(){var b=this;var a=$("<div />");$.each(this.params,function(f,d){if(!d.hidden){var c="param_"+f;var l=$("<div class='form-row' />").appendTo(a);l.append($("<label />").attr("for",c).text(d.label+":"));if(d.type==="bool"){l.append($('<input type="checkbox" />').attr("id",c).attr("name",c).attr("checked",b.values[d.key]))}else{if(d.type==="color"){var h=b.values[d.key];var g=$("<input />").attr("id",c).attr("name",c).val(h);var j=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var e=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(j);var k=$("<div/>").appendTo(e).farbtastic({width:100,height:100,callback:g,color:h});$("<div />").append(g).append(j).appendTo(l).bind("click",function(m){j.css({left:$(this).position().left+($(g).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){j.hide();$(document).unbind("click.color-picker")});m.stopPropagation()})}else{l.append($("<input />").attr("id",c).attr("name",c).val(b.values[d.key]))}}}});return a},update_from_form:function(a){var c=this;var b=false;$.each(this.params,function(d,f){if(!f.hidden){var g="param_"+d;var e=a.find("#"+g).val();if(f.type==="float"){e=parseFloat(e)}else{if(f.type==="int"){e=parseInt(e)}else{if(f.type==="bool"){e=a.find("#"+g).is(":checked")}}}if(e!==c.values[f.key]){c.values[f.key]=e;b=true}}});if(b){this.onchange()}}});var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_url_extra_params={};this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<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,j,n){var c=this,o=c.view;this.filters=(b!==undefined?get_filters_from_dict(b):[]);this.filters_available=false;this.filters_visible=false;this.tool=(j!==undefined?get_tool_from_dict(j):undefined);this.parent_track=n;this.child_tracks=[];if(c.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filters_div=$("<div/>").addClass("filters").hide();this.header_div.after(this.filters_div);this.filters_div.bind("drag",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});$.each(this.filters,function(t,w){var u=$("<div/>").addClass("slider-row").appendTo(c.filters_div);var v=$("<div/>").addClass("slider-label").appendTo(u);var s=$("<span/>").addClass("name").appendTo(v);s.text(w.name+" ");var r=$("<span/>").addClass("values").appendTo(v);var q=$("<div/>").addClass("slider").appendTo(u);w.control_element=$("<div/>").attr("id",w.name+"-filter-control").appendTo(q);w.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(y,z){var x=z.values;r.text("["+x[0]+"-"+x[1]+"]");w.low=x[0];w.high=x[1];c.draw(true,true)},change:function(x,y){w.control_element.slider("option","slide").call(w.control_element,x,y)}});w.slider=w.control_element;w.slider_label=r;$("<div style='clear: both;'/>").appendTo(u)});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(q){q.stopPropagation()}).bind("click",function(q){q.stopPropagation()}).bind("dblclick",function(q){q.stopPropagation()});var m=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var l=this.tool.params;var c=this;$.each(this.tool.params,function(x,s){var v=$("<div>").addClass("slider-row").appendTo(c.dynamic_tool_div);var u=$("<div>").addClass("slider-label").appendTo(v);var z=$("<span class='param-name'>").text(s.label+" ").appendTo(u);var t=$("<span/>").text(s.value);var w=$("<span class='param-value'>").appendTo(u).append("[").append(t).append("]");var y=$("<div/>").addClass("slider").appendTo(v);var q=$("<div id='"+s.name+"-param-control'>").appendTo(y);var r=(s.max<=1?0.01:(s.max<=1000?1:5));q.slider({min:s.min,max:s.max,step:r,value:s.value,slide:function(A,C){var B=C.value;s.value=B;if(0<B&&B<1){B=parseFloat(B).toFixed(2)}t.text(B)},change:function(A,B){s.value=B.value}});w.click(function(){var C=t,B=C.text(),A=(s.max<=1?4:s.max.length);C.text("");$("<input type='text'/>").attr("size",A).attr("maxlength",A).attr("value",B).appendTo(C).focus().select().click(function(D){D.stopPropagation()}).blur(function(){$(this).remove();C.text(B)}).keyup(function(F){if(F.keyCode===27){$(this).trigger("blur")}else{if(F.keyCode===13){var D=$(this),E=parseFloat(D.val());if(isNaN(E)||E>s.max||E<s.min){alert("Parameter value must be in the range ["+s.min+"-"+s.max+"]");return $(this)}C.text(E);q.slider("value",E);s.value=E}}})});$("<div style='clear: both;'/>").appendTo(v)});var p=$("<div>").addClass("slider-row").appendTo(this.dynamic_tool_div);var k=$("<input type='submit'>").attr("value","Run").appendTo(p);var c=this;k.click(function(){c.run_tool()})}c.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();c.container_div.append(c.child_tracks_container);if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_div);var e=(c.track_config&&c.track_config.values.mode?c.track_config.values.mode:c.display_modes[0]);c.mode=e;c.mode_div.text(e);var d=function(q){c.mode_div.text(q);c.mode=q;c.track_config.values.mode=q;c.tile_cache.clear();c.draw()};var a={};for(var f=0,h=c.display_modes.length;f<h;f++){var g=c.display_modes[f];a[g]=function(q){return function(){d(q)}}(g)}make_popupmenu(c.mode_div,a)}else{c.mode_div.hide()}}this.make_name_popup_menu()};$.extend(TiledTrack.prototype,Track.prototype,{make_name_popup_menu:function(){var b=this;var a={};a["Edit configuration"]=function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){b.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(j){if((j.keyCode||j.which)===27){h()}else{if((j.keyCode||j.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);show_modal("Configure Track",b.track_config.build_form(),{Cancel:h,OK:f})};if(b.filters_available>0){var e=(b.filters_div.is(":visible")?"Hide filters":"Show filters");a[e]=function(){b.filters_visible=(b.filters_div.is(":visible"));b.filters_div.toggle();b.make_name_popup_menu()}}if(b.tool){var e=(b.dynamic_tool_div.is(":visible")?"Hide Tool":"Show Tool");a[e]=function(){if(!b.dynamic_tool_div.is(":visible")){b.update_name(b.name+b.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";b.revert_name()}b.dynamic_tool_div.toggle();b.make_name_popup_menu()}}if(b.track_type=="ReadTrack"){var e=(b.show_insertions?"Hide Insertions":"Show Insertions");a[e]=function(){b.show_insertions=!b.show_insertions;b.draw(true);b.make_name_popup_menu()}}if(b.valid_chroms){a["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+b.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var c=view;var d=function(){$("#no-tracks").show()};if(this.parent_track){c=this.parent_track;d=function(){}}a.Remove=function(){c.remove_track(b);if(c.num_tracks===0){d()}};make_popupmenu(b.name_div,a)},draw:function(a,d){console.log(this.name,a,d);var s=this.view.low,g=this.view.high,j=g-s,l=this.view.container.width(),m=this.view.resolution;var e=$("<div style='position: relative;'></div>"),f=l/j;if(!d){this.content_div.children().remove()}this.content_div.append(e);this.max_height=0;var o=Math.floor(s/m/DENSITY);var c={};while((o*DENSITY*m)<g){var r=l+"_"+f+"_"+o;var h=this.tile_cache.get(r);var p=o*DENSITY*this.view.resolution;var b=p+DENSITY*this.view.resolution;if(!a&&h){this.show_tile(h,e,p,f)}else{this.delayed_draw(a,r,p,b,o,m,e,f,c)}o+=1}if(d){var k=this;var q=setInterval(function(){if(obj_length(c)===0){var v=k.content_div.children();var u=false;for(var w=v.length-1,t=0;w>=t;w--){var x=$(v[w]);if(u){x.remove()}else{if(x.children().length!==0){u=true}}}clearInterval(q)}},50)}for(var n=0;n<this.child_tracks.length;n++){this.child_tracks[n].draw(a,d)}},delayed_draw:function(b,j,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(){result=d.data_cache.get_data(view.chrom,g,l,d.mode,e,d.data_url_extra_params);if(view.reference_track&&m>CHAR_WIDTH_PX){$.when(view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params)).then(function(){seq_data=view.reference_track.data_cache.get_data(view.chrom,g,l,d.mode,e,view.reference_track.data_url_extra_params);h(a,result,e,c,k,m,seq_data)})}else{h(a,result,e,c,k,m)}})}}},50);f[a]=true},show_tile:function(h,j,e,k){var a=this;var c=this.view.high-this.view.low,b=(e-this.view.low)*k;if(this.left_offset){b-=this.left_offset}h.css({position:"absolute",top:0,left:b,height:""});j.append(h);a.max_height=Math.max(a.max_height,h.height());a.content_div.css("height",a.max_height+"px");j.children().css("height",a.max_height+"px");if(a.hidden){return}for(var g=0;g<a.filters.length;g++){a.filters[g].update_ui_elt()}var d=false;if(a.example_feature){for(var g=0;g<a.filters.length;g++){if(a.filters[g].applies_to(a.example_feature)){d=true;break}}}if(a.filters_available!==d){a.filters_available=d;if(!a.filters_available){a.filters_div.hide()}a.make_name_popup_menu()}},set_overview:function(){var a=this.view;if(this.initial_canvas&&this.is_overview){a.overview_close.show();a.overview_viewport.append(this.initial_canvas);a.overview_highlight.show().height(this.initial_canvas.height());a.overview_viewport.height(this.initial_canvas.height()+a.overview_box.height())}$(window).trigger("resize")},run_tool:function(){var b={dataset_id:this.original_dataset_id,chrom:this.view.chrom,low:this.view.low,high:this.view.high,tool_id:this.tool.name};$.extend(b,this.tool.get_param_values_dict());var d=this,c=b.tool_id+d.tool_region_and_parameters_str(b.chrom,b.low,b.high),e;if(d.track_type==="FeatureTrack"){e=new ToolDataFeatureTrack(c,view,d.hda_ldda,undefined,{},{},d)}this.add_track(e);e.content_div.text("Starting job.");view.has_changes=true;var a=function(){$.getJSON(run_tool_url,b,function(f){if(f==="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f.error){e.container_div.addClass("error");e.content_div.text(DATA_CANNOT_RUN_TOOL+f.message)}else{if(f==="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!==undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"},add_track:function(a){a.track_id=this.track_id+"_"+this.child_tracks.length;a.container_div.attr("id","track_"+a.track_id);this.child_tracks_container.append(a.container_div);sortable(a.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()})}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.view.container.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";this.hidden=true;Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);a.reference_track=this;this.left_offset=200;this.height_px=12;this.font=DEFAULT_FONT;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:a.dbkey};this.data_cache=new DataManager(CACHED_DATA,this);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.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=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var l=e.get(0).getContext("2d");e.get(0).width=Math.ceil(d*n+f.left_offset);e.get(0).height=f.height_px;l.font=DEFAULT_FONT;l.textAlign="center";for(var h=0,k=m.length;h<k;h++){var a=Math.round(h*n);l.fillText(m[h],a+f.left_offset,10)}return e}this.content_div.css("height","0px")}});var LineTrack=function(e,c,f,a,d){var b=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,e,c,c.viewport_container);TiledTrack.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=f;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new DataManager(CACHED_DATA,this);this.tile_cache=new Cache(CACHED_TILES_LINE);this.track_config=new TrackConfig({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:d,onchange:function(){b.vertical_range=b.prefs.max_value-b.prefs.min_value;$("#linetrack_"+b.track_id+"_minval").text(b.prefs.min_value);$("#linetrack_"+b.track_id+"_maxval").text(b.prefs.max_value);b.tile_cache.clear();b.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;(function(g){var k=false;var j=false;var h=$("<div class='track-resize'>");$(g.container_div).hover(function(){k=true;h.show()},function(){k=false;if(!j){h.hide()}});h.hide().bind("dragstart",function(l,m){j=true;m.original_height=$(g.content_div).height()}).bind("drag",function(m,n){var l=Math.min(Math.max(n.original_height+n.deltaY,g.min_height_px),g.max_height_px);$(g.content_div).css("height",l);g.height_px=l;g.draw(true)}).bind("dragend",function(l,m){g.tile_cache.clear();j=false;if(!k){h.hide()}g.track_config.values.height=g.height_px}).appendTo(g.container_div)})(this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{predraw_init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;return $.getJSON(a.data_url,{stats:true,chrom:a.view.chrom,low:null,high:null,hda_ldda:a.hda_ldda,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");var e=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=e.min;a.prefs.max_value=e.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=e.total_frequency;a.container_div.find(".yaxislabel").remove();var f=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"absolute",top:"24px",left:"10px"});d.prependTo(a.container_div);f.css({position:"absolute",bottom:"2px",left:"10px"});f.prependTo(a.container_div)})},draw_tile:function(j,q,t,c,e){if(this.vertical_range===undefined){return}var o=this,u=t*DENSITY*q,a=DENSITY*q,B=q+"_"+t,v={hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,resolution:this.view.resolution};var b=document.createElement("canvas"),z=j.data;if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);b.get(0).width=Math.ceil(a*e);b.get(0).height=o.height_px;var p=b.get(0).getContext("2d"),k=false,l=o.prefs.min_value,g=o.prefs.max_value,n=o.vertical_range,w=o.total_frequency,d=o.height_px,m=o.mode;var A=Math.round(d+l/n*d);p.beginPath();p.moveTo(0,A);p.lineTo(a*e,A);p.fillStyle="#aaa";p.stroke();p.beginPath();p.fillStyle=o.prefs.color;var x,h,f;if(z.length>1){f=Math.ceil((z[1][0]-z[0][0])*e)}else{f=10}for(var r=0,s=z.length;r<s;r++){x=Math.round((z[r][0]-u)*e);h=z[r][1];if(h===null){if(k&&m==="Filled"){p.lineTo(x,d)}k=false;continue}if(h<l){h=l}else{if(h>g){h=g}}if(m==="Histogram"){h=Math.round(h/n*d);p.fillRect(x,A,f,-h)}else{if(m==="Intensity"){h=255-Math.floor((h-l)/n*255);p.fillStyle="rgb("+h+","+h+","+h+")";p.fillRect(x,0,f,d)}else{h=Math.round(d-(h-l)/n*d);if(k){p.lineTo(x,h)}else{k=true;if(m==="Filled"){p.moveTo(x,d);p.lineTo(x,h)}else{p.moveTo(x,h)}}}}}if(m==="Filled"){if(k){p.lineTo(x,A);p.lineTo(0,A)}p.fill()}else{p.stroke()}return b}});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};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{incremental_slots:function(a,h,p){var q=this.inc_slots[a];if(!q||(q.mode!==p)){q={};q.w_scale=a;q.mode=p;this.inc_slots[a]=q;this.start_end_dct[a]={}}var l=q.w_scale,w=[],x=[],j=0,n=this.view.max_low;for(var u=0,v=h.length;u<v;u++){var g=h[u],k=g[0];if(q[k]!==undefined){j=Math.max(j,q[k]);x.push(q[k])}else{w.push(u)}}var d=this.start_end_dct[a];var m=function(D,E){for(var C=0;C<=MAX_FEATURE_DEPTH;C++){var A=false,F=d[C];if(F!==undefined){for(var z=0,B=F.length;z<B;z++){var y=F[z];if(E>y[0]&&D<y[1]){A=true;break}}}if(!A){return C}}return -1};for(var u=0,v=w.length;u<v;u++){var g=h[w[u]],k=g[0],s=g[1],b=g[2],o=g[3],c=Math.floor((s-n)*l),f=Math.ceil((b-n)*l),t=CONTEXT.measureText(o).width,e;if(o!==undefined&&p==="Pack"){t+=(LABEL_SPACING+PACK_SPACING);if(c-t>=0){c-=t;e="left"}else{f+=t;e="right"}}var r=m(c,f);if(r>=0){if(d[r]===undefined){d[r]=[]}d[r].push([c,f]);q[k]=r;j=Math.max(j,r)}else{}}return j+1},draw_summary_tree:function(b,o,n,l,r,j,f,e){var c=j+LABEL_SPACING+CHAR_HEIGHT_PX;delta_x_px=Math.ceil(n*r);var h=$("<div />").addClass("yaxislabel");h.text(l);h.css({position:"absolute",top:"22px",left:"10px"});h.prependTo(this.container_div);var q=b.get(0).getContext("2d");for(var d=0,g=o.length;d<g;d++){var m=Math.floor((o[d][0]-f)*r);var k=o[d][1];if(!k){continue}var p=k/l*j;q.fillStyle="black";q.fillRect(m+e,c-p,delta_x_px,p);var a=4;if(this.prefs.show_counts&&(q.measureText(k).width+a)<delta_x_px){q.fillStyle="#666";q.textAlign="center";q.fillText(k,m+e+(delta_x_px/2),10)}}},draw_element:function(p,f,g,x,j,r,I,M,N,a,A){var u=x[0],K=x[1],C=x[2]-1,s=x[3],D=Math.floor(Math.max(0,(K-r)*M)),q=Math.ceil(Math.min(a,Math.max(0,(C-r)*M))),B=ERROR_PADDING+(g==="Dense"?0:(0+j))*N,o,G,t=null,O=null,d=this.prefs.block_color,F=this.prefs.label_color;if(g==="Dense"){p.fillStyle=d;p.fillRect(D+A,B,q-D,DENSE_FEATURE_HEIGHT)}else{if(g==="no_detail"){p.fillStyle=d;p.fillRect(D+A,B+5,q-D,DENSE_FEATURE_HEIGHT)}else{var n=x[5],z=x[6],E=x[7],e=x[8];if(z&&E){t=Math.floor(Math.max(0,(z-r)*M));O=Math.ceil(Math.min(a,Math.max(0,(E-r)*M)))}var L,v;if(g==="Squish"){L=1;v=SQUISH_FEATURE_HEIGHT}else{L=5;v=PACK_FEATURE_HEIGHT}if(!e){if(x.strand){if(x.strand==="+"){p.fillStyle=RIGHT_STRAND_INV}else{if(x.strand==="-"){p.fillStyle=LEFT_STRAND_INV}}}else{p.fillStyle=d}p.fillRect(D+A,B,q-D,v)}else{var m,w;if(g==="Squish"){p.fillStyle=CONNECTOR_COLOR;m=B+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;w=1}else{if(n){var m=B;var w=v;if(n==="+"){p.fillStyle=RIGHT_STRAND}else{if(n==="-"){p.fillStyle=LEFT_STRAND}}}else{p.fillStyle=CONNECTOR_COLOR;m+=(SQUISH_FEATURE_HEIGHT/2)+1;w=1}}p.fillRect(D+A,m,q-D,w);for(var J=0,c=e.length;J<c;J++){var h=e[J],b=Math.floor(Math.max(0,(h[0]-r)*M)),y=Math.ceil(Math.min(a,Math.max((h[1]-1-r)*M)));if(b>y){continue}p.fillStyle=d;p.fillRect(b+A,B+(v-L)/2+1,y-b,L);if(t!==undefined&&!(b>O||y<t)){var H=Math.max(b,t),l=Math.min(y,O);p.fillRect(H+A,B+1,l-H,v)}}}if(g==="Pack"&&K>r){p.fillStyle=F;if(f===0&&D-p.measureText(s).width<0){p.textAlign="left";p.fillText(s,q+A+LABEL_SPACING,B+8)}else{p.textAlign="right";p.fillText(s,D+A-LABEL_SPACING,B+8)}p.fillStyle=d}}}},get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="no_detail"){a=NO_DETAIL_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT}}}return a},draw_tile:function(o,x,C,k,m,d){var t=this;var E=C*DENSITY*x,a=(C+1)*DENSITY*x,q=a-E,F={hda_ldda:t.hda_ldda,dataset_id:t.dataset_id,resolution:this.view.resolution,mode:this.mode};var v=Math.ceil(q*m),s=this.mode,H=25,g=this.left_offset,p,h;var c=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(c)}c=$(c);if(s==="Auto"){if(o.dataset_type==="summary_tree"){s=o.dataset_type}else{if(o.extra_info==="no_detail"){s="no_detail"}else{var G=o.data;if((G.length&&G.length<4)||(this.view.high-this.view.low>MIN_SQUISH_VIEW_WIDTH)){s="Squish"}else{s="Pack"}}}}var y=this.get_y_scale(s);if(s==="summary_tree"){h=this.summary_draw_height}if(s==="Dense"){h=H}else{if(s==="no_detail"||s==="Squish"||s==="Pack"){h=this.incremental_slots(m,o.data,s)*y+H;p=this.inc_slots[m]}}c.get(0).width=v+g;c.get(0).height=h;if(o.dataset_type==="summary_tree"){c.get(0).height+=LABEL_SPACING+CHAR_HEIGHT_PX}k.parent().css("height",Math.max(this.height_px,h)+"px");var w=c.get(0).getContext("2d");w.fillStyle=this.prefs.block_color;w.font=this.default_font;w.textAlign="right";this.container_div.find(".yaxislabel").remove();if(s==="summary_tree"){this.draw_summary_tree(c,o.data,o.delta,o.max,m,h,E,g);return c}if(o.message){c.css({"border-top":"1px solid red"});w.fillStyle="red";w.textAlign="left";var r=w.textBaseline;w.textBaseline="top";w.fillText(o.message,g,0);w.textBaseline=r;if(!o.data){return c}}this.example_feature=(o.data.length?o.data[0]:undefined);var G=o.data;for(var z=0,B=G.length;z<B;z++){var j=G[z],l=j[0],u=j[1],b=j[2],e=(p&&p[l]!==undefined?p[l]:null);var A=false;var n;for(var D=0;D<this.filters.length;D++){n=this.filters[D];n.update_attrs(j);if(!n.keep(j)){A=true;break}}if(A){continue}if(is_overlap([u,b],[E,a])&&(s=="Dense"||e!==null)){this.draw_element(w,C,s,j,e,E,a,m,y,v,g,d)}}return c}});var VcfTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="VcfTrack"};$.extend(VcfTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{draw_element:function(u,p,j,e,x,c,m,v,s){var j=data[i],l=j[0],t=j[1],d=j[2]-1,o=j[3],g=Math.floor(Math.max(0,(t-x)*m)),k=Math.ceil(Math.min(s,Math.max(0,(d-x)*m))),f=ERROR_PADDING+(p==="Dense"?0:(0+e))*v,a,y,b=null,n=null;if(no_label){u.fillStyle=block_color;u.fillRect(g+left_offset,f+5,k-g,1)}else{var w=j[4],r=j[5],h=j[6];a=9;y=1;u.fillRect(g+left_offset,f,k-g,a);if(p!=="Dense"&&o!==undefined&&t>x){u.fillStyle=label_color;if(tile_index===0&&g-u.measureText(o).width<0){u.textAlign="left";u.fillText(o,k+2+left_offset,f+8)}else{u.textAlign="right";u.fillText(o,g-2+left_offset,f+8)}u.fillStyle=block_color}var q=w+" / "+r;if(t>x&&u.measureText(q).width<(k-g)){u.fillStyle="white";u.textAlign="center";u.fillText(q,left_offset+g+(k-g)/2,f+8);u.fillStyle=block_color}}}});var ReadTrack=function(d,b,f,a,c,e){FeatureTrack.call(this,d,b,f,a,c,e);this.track_type="ReadTrack";this.difference_mode=true;this.show_insertions=false;this.make_name_popup_menu()};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{get_y_scale:function(b){var a;if(b==="summary_tree"){}if(b==="Dense"){a=DENSE_TRACK_HEIGHT}else{if(b==="Squish"){a=SQUISH_TRACK_HEIGHT}else{a=PACK_TRACK_HEIGHT;if(this.show_insertions){a*=2}}}return a},draw_read:function(m,d,J,n,D,G,e,o,y,a){m.textAlign="center";var l=this,u=[n,D],C=0,z=0,f=0;var r=[];if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){f=Math.ceil(CHAR_WIDTH_PX/2+1)}if(!e){e=[[0,o.length]]}for(var h=0,k=e.length;h<k;h++){var b=e[h],g="MIDNSHP=X"[b[0]],v=b[1];if(g==="H"||g==="S"){C-=v}var x=G+C,B=Math.floor(Math.max(0,(x-n)*J)),E=Math.floor(Math.max(0,(x+v-n)*J));switch(g){case"H":break;case"S":case"M":case"=":var p=compute_overlap([x,x+v],u);if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(f>0){m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset-f,y+1,E-B,9);m.fillStyle=CONNECTOR_COLOR;for(var I=0,j=q.length;I<j;I++){if(this.difference_mode&&a){var s=a[x-n+I];if(!s||s.toLowerCase()===q[I].toLowerCase()){continue}}if(x+I>=n&&x+I<=D){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset,y+9)}}}else{m.fillStyle=this.prefs.block_color;m.fillRect(B+this.left_offset,y+(this.mode!=="Dense"?4:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}z+=v;C+=v;break;case"N":m.fillStyle=CONNECTOR_COLOR;m.fillRect(B+this.left_offset-f,y+5,E-B,1);C+=v;break;case"D":m.fillStyle="red";m.fillRect(B+this.left_offset-f,y+4,E-B,3);C+=v;break;case"P":break;case"I":var p=compute_overlap([x,x+v],u),K=this.left_offset+B-f;if(p!==NO_OVERLAP){var q=o.slice(z,z+v);if(this.show_insertions){var w=this.left_offset+B-(E-B)/2;if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){m.fillStyle="yellow";m.fillRect(w-f,y-9,E-B,9);r[r.length]={type:"triangle",data:[K,y+4,5]};m.fillStyle=CONNECTOR_COLOR;switch(p){case (OVERLAP_START):q=q.slice(n-x);break;case (OVERLAP_END):q=q.slice(0,x-D);break;case (CONTAINED_BY):break;case (CONTAINS):q=q.slice(n-x,x-D);break}for(var I=0,j=q.length;I<j;I++){var A=Math.floor(Math.max(0,(x+I-n)*J));m.fillText(q[I],A+this.left_offset-(E-B)/2,y)}}else{m.fillStyle="yellow";m.fillRect(w,y+(this.mode!=="Dense"?2:5),E-B,(d!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((d==="Pack"||this.mode==="Auto")&&o!==undefined&&J>CHAR_WIDTH_PX){r[r.length]={type:"text",data:[q.length,K,y+9]}}else{}}}z+=v;break;case"X":z+=v;break}}m.fillStyle="yellow";var t,L,H;for(var F=0;F<r.length;F++){t=r[F];L=t.type;H=t.data;if(L==="text"){m.font="bold "+DEFAULT_FONT;m.fillText(H[0],H[1],H[2]);m.font=DEFAULT_FONT}else{if(L=="triangle"){m.drawDownwardEquilateralTriangle(H[0],H[1],H[2])}}}},draw_element:function(w,y,r,k,e,A,b,n,x,u,f,c){var m=k[0],v=k[1],d=k[2],o=k[3],h=Math.floor(Math.max(0,(v-A)*n)),j=Math.ceil(Math.min(u,Math.max(0,(d-A)*n))),g=(r==="Dense"?1:(1+e))*x,z=this.prefs.block_color,l=this.prefs.label_color;t=0;w.fillStyle=z;if(k[5] instanceof Array){var s=Math.floor(Math.max(0,(k[4][0]-A)*n)),q=Math.ceil(Math.min(u,Math.max(0,(k[4][1]-A)*n))),p=Math.floor(Math.max(0,(k[5][0]-A)*n)),a=Math.ceil(Math.min(u,Math.max(0,(k[5][1]-A)*n)));if(k[4][1]>=A&&k[4][0]<=b&&k[4][2]){this.draw_read(w,r,n,A,b,k[4][0],k[4][2],k[4][3],g,c)}if(k[5][1]>=A&&k[5][0]<=b&&k[5][2]){this.draw_read(w,r,n,A,b,k[5][0],k[5][2],k[5][3],g,c)}if(p>q){w.fillStyle=CONNECTOR_COLOR;w.dashedLine(q+f,g+5,f+p,g+5)}}else{w.fillStyle=z;this.draw_read(w,r,n,A,b,v,k[4],k[5],g,c)}if(r==="Pack"&&v>A){w.fillStyle=this.prefs.label_color;if((r==="Pack"||this.mode==="Auto")&&n>CHAR_WIDTH_PX){var t=Math.round(n/2)}if(y===0&&h-w.measureText(o).width<0){w.textAlign="left";w.fillText(o,j+f+LABEL_SPACING-t,g+8)}else{w.textAlign="right";w.fillText(o,h+f-LABEL_SPACING-t,g+8)}w.fillStyle=z}}});var ToolDataFeatureTrack=function(e,c,g,a,d,f,b){FeatureTrack.call(this,e,c,g,a,d,f,{},b);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{predraw_init:function(){var b=this;var a=function(){if(b.data_cache.size()===0){setTimeout(a,300)}else{b.data_url=default_data_url;b.data_query_wait=DEFAULT_DATA_QUERY_WAIT;b.dataset_state_url=converted_datasets_state_url;$.getJSON(b.dataset_state_url,{dataset_id:b.dataset_id,hda_ldda:b.hda_ldda},function(c){})}};a()}}); \ No newline at end of file --- a/static/scripts/trackster.js Thu Mar 24 15:03:12 2011 -0400 +++ b/static/scripts/trackster.js Thu Mar 24 15:05:28 2011 -0400 @@ -243,13 +243,30 @@ }); /** - * Data-specific cache. + * Data manager for a track. */ -var DataCache = function(num_elements) { - Cache.call(this, num_elements); +var DataManager = function(num_elements, track) { + Cache.call(this, num_elements); + this.track = track; }; -$.extend(DataCache.prototype, Cache.prototype, { - get_data: function(low, high, mode) { +$.extend(DataManager.prototype, Cache.prototype, { + /** + * Load data from server; returns AJAX object so that use of Deferred is possible. + */ + load_data: function(chrom, low, high, mode, resolution, extra_params) { + var params = {"chrom": chrom, "low": low, "high": high, "mode": mode, + "resolution": resolution, "dataset_id" : this.track.dataset_id, + "hda_ldda": this.track.hda_ldda}; + $.extend(params, extra_params); + var manager = this; + return $.getJSON(this.track.data_url, params, function (result) { + manager.set_data(low, high, mode, result); + }); + }, + /** + * Get data and do callback. + */ + get_data: function(chrom, low, high, mode, resolution, extra_params) { // Debugging: //console.log("get_data", low, high, mode); /* @@ -259,7 +276,7 @@ } */ - // Look for key in cache and, if found, return it. + // Look for key in cache and, if found, do callback. var entry = this.get(this.gen_key(low, high, mode)); if (entry) { return entry; @@ -290,18 +307,25 @@ } } - return undefined; + // + // Load data from server. + // + return this.load_data(chrom, low, high, mode, resolution, extra_params); }, set_data: function(low, high, mode, result) { //console.log("set_data", low, high, mode, result); return this.set(this.gen_key(low, high, mode), result); }, - // Generate key for cache. + /** + * Generate key for cache. + */ gen_key: function(low, high, mode) { var key = low + "_" + high + "_" + mode; return key; }, - // Split key from cache into array with format [low, high, mode] + /** + * Split key from cache into array with format [low, high, mode] + */ split_key: function(key) { return key.split("_"); } @@ -1028,6 +1052,7 @@ this.view = view; this.parent_element = parent_element; this.data_url = (data_url ? data_url : default_data_url); + this.data_url_extra_params = {} this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT); this.dataset_check_url = converted_datasets_state_url; @@ -1496,45 +1521,12 @@ make_popupmenu(track.name_div, track_dropdown); }, - tile_data: function(resolution, tile_index, extra_params, callback, key) { - var track = this, - low = tile_index * DENSITY * resolution, - high = ( tile_index + 1 ) * DENSITY * resolution, - params = { "chrom": this.view.chrom, "low": low, "high": high, "dbkey": this.view.dbkey }; - - if (key === undefined) { - key = resolution + "_" + tile_index; - } - var cached = track.data_cache.get(key); - if (cached) { - return callback(cached); - } - $.extend(params, extra_params); - $.ajax({ 'url': this.data_url, 'dataType': 'json', 'data': params, - success: function (result) { - track.data_cache.set(key, result); - return callback(result); - }, error: function(r, t, e) { - console.log(r, t, e); - } - }); - }, /** * Draw track. It is possible to force a redraw rather than use cached tiles and/or clear old * tiles after drawing new tiles. - * - * NOTE/TODO: clear_after only works when no data needs to be loaded. Because tiles fetch their own - * data and then draw themselves, there's no way to determine when all track tiles have been drawn - * because a tile may be waiting on data or drawing itself and there is no way to track a tile's status - * when it requests data and subsequently draws itself. Without the ability to determine when - * a track has been drawn, clear_after may not clear old tiles because it may be called too soon and - * miss old tiles that are being/will be drawn over. - * - * This problem can be fixed by either (a) fetching the data before drawing tiles so that tile drawing - * status can be fully monitored; or (b) keeping a global dictionary of tiles being drawn and their - * status. (a) is probably the better approach. */ draw: function(force, clear_after) { + console.log(this.name, force, clear_after); var low = this.view.low, high = this.view.high, range = high - low, @@ -1544,9 +1536,7 @@ var parent_element = $("<div style='position: relative;'></div>"), w_scale = width / range; - if (!clear_after) { - this.content_div.children().remove(); - } + if (!clear_after) { this.content_div.children().remove(); } this.content_div.append( parent_element ); this.max_height = 0; // Index of first tile that overlaps visible region @@ -1571,7 +1561,7 @@ } // - // Actions to take after new tiles have been loaded/drawn: + // Actions to take after tiles have been drawn: // (1) remove old tile(s); // (2) update filtering UI elements. // @@ -1612,44 +1602,66 @@ delayed_draw: function(force, key, tile_low, tile_high, tile_index, resolution, parent_element, w_scale, draw_tile_dict) { var track = this; // Put a 50ms delay on drawing so that if the user scrolls fast, we don't load extra data - var draw_tile = function(tile_element) { + var draw_and_show_tile = function(id, result, resolution, tile_index, parent_element, w_scale, seq_data) { + returned_tile = track.draw_tile(result, resolution, tile_index, parent_element, w_scale, seq_data) + + // Wrap element in div for background + var wrapper_element = $("<div class='track-tile'>").prepend(returned_tile); + tile_element = wrapper_element; + track.tile_cache.set(key, tile_element); track.show_tile(tile_element, parent_element, tile_low, w_scale); + + // TODO: this should go in a post-draw function. + // Store initial canvas in case we need to use it for overview + /* This is completely broken, just saves the first tile it sees + regardless of if it should be the overview + if (!track.initial_canvas && !window.G_vmlCanvasManager) { + track.initial_canvas = $(tile_element).clone(); + var src_ctx = tile_element.get(0).getContext("2d"); + var tgt_ctx = track.initial_canvas.get(0).getContext("2d"); + var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); + tgt_ctx.putImageData(data, 0, 0); + track.set_overview(); + } + */ + + delete draw_tile_dict[id]; }; var id = setTimeout(function() { if (tile_low <= track.view.high && tile_high >= track.view.low) { // Show/draw tile: check cache for tile; if tile not in cache, draw it. - var tile_element; - if (!force) { - tile_element = track.tile_cache.get(key); + var tile_element = (force ? undefined : track.tile_cache.get(key)); + if (tile_element) { + track.show_tile(tile_element, parent_element, tile_low, w_scale); + delete draw_tile_dict[id]; } - if (!tile_element) { - track.draw_tile(resolution, tile_index, parent_element, w_scale, function(returned_tile) { - if ( returned_tile ) { - // Wrap element in div for background - var wrapper_element = $("<div class='track-tile'>").prepend( returned_tile ); - tile_element = wrapper_element; + else { + // + // Really draw tile: get data, seq data if available, and draw tile. + // + $.when(track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, + resolution, track.data_url_extra_params)).then(function() { + // Data available for track. + result = track.data_cache.get_data(view.chrom, tile_low, tile_high, track.mode, + resolution, track.data_url_extra_params); + // If sequence data needed, get that and draw. Otherwise draw. + if (view.reference_track && w_scale > CHAR_WIDTH_PX) { + $.when(view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, + track.mode, resolution, + view.reference_track.data_url_extra_params)).then(function() { + seq_data = view.reference_track.data_cache.get_data(view.chrom, tile_low, tile_high, + track.mode, resolution, + view.reference_track.data_url_extra_params); + draw_and_show_tile(id, result, resolution, tile_index, parent_element, w_scale, seq_data); + }); } - draw_tile(tile_element); - }); - } - if (tile_element) { - // Store initial canvas in case we need to use it for overview - /* This is completely broken, just saves the first tile it sees - regardless of if it should be the overview - if (!track.initial_canvas && !window.G_vmlCanvasManager) { - track.initial_canvas = $(tile_element).clone(); - var src_ctx = tile_element.get(0).getContext("2d"); - var tgt_ctx = track.initial_canvas.get(0).getContext("2d"); - var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); - tgt_ctx.putImageData(data, 0, 0); - track.set_overview(); - } - */ - draw_tile(tile_element); + else { + draw_and_show_tile(id, result, resolution, tile_index, parent_element, w_scale); + } + }); } } - delete draw_tile_dict[id]; }, 50); draw_tile_dict[id] = true; }, @@ -1846,8 +1858,8 @@ var ReferenceTrack = function (view) { this.track_type = "ReferenceTrack"; this.hidden = true; - Track.call( this, null, view, view.top_labeltrack ); - TiledTrack.call( this ); + Track.call(this, null, view, view.top_labeltrack); + TiledTrack.call(this); view.reference_track = this; this.left_offset = 200; @@ -1858,42 +1870,43 @@ this.content_div.css("min-height", "0px"); this.content_div.css("border", "none"); this.data_url = reference_url; - this.data_cache = new DataCache(CACHED_DATA); + this.data_url_extra_params = {dbkey: view.dbkey}; + this.data_cache = new DataManager(CACHED_DATA, this); this.tile_cache = new Cache(CACHED_TILES_LINE); }; -$.extend( ReferenceTrack.prototype, TiledTrack.prototype, { - draw_tile: function( resolution, tile_index, parent_element, w_scale, callback ) { +$.extend(ReferenceTrack.prototype, TiledTrack.prototype, { + /** + * Draw ReferenceTrack tile. + */ + draw_tile: function(seq, resolution, tile_index, parent_element, w_scale) { var track = this, tile_length = DENSITY * resolution; if (w_scale > CHAR_WIDTH_PX) { - track.tile_data(resolution, tile_index, {}, function(seq) { - if (seq === null) { - track.content_div.css("height", "0px"); - return; - } - var canvas = document.createElement("canvas"); - if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } // EXCANVAS HACK - canvas = $(canvas); + if (seq === null) { + track.content_div.css("height", "0px"); + return; + } + var canvas = document.createElement("canvas"); + if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } // EXCANVAS HACK + canvas = $(canvas); - var ctx = canvas.get(0).getContext("2d"); - canvas.get(0).width = Math.ceil( tile_length * w_scale + track.left_offset); - canvas.get(0).height = track.height_px; - ctx.font = DEFAULT_FONT; - ctx.textAlign = "center"; - for (var c = 0, str_len = seq.length; c < str_len; c++) { - var c_start = Math.round(c * w_scale); - ctx.fillText(seq[c], c_start + track.left_offset, 10); - } - // parent_element.append(canvas); - return callback(canvas); - }); + var ctx = canvas.get(0).getContext("2d"); + canvas.get(0).width = Math.ceil( tile_length * w_scale + track.left_offset); + canvas.get(0).height = track.height_px; + ctx.font = DEFAULT_FONT; + ctx.textAlign = "center"; + for (var c = 0, str_len = seq.length; c < str_len; c++) { + var c_start = Math.round(c * w_scale); + ctx.fillText(seq[c], c_start + track.left_offset, 10); + } + return canvas; } this.content_div.css("height", "0px"); } }); -var LineTrack = function ( name, view, hda_ldda, dataset_id, prefs ) { +var LineTrack = function (name, view, hda_ldda, dataset_id, prefs) { var track = this; this.track_type = "LineTrack"; this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; @@ -1907,7 +1920,7 @@ this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; - this.data_cache = new DataCache(CACHED_DATA); + this.data_cache = new DataManager(CACHED_DATA, this); this.tile_cache = new Cache(CACHED_TILES_LINE); // Define track configuration @@ -1968,7 +1981,7 @@ }).appendTo( track.container_div ); })(this); }; -$.extend( LineTrack.prototype, TiledTrack.prototype, { +$.extend(LineTrack.prototype, TiledTrack.prototype, { predraw_init: function() { var track = this, track_id = track.view.tracks.indexOf(track); @@ -2001,7 +2014,10 @@ min_label.prependTo(track.container_div); }); }, - draw_tile: function( resolution, tile_index, parent_element, w_scale, callback ) { + /** + * Draw LineTrack tile. + */ + draw_tile: function(result, resolution, tile_index, parent_element, w_scale) { if (this.vertical_range === undefined) { return; } @@ -2012,94 +2028,93 @@ key = resolution + "_" + tile_index, params = { hda_ldda: this.hda_ldda, dataset_id: this.dataset_id, resolution: this.view.resolution }; - this.tile_data(resolution, tile_index, params, function(result) { - var canvas = document.createElement("canvas"), - data = result.data; - if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } // EXCANVAS HACK - canvas = $(canvas); - canvas.get(0).width = Math.ceil( tile_length * w_scale ); - canvas.get(0).height = track.height_px; - var ctx = canvas.get(0).getContext("2d"), - in_path = false, - min_value = track.prefs.min_value, - max_value = track.prefs.max_value, - vertical_range = track.vertical_range, - total_frequency = track.total_frequency, - height_px = track.height_px, - mode = track.mode; + var canvas = document.createElement("canvas"), + data = result.data; + if (window.G_vmlCanvasManager) { G_vmlCanvasManager.initElement(canvas); } // EXCANVAS HACK + canvas = $(canvas); + + canvas.get(0).width = Math.ceil( tile_length * w_scale ); + canvas.get(0).height = track.height_px; + var ctx = canvas.get(0).getContext("2d"), + in_path = false, + min_value = track.prefs.min_value, + max_value = track.prefs.max_value, + vertical_range = track.vertical_range, + total_frequency = track.total_frequency, + height_px = track.height_px, + mode = track.mode; - // Pixel position of 0 on the y axis - var y_zero = Math.round( height_px + min_value / vertical_range * height_px ); + // Pixel position of 0 on the y axis + var y_zero = Math.round( height_px + min_value / vertical_range * height_px ); - // Line at 0.0 - ctx.beginPath(); - ctx.moveTo( 0, y_zero ); - ctx.lineTo( tile_length * w_scale, y_zero ); - // ctx.lineWidth = 0.5; - ctx.fillStyle = "#aaa"; - ctx.stroke(); - - ctx.beginPath(); - ctx.fillStyle = track.prefs.color; - var x_scaled, y, delta_x_px; - if (data.length > 1) { - delta_x_px = Math.ceil((data[1][0] - data[0][0]) * w_scale); + // Line at 0.0 + ctx.beginPath(); + ctx.moveTo( 0, y_zero ); + ctx.lineTo( tile_length * w_scale, y_zero ); + // ctx.lineWidth = 0.5; + ctx.fillStyle = "#aaa"; + ctx.stroke(); + + ctx.beginPath(); + ctx.fillStyle = track.prefs.color; + var x_scaled, y, delta_x_px; + if (data.length > 1) { + delta_x_px = Math.ceil((data[1][0] - data[0][0]) * w_scale); + } else { + delta_x_px = 10; + } + for (var i = 0, len = data.length; i < len; i++) { + x_scaled = Math.round((data[i][0] - tile_low) * w_scale); + y = data[i][1]; + if (y === null) { + if (in_path && mode === "Filled") { + ctx.lineTo(x_scaled, height_px); + } + in_path = false; + continue; + } + if (y < min_value) { + y = min_value; + } else if (y > max_value) { + y = max_value; + } + + if (mode === "Histogram") { + // y becomes the bar height in pixels, which is the negated for canvas coords + y = Math.round( y / vertical_range * height_px ); + ctx.fillRect(x_scaled, y_zero, delta_x_px, - y ); + } else if (mode === "Intensity" ) { + y = 255 - Math.floor( (y - min_value) / vertical_range * 255 ); + ctx.fillStyle = "rgb(" +y+ "," +y+ "," +y+ ")"; + ctx.fillRect(x_scaled, 0, delta_x_px, height_px); } else { - delta_x_px = 10; - } - for (var i = 0, len = data.length; i < len; i++) { - x_scaled = Math.round((data[i][0] - tile_low) * w_scale); - y = data[i][1]; - if (y === null) { - if (in_path && mode === "Filled") { - ctx.lineTo(x_scaled, height_px); - } - in_path = false; - continue; - } - if (y < min_value) { - y = min_value; - } else if (y > max_value) { - y = max_value; - } - - if (mode === "Histogram") { - // y becomes the bar height in pixels, which is the negated for canvas coords - y = Math.round( y / vertical_range * height_px ); - ctx.fillRect(x_scaled, y_zero, delta_x_px, - y ); - } else if (mode === "Intensity" ) { - y = 255 - Math.floor( (y - min_value) / vertical_range * 255 ); - ctx.fillStyle = "rgb(" +y+ "," +y+ "," +y+ ")"; - ctx.fillRect(x_scaled, 0, delta_x_px, height_px); + // console.log(y, track.min_value, track.vertical_range, (y - track.min_value) / track.vertical_range * track.height_px); + y = Math.round( height_px - (y - min_value) / vertical_range * height_px ); + // console.log(canvas.get(0).height, canvas.get(0).width); + if (in_path) { + ctx.lineTo(x_scaled, y); } else { - // console.log(y, track.min_value, track.vertical_range, (y - track.min_value) / track.vertical_range * track.height_px); - y = Math.round( height_px - (y - min_value) / vertical_range * height_px ); - // console.log(canvas.get(0).height, canvas.get(0).width); - if (in_path) { + in_path = true; + if (mode === "Filled") { + ctx.moveTo(x_scaled, height_px); ctx.lineTo(x_scaled, y); } else { - in_path = true; - if (mode === "Filled") { - ctx.moveTo(x_scaled, height_px); - ctx.lineTo(x_scaled, y); - } else { - ctx.moveTo(x_scaled, y); - } + ctx.moveTo(x_scaled, y); } } } - if (mode === "Filled") { - if (in_path) { - ctx.lineTo( x_scaled, y_zero ); - ctx.lineTo( 0, y_zero ); - } - ctx.fill(); - } else { - ctx.stroke(); + } + if (mode === "Filled") { + if (in_path) { + ctx.lineTo( x_scaled, y_zero ); + ctx.lineTo( 0, y_zero ); } - callback(canvas); - }); + ctx.fill(); + } else { + ctx.stroke(); + } + return canvas; } }); @@ -2147,10 +2162,10 @@ this.inc_slots = {}; this.start_end_dct = {}; this.tile_cache = new Cache(CACHED_TILES_FEATURE); - this.data_cache = new DataCache(20); + this.data_cache = new DataManager(20, this); this.left_offset = 200; }; -$.extend( FeatureTrack.prototype, TiledTrack.prototype, { +$.extend(FeatureTrack.prototype, TiledTrack.prototype, { /** * Place features in slots for drawing (i.e. pack features). * this.inc_slots[level] is created in this method. this.inc_slots[level] @@ -2501,14 +2516,10 @@ /** * Draw FeatureTrack tile. */ - draw_tile: function(resolution, tile_index, parent_element, w_scale, callback, ref_seq, result) { + draw_tile: function(result, resolution, tile_index, parent_element, w_scale, ref_seq) { // Fetch reference sequence data if it exists and we are displaying var track = this; - if (track.view.reference_track && w_scale > CHAR_WIDTH_PX && ref_seq === undefined) { - return track.view.reference_track.tile_data(resolution, tile_index, {}, function(ret_ref_seq) { - track.draw_tile(resolution, tile_index, parent_element, w_scale, callback, ret_ref_seq); - }); - } + var tile_low = tile_index * DENSITY * resolution, tile_high = ( tile_index + 1 ) * DENSITY * resolution, tile_span = tile_high - tile_low, @@ -2516,21 +2527,6 @@ resolution: this.view.resolution, mode: this.mode }; // - // Get tile data; if data not available, issue get_data request and rerun with data - // - if (result === undefined) { - var cached = this.data_cache.get_data(tile_low, tile_high, this.mode), - key = resolution + "_" + tile_index + "_" + this.mode; - if (cached === undefined) { - return track.tile_data(resolution, tile_index, params, function(get_data_result) { - track.data_cache.set_data(tile_low, tile_high, this.mode, get_data_result); - track.draw_tile(resolution, tile_index, parent_element, w_scale, callback, ref_seq, get_data_result); - }, key); - } - result = cached; - } - - // // Create/set/compute some useful vars. // var width = Math.ceil( tile_span * w_scale ), @@ -2611,7 +2607,7 @@ if (mode === "summary_tree") { this.draw_summary_tree(canvas, result.data, result.delta, result.max, w_scale, required_height, tile_low, left_offset); - return callback(canvas); + return canvas; } // @@ -2631,7 +2627,7 @@ // If there's no data, return. if (!result.data) { - return callback(canvas); + return canvas; } } @@ -2674,7 +2670,7 @@ width, left_offset, ref_seq); } } - callback(canvas); + return canvas; } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: fixed calculation of codon starts
by Bitbucket 24 Mar '11

24 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5b0edf34839e/ changeset: r5268:5b0edf34839e user: richard_burhans date: 2011-03-24 20:03:12 summary: fixed calculation of codon starts affected #: 1 file (59 bytes) --- a/tools/filters/ucsc_gene_bed_to_exon_bed.py Thu Mar 24 14:33:05 2011 -0400 +++ b/tools/filters/ucsc_gene_bed_to_exon_bed.py Thu Mar 24 15:03:12 2011 -0400 @@ -103,13 +103,12 @@ i+=1 #for non-intron regions: else: - shift = 0 for start, end in zip( exon_starts, exon_ends ): start = max( start, region_start ) end = min( end, region_end ) if start < end: if options.region == 'codon': - start += shift + start += (3 - ((start-region_start)%3))%3 c_start = start while c_start+3 <= end: if strand: @@ -117,7 +116,6 @@ else: print_tab_sep(out_file, chrom, c_start, c_start+3) c_start += 3 - shift = (3 - ((end-start)%3))%3 else: if strand: print_tab_sep(out_file, chrom, start, end, name, "0", strand ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Update the check_galaxy script for the recent changes to the User controller
by Bitbucket 24 Mar '11

24 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b41ea12642ad/ changeset: r5267:b41ea12642ad user: natefoo date: 2011-03-24 19:33:05 summary: Update the check_galaxy script for the recent changes to the User controller affected #: 1 file (14 bytes) --- a/scripts/check_galaxy.py Thu Mar 24 13:52:04 2011 -0400 +++ b/scripts/check_galaxy.py Thu Mar 24 14:33:05 2011 -0400 @@ -274,7 +274,7 @@ self.get("/root/delete?id=%s" % did) def check_if_logged_in(self): - self.get("/user") + self.get("/user?cntrller=user") p = loggedinParser() p.feed(tc.browser.get_html()) return p.logged_in Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: small fix for read drawing and added note about larger issue.
by Bitbucket 24 Mar '11

24 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c0330af57060/ changeset: r5266:c0330af57060 user: jgoecks date: 2011-03-24 18:52:04 summary: Trackster: small fix for read drawing and added note about larger issue. affected #: 1 file (213 bytes) --- a/static/scripts/trackster.js Thu Mar 24 11:45:50 2011 -0400 +++ b/static/scripts/trackster.js Thu Mar 24 13:52:04 2011 -0400 @@ -2782,8 +2782,10 @@ // Keep list of items that need to be drawn on top of initial drawing layer. var draw_last = []; + // Gap is needed so that read is offset and hence first base can be drawn on read. + // TODO-FIX: using this gap offsets reads so that their start is not visually in sync with other tracks. if ((mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > CHAR_WIDTH_PX) { - gap = Math.round(w_scale/2); + gap = Math.ceil(CHAR_WIDTH_PX/2 + 1); } if (!cigar) { // If no cigar string, then assume all matches Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add more verbose error reporting to FASTQ Groomer tool.
by Bitbucket 24 Mar '11

24 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/acf9c73836f3/ changeset: r5265:acf9c73836f3 user: dan date: 2011-03-24 16:45:50 summary: Add more verbose error reporting to FASTQ Groomer tool. affected #: 2 files (2.3 KB) --- a/lib/galaxy_utils/sequence/fastq.py Wed Mar 23 19:32:32 2011 -0400 +++ b/lib/galaxy_utils/sequence/fastq.py Thu Mar 24 11:45:50 2011 -0400 @@ -455,6 +455,44 @@ while True: yield self.next() +class ReadlineCountFile( object ): + def __init__( self, f ): + self.__file = f + self.readline_count = 0 + def readline( self, *args, **kwds ): + self.readline_count += 1 + return self.__file.readline( *args, **kwds ) + def __getattr__( self, name ): + return getattr( self.__file, name ) + +class fastqVerboseErrorReader( fastqReader ): + MAX_PRINT_ERROR_BYTES = 1024 + def __init__( self, fh, **kwds ): + super( fastqVerboseErrorReader, self ).__init__( ReadlineCountFile( fh ), **kwds ) + self.last_good_identifier = None + def next( self ): + last_good_end_offset = self.file.tell() + last_readline_count = self.file.readline_count + try: + block = super( fastqVerboseErrorReader, self ).next() + self.last_good_identifier = block.identifier + return block + except StopIteration, e: + raise e + except Exception, e: + print "There was an error reading your input file. Your input file is likely malformed.\nIt is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below.\nHowever, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism.\n\nThe reported error is: '%s'." % e + if self.last_good_identifier is not None: + print "The last valid FASTQ read had an identifier of '%s'." % self.last_good_identifier + else: + print "The error occurred at the start of your file and no valid FASTQ reads were found." + error_offset = self.file.tell() + error_byte_count = error_offset - last_good_end_offset + print_error_bytes = min( self.MAX_PRINT_ERROR_BYTES, error_byte_count ) + print "The error in your file occurs between lines '%i' and '%i', which corresponds to byte-offsets '%i' and '%i', and contains the text (%i of %i bytes shown):\n" % ( last_readline_count + 1, self.file.readline_count, last_good_end_offset, error_offset, print_error_bytes, error_byte_count ) + self.file.seek( last_good_end_offset ) + print self.file.read( print_error_bytes ) + raise e + class fastqNamedReader( object ): def __init__( self, fh, format = 'sanger' ): self.file = fh --- a/tools/fastq/fastq_groomer.py Wed Mar 23 19:32:32 2011 -0400 +++ b/tools/fastq/fastq_groomer.py Thu Mar 24 11:45:50 2011 -0400 @@ -1,6 +1,6 @@ #Dan Blankenberg import sys -from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator, fastqWriter +from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter def main(): input_filename = sys.argv[1] @@ -15,7 +15,11 @@ aggregator = fastqAggregator() out = fastqWriter( open( output_filename, 'wb' ), format = output_type, force_quality_encoding = force_quality_encoding ) read_count = None - for read_count, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): + if summarize_input: + reader = fastqVerboseErrorReader + else: + reader = fastqReader + for read_count, fastq_read in enumerate( reader( open( input_filename ), format = input_type ) ): if summarize_input: aggregator.consume_read( fastq_read ) out.write( fastq_read ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: fubar: still having a problem with getting clustalw2 to print sequence indices - test does not cover so passes
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/620b060c31c7/ changeset: r5264:620b060c31c7 user: fubar date: 2011-03-24 00:32:32 summary: still having a problem with getting clustalw2 to print sequence indices - test does not cover so passes affected #: 1 file (35 bytes) --- a/tools/rgenetics/rgClustalw.xml Wed Mar 23 19:14:14 2011 -0400 +++ b/tools/rgenetics/rgClustalw.xml Wed Mar 23 19:32:32 2011 -0400 @@ -7,9 +7,9 @@ #end if #if ($outcontrol.outform=="clustal") -f "CLUSTAL" + #if ($outcontrol.out_seqnos=="ON") +-q "ON" #end if - #if ($outcontrol.outform=="clustal" and $outcontrol.out_seqnos=="ON") --q "ON" #end if #if ($outcontrol.outform=="phylip") -f "PHYLIP" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: fubar: python wrapper for clustalw tool
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/cd05024e5b2a/ changeset: r5263:cd05024e5b2a user: fubar date: 2011-03-24 00:14:14 summary: python wrapper for clustalw tool affected #: 1 file (0 bytes) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Allow users to import copies of their own workflows.
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/589e769ceab5/ changeset: r5262:589e769ceab5 user: dan date: 2011-03-23 23:06:04 summary: Allow users to import copies of their own workflows. affected #: 1 file (189 bytes) --- a/lib/galaxy/web/controllers/workflow.py Wed Mar 23 17:20:47 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Wed Mar 23 18:06:04 2011 -0400 @@ -329,8 +329,6 @@ stored = self.get_stored_workflow( trans, id, check_ownership=False ) if stored.importable == False: return trans.show_error_message( "The owner of this workflow has disabled imports via this link.<br>You can %s" % referer_message, use_panels=True ) - elif stored.user == trans.user: - return trans.show_error_message( "You can't import this workflow because you own it.<br>You can %s" % referer_message, use_panels=True ) elif stored.deleted: return trans.show_error_message( "You can't import this workflow because it has been deleted.<br>You can %s" % referer_message, use_panels=True ) else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 23 Mar '11

23 Mar '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6f1d1bcb0b9c/ changeset: r5260:6f1d1bcb0b9c user: fubar date: 2011-03-23 22:18:29 summary: Fixes to clustalw tool - need a python wrapper to take care of Clustalw's bad habit of writing to an output path determined from the input path - naughty..Also added the dendrogram to the log output so test output sample updated; version bumped affected #: 1 file (34 bytes) --- a/tools/rgenetics/rgClustalw.xml Wed Mar 23 16:42:14 2011 -0400 +++ b/tools/rgenetics/rgClustalw.xml Wed Mar 23 17:18:29 2011 -0400 @@ -1,21 +1,22 @@ <tool id="clustalw" name="ClustalW" version="0.1"><description>multiple sequence alignment program for DNA or proteins</description> - <command> + <command interpreter="python"> + rgClustalw.py -i "$input" -o "$output" -s "$out_order" -l "$outlog" -t "$outname" -d "$dnarna" #if ($range.mode=="part") - clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_order -RANGE=$range.seq_range_start,$range.seq_range_end - #elif ($range.mode=="complete") - clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_order +-b "$range.seq_range_start" -e "$range.seq_range_end" #end if #if ($outcontrol.outform=="clustal") - -SEQNOS=$outcontrol.out_seqnos +-f "CLUSTAL" + #end if + #if ($outcontrol.outform=="clustal" and $outcontrol.out_seqnos=="ON") +-q "ON" #end if #if ($outcontrol.outform=="phylip") - -OUTPUT=PHYLIP +-f "PHYLIP" #end if #if ($outcontrol.outform=="fasta") - -OUTPUT=FASTA +-f "FASTA" #end if - -TYPE=$dnarna 1>$outlog 2>&1 </command><inputs><page> http://bitbucket.org/galaxy/galaxy-central/changeset/72f60642853b/ changeset: r5261:72f60642853b user: fubar date: 2011-03-23 22:20:47 summary: test data updated for clustalw test affected #: 1 file (664 bytes) --- a/test-data/rgClustal_testout.log Wed Mar 23 17:18:29 2011 -0400 +++ b/test-data/rgClustal_testout.log Wed Mar 23 17:20:47 2011 -0400 @@ -87,7 +87,7 @@ Sequences (10:11) Aligned. Score: 64 Sequences (10:12) Aligned. Score: 76 Sequences (11:12) Aligned. Score: 46 -Guide tree file created: [/share/shared/galaxy/database/files/002/dataset_2705.dnd] +Guide tree file created: [infile_copy.dnd] There are 11 groups Start of Multiple Alignment @@ -105,8 +105,40 @@ Group 10: Sequences: 4 Score:945 Group 11: Sequences: 12 Score:380 Alignment Score 6283 -firstres = 1 lastres = 63 -FASTA file created! -Fasta-Alignment file created [/share/shared/galaxy/database/files/002/dataset_2726.dat] +CLUSTAL-Alignment file created [/share/shared/galaxy/database/files/002/dataset_2801.dat] + +Clustal created the following dnd file for your information: +( +( +c_briggsae-chrII_+_/43862-46313:0.07349, +c_brenneri-Cbre_Contig60_+_/627772-630087:0.04317) +:0.02387, +( +c_remanei-Crem_Contig172_-_/123228-124941:0.06114, +c_elegans-II_+_/9706834-9708803:0.07219) +:0.01779, +( +( +( +c_briggsae-chrIfooI_+_/43862-46313:0.10368, +c_brenneri-Cbre_Contig60gak_+_/627772-630087:0.06298) +:0.01654, +( +c_remanei-Crem_Contig172foo_-_/123228-124941:0.05765, +c_elegans-II_+_more/9706834-9708803:0.05902) +:0.06262) +:0.31533, +( +( +c_briggsae-chrII_+_bar/43862-46313:0.02327, +c_brenneri-Cbre_Contig60fee_+_/627772-630087:0.13463) +:0.05016, +( +c_remanei-Crem_Contig172zot_-_/123228-124941:0.11667, +c_elegans-II_+_meh/9706834-9708803:0.11737) +:0.12013) +:0.20951) +:0.30133); + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Slight output difference on the buildbot for weblogo, hopefully the difference is static.
by Bitbucket 23 Mar '11

23 Mar '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a9d745a274e3/ changeset: r5259:a9d745a274e3 user: natefoo date: 2011-03-23 21:42:14 summary: Slight output difference on the buildbot for weblogo, hopefully the difference is static. affected #: 1 file (34 bytes) Binary file test-data/rgWebLogo3_test.jpg has changed Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0