diff --git a/lib/galaxy/visualization/tracks/data_providers.py b/lib/galaxy/visualization/tracks/data_providers.py
index e150e58a8d6..5e3efcf972b 100644
--- a/lib/galaxy/visualization/tracks/data_providers.py
+++ b/lib/galaxy/visualization/tracks/data_providers.py
@@ -235,11 +235,13 @@ class BamDataProvider( TracksDataProvider ):
             else:
                 return None
         # Encode reads as list of lists; each read is a list with the format 
-        #   [<name>, <start>, <end>, <read_1_seq>, <cigar>, <read_1>, <read_2>] 
+        #   [<guid>, <start>, <end>, <name>, <read_1>, <read_2>] 
         # where <read_1> has the format
-        #   [<start>, <end>, ?<read_seq>?]
+        #   [<start>, <end>, <cigar>, ?<read_seq>?]
         # and <read_2> has the format
-        #   [<start>, <end>, ?<read_seq>?]
+        #   [<start>, <end>, <cigar>, ?<read_seq>?]
+        # For single-end reads, read has format:
+        #   [<guid>, <start>, <end>, <name>, cigar, seq] 
         # NOTE: read end and sequence data are not valid for reads outside of
         # requested region and should not be used.
         results = []
@@ -258,32 +260,38 @@ class BamDataProvider( TracksDataProvider ):
             if read.is_proper_pair:
                 if qname in paired_pending: # one in dict is always first
                     pair = paired_pending[qname]
-                    results.append( [ qname, pair['start'], read.pos + read_len, seq, read.cigar, [pair['start'], pair['end'], pair['seq']], [read.pos, read.pos + read_len, seq] ] )
+                    results.append( [ "%i_%s" % ( read.pos-start, qname ), 
+                                      pair['start'], 
+                                      read.pos + read_len, 
+                                      qname, 
+                                      [ pair['start'], pair['end'], pair['cigar'], pair['seq'] ], 
+                                      [ read.pos, read.pos + read_len, read.cigar, seq] 
+                                     ] )
                     del paired_pending[qname]
                 else:
                     paired_pending[qname] = { 'start': read.pos, 'end': read.pos + read_len, 'seq': seq, 'mate_start': read.mpos, 'rlen': read_len, 'cigar': read.cigar }
             else:
-                results.append( [qname, read.pos, read.pos + read_len, seq, read.cigar] )
+                results.append( [ "%i_%s" % ( read.pos-start, qname ), read.pos, read.pos + read_len, qname, read.cigar, read.seq] )
         # Take care of reads whose mates are out of range.
         for qname, read in paired_pending.iteritems():
             if read['mate_start'] < read['start']:
                 # Mate is before read.
-                start = read['mate_start']
-                end = read['end']
+                read_start = read['mate_start']
+                read_end = read['end']
                 # Make read_1 start=end so that length is 0 b/c we don't know
                 # read length.
-                r1 = [read['mate_start'], read['mate_start']]
-                r2 = [read['start'], read['end'], read['seq']]
+                r1 = [ read['mate_start'], read['mate_start'] ]
+                r2 = [ read['start'], read['end'], read['cigar'], read['seq'] ]
             else:
                 # Mate is after read.
-                start = read['start']
+                read_start = read['start']
                 # Make read_2 start=end so that length is 0 b/c we don't know
                 # read length. Hence, end of read is start of read_2.
-                end = read['mate_start']
-                r1 = [read['start'], read['end'], read['seq']]
-                r2 = [read['mate_start'], read['mate_start']]
+                read_end = read['mate_start']
+                r1 = [ read['start'], read['end'], read['cigar'], read['seq'] ]
+                r2 = [ read['mate_start'], read['mate_start'] ]
 
-            results.append( [ qname, start, end, read['seq'], read['cigar'], r1, r2 ] )
+            results.append( [ "%i_%s" % ( read_start-start, qname ), read_start, read_end, qname, r1, r2 ] )
 
         bamfile.close()
         return { 'data': results, 'message': message }
@@ -437,6 +445,11 @@ class IntervalIndexDataProvider( TracksDataProvider ):
         if chrom not in index.indexes and chrom[3:] in index.indexes:
             chrom = chrom[3:]
 
+        #
+        # Build data to return. Payload format is:
+        # [ <guid/offset>, <start>, <end>, <name>, <strand>, <blocks>]
+        # 
+        no_detail = ( "no_detail" in kwargs )
         for start, end, offset in index.find(chrom, start, end):
             if count >= MAX_VALS:
                 message = "Only the first %s features are being displayed." % MAX_VALS
@@ -445,16 +458,16 @@ class IntervalIndexDataProvider( TracksDataProvider ):
             source.seek( offset )
             # TODO: can we use column metadata to fill out payload?
             # TODO: use function to set payload data
-            if "no_detail" not in kwargs:
-                if isinstance( self.original_dataset.datatype, Gff ):
-                    # GFF dataset.
-                    reader = GFFReaderWrapper( source, fix_strand=True )
-                    feature = reader.next()
-                    payload = package_gff_feature( feature )
-                    payload.insert( 0, offset )
-                elif isinstance( self.original_dataset.datatype, Bed ):
-                    # BED dataset.
-                    payload = [ offset, start, end ]
+            if isinstance( self.original_dataset.datatype, Gff ):
+                # GFF dataset.
+                reader = GFFReaderWrapper( source, fix_strand=True )
+                feature = reader.next()
+                payload = package_gff_feature( feature, no_detail )
+                payload.insert( 0, offset )
+            elif isinstance( self.original_dataset.datatype, Bed ):
+                # BED dataset.
+                payload = [ offset, start, end ]
+                if not no_detail:
                     feature = source.readline().split()
                     length = len(feature)
                     if length >= 4:
@@ -472,7 +485,7 @@ class IntervalIndexDataProvider( TracksDataProvider ):
                         block_starts = [ int(n) for n in feature[11].split(',') if n != '' ]
                         blocks = zip( block_sizes, block_starts )
                         payload.append( [ ( start + block[1], start + block[1] + block[0] ) for block in blocks ] )
-                        
+                    
                     if length >= 5:
                         payload.append( int(feature[4]) ) # score
 
@@ -564,9 +577,15 @@ def get_data_provider( name=None, original_dataset=None ):
                 pass
     return data_provider
 
-def package_gff_feature( feature ):
+def package_gff_feature( feature, no_detail=False ):
     """ Package a GFF feature in an array for data providers. """
     feature = convert_gff_coords_to_bed( feature )
+    
+    # No detail means only start, end.
+    if no_detail:
+        return [ feature.start, feature.end ]
+    
+    # Return full feature.
     payload = [ feature.start, 
                 feature.end, 
                 feature.name(), 
diff --git a/static/scripts/packed/trackster.js b/static/scripts/packed/trackster.js
index da71b17e905..c663a438b7e 100644
--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1 +1 @@
-var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=50,DEFAULT_DATA_QUERY_WAIT=5000,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_LOADING="Loading data...",FILTERABLE_CLASS="filterable",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)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;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()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var View=function(a,d,c,b,e){this.container=a;this.chrom=null;this.vis_id=c;this.dbkey=b;this.title=d;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(e);this.reset()};$.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_form=$("<form/>").attr("action",function(){}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);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=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);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=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(f){a.zoom_in(f.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(f){this.current_x=f.offsetX}).bind("drag",function(f){var h=f.offsetX-this.current_x;this.current_x=f.offsetX;var g=Math.round(h/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-g)});this.overview_close.bind("click",function(){for(var f=0,e=a.tracks.length;f<e;f++){a.tracks[f].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",a.overview_box.height());a.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("dragstart",function(f){this.original_low=a.low;this.current_height=f.clientY;this.current_x=f.offsetX;this.enable_pan=(f.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(h){if(!this.enable_pan||this.in_reordering){return}var f=$(this);var j=h.offsetX-this.current_x;var g=f.scrollTop()-(h.clientY-this.current_height);f.scrollTop(g);this.current_height=h.clientY;this.current_x=h.offsetX;var i=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)});this.top_labeltrack.bind("dragstart",function(f){this.drag_origin_x=f.clientX;this.drag_origin_pos=f.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var g=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,f=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low);this.drag_div.css({left:g+"px",width:(f-g)+"px"})}).bind("dragend",function(k){var g=Math.min(k.clientX,this.drag_origin_x),f=Math.max(k.clientX,this.drag_origin_x),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;this.drag_div.remove();a.redraw()});this.add_label_track(new LabelTrack(this,this.top_labeltrack));this.add_label_track(new LabelTrack(this,this.nav_labeltrack));$(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))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}if(e!==d.chrom){d.chrom=e;if(!d.chrom){d.intro_div.show()}else{d.intro_div.hide()}d.chrom_select.val(d.chrom);d.max_high=f.len;d.reset();d.redraw(true);for(var h=0,a=d.tracks.length;h<a;h++){var c=d.tracks[h];if(c.init){c.init()}}}if(b!==undefined&&g!==undefined){d.low=Math.max(b,0);d.high=Math.min(g,d.max_high)}d.reset_overview();d.redraw()},go_to:function(f){var j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.change_chrom(h,a,d)},move_fraction:function(c){var a=this;var b=a.high-a.low;this.move_delta(c*b)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(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 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.init_global()};$.extend(Track.prototype,{init_global:function(){this.container_div=$("<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)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom){$.getJSON(a.data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$(" <a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("View error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},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(c,l,p){var d=this,q=d.view;this.filters=(c!==undefined?get_filters_from_dict(c):[]);this.tool=(l!==undefined?get_tool_from_dict(l):undefined);this.parent_track=p;this.child_tracks=[];if(d.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.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(u,x){var t=$("<tr>").appendTo(b);var w=$("<th class='filter-info'>").appendTo(t);var s=$("<span class='name'>").appendTo(w);s.text(x.name+"  ");var i=$("<span class='values'>").appendTo(w);var v=$("<td>").appendTo(t);x.control_element=$("<div id='"+x.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(v);x.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(z,A){var y=A.values;i.text("["+y[0]+"-"+y[1]+"]");x.low=y[0];x.high=y[1];d.draw(true)},change:function(y,z){x.control_element.slider("option","slide").call(x.control_element,y,z)}});x.slider=x.control_element;x.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var o=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var n=this.tool.params;var d=this;$.each(this.tool.params,function(y,t){var w=$("<div>").addClass("param-row").appendTo(d.dynamic_tool_div);var v=$("<div>").addClass("slider-label").appendTo(w);var A=$("<span class='param-name'>").text(t.label+"  ").appendTo(v);var u=$("<span/>").text(t.value);var x=$("<span class='param-value'>").appendTo(v).append("[").append(u).append("]");var z=$("<div/>").addClass("slider").appendTo(w);var i=$("<div id='"+t.name+"-param-control'>").appendTo(z);var s=(t.max<=1?0.01:(t.max<=1000?1:5));i.slider({min:t.min,max:t.max,step:s,value:t.value,slide:function(B,D){var C=D.value;t.value=C;if(0<C&&C<1){C=parseFloat(C).toFixed(2)}u.text(C)},change:function(B,C){t.value=C.value}});x.click(function(){var D=u,C=D.text(),B=(t.max<=1?4:t.max.length);D.text("");$("<input type='text'/>").attr("size",B).attr("maxlength",B).attr("value",C).appendTo(D).focus().select().click(function(E){E.stopPropagation()}).blur(function(){$(this).remove();D.text(C)}).keyup(function(G){if(G.keyCode===27){$(this).trigger("blur")}else{if(G.keyCode===13){var E=$(this),F=parseFloat(E.val());if(isNaN(F)||F>t.max||F<t.min){alert("Parameter value must be in the range ["+t.min+"-"+t.max+"]");return $(this)}D.text(F);i.slider("value",F);t.value=F}}})});$("<div style='clear: both;'/>").appendTo(w)});var r=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var m=$("<input type='submit'>").attr("value","Run").appendTo(r);var d=this;m.click(function(){d.run_tool()})}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var g=d.display_modes[0];d.mode=g;d.mode_div.text(g);var e=function(i){d.mode_div.text(i);d.mode=i;d.tile_cache.clear();d.draw()};var a={};for(var h=0,k=d.display_modes.length;h<k;h++){var j=d.display_modes[h];a[j]=function(i){return function(){e(i)}}(j)}make_popupmenu(d.mode_div,a)}else{d.mode_div.hide()}}var f={};f["Edit configuration"]=function(){var t=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){d.update_options(d.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},s=function(u){if((u.keyCode||u.which)===27){t()}else{if((u.keyCode||u.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",s);show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:t,OK:i})};f["Set as overview"]=function(){q.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var i in q.tracks){if(q.tracks[i]!==d){q.tracks[i].is_overview=false}}};if(d.filters.length>0){f["Show filters"]=function(){var i;if(!d.filtering_div.is(":visible")){i="Hide filters";d.filters_visible=true}else{i="Show filters";d.filters_visible=false}d.filtering_div.toggle()}}if(d.tool){f["Toggle Tool"]=function(){var i;if(!d.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";d.update_name(d.name+d.tool_region_and_parameters_str())}else{i="Show dynamic tool";d.revert_name()}d.dynamic_tool_div.toggle()}}f.Remove=function(){q.remove_track(d);if(q.num_tracks===0){$("#no-tracks").show()}};d.popup_menu=make_popupmenu(d.name_div,f)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var k=this.view.low,g=this.view.high,h=g-k,f=this.view.resolution;var n=$("<div style='position: relative;'></div>"),o=this.content_div.width()/h;this.content_div.append(n);this.max_height=0;var b=Math.floor(k/f/DENSITY);var j={};while((b*DENSITY*f)<g){var l=this.content_div.width()+"_"+o+"_"+b;var e=this.tile_cache.get(l);if(!a&&e){var i=b*DENSITY*f;var d=(i-k)*o;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,n)}else{this.delayed_draw(this,l,k,g,b,f,n,o,j)}b+=1}var c=this;var m=setInterval(function(){if(obj_length(j)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var p=0;p<c.filters.length;p++){c.filters[p].update_ui_elt()}clearInterval(m)}},50)},delayed_draw:function(c,h,g,e,b,d,i,j,f){var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},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,undefined,{},{},{},d)}view.add_track(e);var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!=undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.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.content_div.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);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,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",top:a.height_px+12+"px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,w=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(w)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(w);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(d-(h-k)/m*d);n.fillRect(u,h,f,d-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,d)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,b,q){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=a;this.inc_slots[a].mode=q;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,y=[],h=0,n=this.view.max_low;var A=[];if(this.inc_slots[a].mode!==q){delete this.inc_slots[a];this.inc_slots[a]={mode:q,w_scale:m};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var v=0,w=g.length;v<w;v++){var f=g[v],l=f[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);A.push(this.inc_slots[a][l])}else{y.push(v)}}for(var v=0,w=y.length;v<w;v++){var f=g[y[v]],l=f[0],r=f[1],c=f[2],p=f[3],d=Math.floor((r-n)*m),e=Math.ceil((c-n)*m);if(p!==undefined&&!b){var s=CONTEXT.measureText(p).width;if(d-s<0){e+=s}else{d-=s}}var u=0;while(u<=MAX_FEATURE_DEPTH){var o=true;if(this.s_e_by_tile[a][u]!==undefined){for(var t=0,z=this.s_e_by_tile[a][u].length;t<z;t++){var x=this.s_e_by_tile[a][u][t];if(e>x[0]&&d<x[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][u]===undefined){this.s_e_by_tile[a][u]=[]}this.s_e_by_tile[a][u].push([d,e]);this.inc_slots[a][l]=u;h=Math.max(h,u);break}u++}}return h},rect_or_text:function(r,l,t,b,q,f,i,e){r.textAlign="center";var k=0,p=Math.round(l/2);for(var m=0,s=i.length;m<s;m++){var j=i[m],d="MIDNSHP"[j[0]],n=j[1];if(d==="H"||d==="S"){k-=n}var g=q+k,w=Math.floor(Math.max(0,(g-t)*l)),h=Math.floor(Math.max(0,(g+n-t)*l));switch(d){case"S":case"H":case"M":var o=f.slice(k,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+1,h-w,9);r.fillStyle=CONNECTOR_COLOR;for(var u=0,a=o.length;u<a;u++){if(g+u>=t&&g+u<=b){var 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q=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(q)}q=$(q);if(I.dataset_type==="summary_tree"){D=this.summary_draw_height}else{if(r==="Dense"){D=z;av=10}else{av=(ad?this.vertical_nodetail_px:this.vertical_detail_px);var A=(au<0.0001?1/this.view.zoom_res:au);D=this.incremental_slots(A,I.data,ad,r)*av+z;at=this.inc_slots[A]}}q.css({position:"absolute",top:0,left:(N-this.view.low)*au-W});q.get(0).width=a+W;q.get(0).height=D;s.parent().css("height",Math.max(this.height_px,D)+"px");var J=q.get(0).getContext("2d");J.fillStyle=l;J.font=this.default_font;J.textAlign="right";this.container_div.find(".yaxislabel").remove();if(I.dataset_type=="summary_tree"){var Y=I.data,L=I.max,b=Math.ceil(I.delta*au);var p=$("<div />").addClass("yaxislabel").text(L);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var ao=0,H=Y.length;ao<H;ao++){var aa=Math.floor((Y[ao][0]-N)*au);var Z=Y[ao][1];if(!Z){continue}var al=Z/L*this.summary_draw_height;J.fillStyle="black";J.fillRect(aa+W,this.summary_draw_height-al,b,al);if(this.prefs.show_counts&&J.measureText(Z).width<b){J.fillStyle="#bbb";J.textAlign="center";J.fillText(Z,aa+W+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(q);return q}if(I.message){q.css({border:"solid red","border-width":"2px 2px 2px 0px"});J.fillStyle="red";J.textAlign="left";J.fillText(I.message,100+W,av);return q}for(var aq=0;aq<this.filters.length;aq++){if(this.filters[aq].applies_to(I.data[0])){q.addClass(FILTERABLE_CLASS);break}}var ar=I.data;var an=0;for(var ao=0,H=ar.length;ao<H;ao++){var S=ar[ao],R=S[0],ap=S[1],ac=S[2],O=S[3];if(this.mode!="Dense"&&at[R]===undefined){continue}var ab=false;var U;for(var aq=0;aq<this.filters.length;aq++){U=this.filters[aq];U.update_attrs(S);if(!U.keep(S)){ab=true;break}}if(ab){continue}if(ap<=ak&&ac>=N){var ae=Math.floor(Math.max(0,(ap-N)*au)),K=Math.ceil(Math.min(a,Math.max(0,(ac-N)*au))),X=(r==="Dense"?1:(1+at[R]))*av;var G,ai,P=null,aw=null;if(I.dataset_type==="bai"){var v=S[4];J.fillStyle=l;if(S[5] instanceof Array){var E=Math.floor(Math.max(0,(S[5][0]-N)*au)),Q=Math.ceil(Math.min(a,Math.max(0,(S[5][1]-N)*au))),C=Math.floor(Math.max(0,(S[6][0]-N)*au)),w=Math.ceil(Math.min(a,Math.max(0,(S[6][1]-N)*au)));if(S[5][1]>=N&&S[5][0]<=ak){this.rect_or_text(J,au,N,ak,S[5][0],S[5][2],v,X)}if(S[6][1]>=N&&S[6][0]<=ak){this.rect_or_text(J,au,N,ak,S[6][0],S[6][2],v,X)}if(C>Q){J.fillStyle=CONNECTOR_COLOR;J.fillRect(Q+W,X+5,C-Q,1)}}else{J.fillStyle=l;this.rect_or_text(J,au,N,ak,ap,O,v,X)}if(r!=="Dense"&&!ad&&ap>N){J.fillStyle=this.prefs.label_color;if(o===0&&ae-J.measureText(O).width<0){J.textAlign="left";J.fillText(R,K+2+W,X+8)}else{J.textAlign="right";J.fillText(R,ae-2+W,X+8)}J.fillStyle=l}}else{if(I.dataset_type==="interval_index"){if(ad){J.fillStyle=l;J.fillRect(ae+W,X+5,K-ae,1)}else{var F=S[4],V=S[5],ag=S[6],h=S[7];if(V&&ag){P=Math.floor(Math.max(0,(V-N)*au));aw=Math.ceil(Math.min(a,Math.max(0,(ag-N)*au)))}if(r!=="Dense"&&O!==undefined&&ap>N){J.fillStyle=ah;if(o===0&&ae-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,ae-2+W,X+8)}J.fillStyle=l}if(h){if(F){if(F=="+"){J.fillStyle=RIGHT_STRAND}else{if(F=="-"){J.fillStyle=LEFT_STRAND}}J.fillRect(ae+W,X,K-ae,10);J.fillStyle=l}for(var am=0,g=h.length;am<g;am++){var u=h[am],d=Math.floor(Math.max(0,(u[0]-N)*au)),T=Math.ceil(Math.min(a,Math.max((u[1]-N)*au)));if(d>T){continue}G=5;ai=3;J.fillRect(d+W,X+ai,T-d,G);if(P!==undefined&&!(d>aw||T<P)){G=9;ai=1;var aj=Math.max(d,P),B=Math.min(T,aw);J.fillRect(aj+W,X+ai,B-aj,G)}}}else{G=9;ai=1;J.fillRect(ae+W,X+ai,K-ae,G);if(S.strand){if(S.strand=="+"){J.fillStyle=RIGHT_STRAND_INV}else{if(S.strand=="-"){J.fillStyle=LEFT_STRAND_INV}}J.fillRect(ae+W,X,K-ae,10);J.fillStyle=l}}}}else{if(I.dataset_type==="vcf"){if(ad){J.fillStyle=l;J.fillRect(ae+W,X+5,K-ae,1)}else{var t=S[4],n=S[5],c=S[6];G=9;ai=1;J.fillRect(ae+W,X,K-ae,G);if(r!=="Dense"&&O!==undefined&&ap>N){J.fillStyle=ah;if(o===0&&ae-J.measureText(O).width<0){J.textAlign="left";J.fillText(O,K+2+W,X+8)}else{J.textAlign="right";J.fillText(O,ae-2+W,X+8)}J.fillStyle=l}var m=t+" / "+n;if(ap>N&&J.measureText(m).width<(K-ae)){J.fillStyle="white";J.textAlign="center";J.fillText(m,W+ae+(K-ae)/2,X+8);J.fillStyle=l}}}}}an++}}return q},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input 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ReadTrack=function(d,b,a,c,e){FeatureTrack.call(this,d,b,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(d,b,a,c,e){FeatureTrack.call(this,d,b,a,c,e);this.track_type="ToolDataFeatureTrack"};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{init:function(){var b=this,c="initial";b.data_url=raw_data_url;b.data_query_wait=1000;var a={low:b.view.max_low,high:b.view.max_high,dataset_id:b.dataset_id,chrom:b.view.chrom,resolution:this.view.resolution,mode:b.mode};this.init_each(a,function(d){b.mode_div.show();b.data_cache.set(c,d);b.draw();var e=function(){if(b.data_cache.num_elements==0){setTimeout(e,300)}else{b.data_url=default_data_url}};e()})}});
\ No newline at end of file
+var DENSITY=200,FEATURE_LEVELS=10,MAX_FEATURE_DEPTH=100,DEFAULT_DATA_QUERY_WAIT=5000,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_LOADING="Loading data...",FILTERABLE_CLASS="filterable",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)}CONTEXT=DUMMY_CANVAS.getContext("2d");PX_PER_CHAR=CONTEXT.measureText("A").width;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.key_ary.splice(a,1);this.key_ary.push(b)}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},clear:function(){this.obj_cache={};this.key_ary=[]}});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=$("<a href='javascript:void(0);'>Close 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false}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress focusout",b).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);this.location_span.bind("click",function(){a.location_span.hide();a.chrom_select.hide();a.nav_input.css("display","inline-block");a.nav_input.select();a.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zo_link=$("<a id='zoom-out' />").click(function(){a.zoom_out();a.redraw()}).appendTo(this.chrom_form);this.zi_link=$("<a id='zoom-in' />").click(function(){a.zoom_in();a.redraw()}).appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(f){if(f.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=f.chrom_info;var j='<option value="">Select Chrom/Contig</option>';for(var h=0,e=a.chrom_data.length;h<e;h++){var g=a.chrom_data[h].chrom;j+='<option value="'+g+'">'+g+"</option>"}a.chrom_select.html(j);a.intro_div.show();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())});if(d){d()}},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("click",function(f){$(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){this.current_x=f.offsetX}).bind("drag",function(f){var h=f.offsetX-this.current_x;this.current_x=f.offsetX;var g=Math.round(h/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();$(this).hide()});this.viewport_container.bind("dragstart",function(f){this.original_low=a.low;this.current_height=f.clientY;this.current_x=f.offsetX;this.enable_pan=(f.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(h){if(!this.enable_pan||this.in_reordering){return}var f=$(this);var j=h.offsetX-this.current_x;var g=f.scrollTop()-(h.clientY-this.current_height);f.scrollTop(g);this.current_height=h.clientY;this.current_x=h.offsetX;var i=Math.round(j/a.viewport_container.width()*(a.high-a.low));a.move_delta(i)});this.top_labeltrack.bind("dragstart",function(f){this.drag_origin_x=f.clientX;this.drag_origin_pos=f.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height()+a.top_labeltrack.height()+a.nav_labeltrack.height(),top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(j){var g=Math.min(j.clientX,this.drag_origin_x)-a.container.offset().left,f=Math.max(j.clientX,this.drag_origin_x)-a.container.offset().left,i=(a.high-a.low),h=a.viewport_container.width();a.update_location(Math.round(g/h*i)+a.low,Math.round(f/h*i)+a.low);this.drag_div.css({left:g+"px",width:(f-g)+"px"})}).bind("dragend",function(k){var g=Math.min(k.clientX,this.drag_origin_x),f=Math.max(k.clientX,this.drag_origin_x),i=(a.high-a.low),h=a.viewport_container.width(),j=a.low;a.low=Math.round(g/h*i)+j;a.high=Math.round(f/h*i)+j;this.drag_div.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();$(window).trigger("resize")},update_location:function(a,b){this.location_span.text(commatize(a)+" - "+commatize(b));this.nav_input.val(this.chrom+":"+commatize(a)+"-"+commatize(b))},change_chrom:function(e,b,g){var d=this;var f=$.grep(d.chrom_data,function(j,k){return j.chrom===e})[0];if(f===undefined){return}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;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 j=this,a,d,b=f.split(":"),h=b[0],i=b[1];if(i!==undefined){try{var g=i.split("-");a=parseInt(g[0].replace(/,/g,""),10);d=parseInt(g[1].replace(/,/g,""),10)}catch(c){return false}}j.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);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};$.extend(NumberFilter.prototype,{applies_to:function(a){if(a.length>this.index){return true}return false},keep:function(a){if(!this.applies_to(a)){return true}return(a[this.index]>=this.low&&a[this.index]<=this.high)},update_attrs:function(b){var a=false;if(!this.applies_to(b)){return a}if(b[this.index]<this.slider_min){this.slider_min=b[this.index];a=true}if(b[this.index]>this.slider_max){this.slider_max=b[this.index];a=false}return a},update_ui_elt:function(){var b=this.slider.slider("option","min"),a=this.slider.slider("option","max");if(this.slider_min<b||this.slider_max>a){this.slider.slider("option","min",this.slider_min);this.slider.slider("option","max",this.slider_max);this.slider.slider("option","values",[this.slider_min,this.slider_max])}}});var get_filters_from_dict=function(a){var g=[];for(var d=0;d<a.length;d++){var f=a[d];var c=f.name,e=f.type,b=f.index;if(e=="int"||e=="float"){g[d]=new NumberFilter(c,b)}else{g[d]=new Filter(c,b,e)}}return g};var Track=function(b,a,e,c,d){this.name=b;this.view=a;this.parent_element=e;this.data_url=(c?c:default_data_url);this.data_query_wait=(d?d:DEFAULT_DATA_QUERY_WAIT);this.init_global()};$.extend(Track.prototype,{init_global:function(){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=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.initial_canvas=undefined;a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(!a.dataset_id){return}if(a.view.chrom){$.getJSON(a.data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$(" <a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("View error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},a.data_query_wait)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}},restore_prefs:function(a){var b=this;$.each(a,function(c,d){if(d!==undefined){b.prefs[c]=d}})},update_name:function(a){this.old_name=this.name;this.name=a;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var TiledTrack=function(c,l,p){var d=this,q=d.view;this.filters=(c!==undefined?get_filters_from_dict(c):[]);this.tool=(l!==undefined?get_tool_from_dict(l):undefined);this.parent_track=p;this.child_tracks=[];if(d.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}this.filtering_div=$("<div/>").addClass("track-filters").hide();this.header_div.after(this.filtering_div);this.filtering_div.bind("drag",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var b=$("<table class='filters'>").appendTo(this.filtering_div);$.each(this.filters,function(u,x){var t=$("<tr>").appendTo(b);var w=$("<th class='filter-info'>").appendTo(t);var s=$("<span class='name'>").appendTo(w);s.text(x.name+"  ");var i=$("<span class='values'>").appendTo(w);var v=$("<td>").appendTo(t);x.control_element=$("<div id='"+x.name+"-filter-control' style='width: 200px; position: relative'>").appendTo(v);x.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(z,A){var y=A.values;i.text("["+y[0]+"-"+y[1]+"]");x.low=y[0];x.high=y[1];d.draw(true)},change:function(y,z){x.control_element.slider("option","slide").call(x.control_element,y,z)}});x.slider=x.control_element;x.slider_label=i});if(this.tool){this.dynamic_tool_div=$("<div/>").addClass("dynamic-tool").hide();this.header_div.after(this.dynamic_tool_div);this.dynamic_tool_div.bind("drag",function(i){i.stopPropagation()}).bind("click",function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()});var o=$("<div class='tool-name'>").appendTo(this.dynamic_tool_div).text(this.tool.name);var n=this.tool.params;var d=this;$.each(this.tool.params,function(y,t){var w=$("<div>").addClass("param-row").appendTo(d.dynamic_tool_div);var v=$("<div>").addClass("slider-label").appendTo(w);var A=$("<span class='param-name'>").text(t.label+"  ").appendTo(v);var u=$("<span/>").text(t.value);var x=$("<span class='param-value'>").appendTo(v).append("[").append(u).append("]");var z=$("<div/>").addClass("slider").appendTo(w);var i=$("<div id='"+t.name+"-param-control'>").appendTo(z);var s=(t.max<=1?0.01:(t.max<=1000?1:5));i.slider({min:t.min,max:t.max,step:s,value:t.value,slide:function(B,D){var C=D.value;t.value=C;if(0<C&&C<1){C=parseFloat(C).toFixed(2)}u.text(C)},change:function(B,C){t.value=C.value}});x.click(function(){var D=u,C=D.text(),B=(t.max<=1?4:t.max.length);D.text("");$("<input type='text'/>").attr("size",B).attr("maxlength",B).attr("value",C).appendTo(D).focus().select().click(function(E){E.stopPropagation()}).blur(function(){$(this).remove();D.text(C)}).keyup(function(G){if(G.keyCode===27){$(this).trigger("blur")}else{if(G.keyCode===13){var E=$(this),F=parseFloat(E.val());if(isNaN(F)||F>t.max||F<t.min){alert("Parameter value must be in the range ["+t.min+"-"+t.max+"]");return $(this)}D.text(F);i.slider("value",F);t.value=F}}})});$("<div style='clear: both;'/>").appendTo(w)});var r=$("<div>").addClass("param-row").appendTo(this.dynamic_tool_div);var m=$("<input type='submit'>").attr("value","Run").appendTo(r);var d=this;m.click(function(){d.run_tool()})}if(d.display_modes!==undefined){if(d.mode_div===undefined){d.mode_div=$("<div class='right-float menubutton popup' />").appendTo(d.header_div);var g=d.display_modes[0];d.mode=g;d.mode_div.text(g);var e=function(i){d.mode_div.text(i);d.mode=i;d.tile_cache.clear();d.draw()};var a={};for(var h=0,k=d.display_modes.length;h<k;h++){var j=d.display_modes[h];a[j]=function(i){return function(){e(i)}}(j)}make_popupmenu(d.mode_div,a)}else{d.mode_div.hide()}}var f={};f["Edit configuration"]=function(){var t=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},i=function(){d.update_options(d.track_id);hide_modal();$(window).unbind("keypress.check_enter_esc")},s=function(u){if((u.keyCode||u.which)===27){t()}else{if((u.keyCode||u.which)===13){i()}}};$(window).bind("keypress.check_enter_esc",s);show_modal("Configure Track",d.gen_options(d.track_id),{Cancel:t,OK:i})};f["Set as overview"]=function(){q.overview_viewport.find("canvas").remove();d.is_overview=true;d.set_overview();for(var i in q.tracks){if(q.tracks[i]!==d){q.tracks[i].is_overview=false}}};if(d.filters.length>0){f["Show filters"]=function(){var i;if(!d.filtering_div.is(":visible")){i="Hide filters";d.filters_visible=true}else{i="Show filters";d.filters_visible=false}d.filtering_div.toggle()}}if(d.tool){f["Toggle Tool"]=function(){var i;if(!d.dynamic_tool_div.is(":visible")){i="Hide dynamic tool";d.update_name(d.name+d.tool_region_and_parameters_str())}else{i="Show dynamic tool";d.revert_name()}d.dynamic_tool_div.toggle()}}f.Remove=function(){q.remove_track(d);if(q.num_tracks===0){$("#no-tracks").show()}};d.popup_menu=make_popupmenu(d.name_div,f)};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(a){var k=this.view.low,g=this.view.high,h=g-k,f=this.view.resolution;var n=$("<div style='position: relative;'></div>"),o=this.content_div.width()/h;this.content_div.append(n);this.max_height=0;var b=Math.floor(k/f/DENSITY);var j={};while((b*DENSITY*f)<g){var l=this.content_div.width()+"_"+o+"_"+b;var e=this.tile_cache.get(l);if(!a&&e){var i=b*DENSITY*f;var d=(i-k)*o;if(this.left_offset){d-=this.left_offset}e.css({left:d});this.show_tile(e,n)}else{this.delayed_draw(this,l,k,g,b,f,n,o,j)}b+=1}var c=this;var m=setInterval(function(){if(obj_length(j)===0){if(c.content_div.children().length>1){c.content_div.children(":first").remove()}for(var p=0;p<c.filters.length;p++){c.filters[p].update_ui_elt()}clearInterval(m)}},50)},delayed_draw:function(c,h,g,e,b,d,i,j,f){var a=setTimeout(function(){if(g<=c.view.high&&e>=c.view.low){var k=c.draw_tile(d,b,i,j);if(k){if(!c.initial_canvas&&!window.G_vmlCanvasManager){c.initial_canvas=$(k).clone();var n=k.get(0).getContext("2d");var l=c.initial_canvas.get(0).getContext("2d");var m=n.getImageData(0,0,n.canvas.width,n.canvas.height);l.putImageData(m,0,0);c.set_overview()}c.tile_cache.set(h,k);c.show_tile(k,i)}}delete f[a]},50);f[a]=true},show_tile:function(a,c){var b=this;c.append(a);b.max_height=Math.max(b.max_height,a.height());b.content_div.css("height",b.max_height+"px");if(b.hidden){return}if(a.hasClass(FILTERABLE_CLASS)){show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters");if(b.filters_visible){b.filtering_div.show()}}else{show_hide_popupmenu_options(b.popup_menu,"(Show|Hide) filters",false);b.filtering_div.hide()}},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,undefined,{},{},{},d)}view.add_track(e);var a=function(){$.getJSON(run_tool_url,b,function(f){if(f=="no converter"){e.container_div.addClass("error");e.content_div.text(DATA_NOCONVERTER)}else{if(f=="pending"){e.container_div.addClass("pending");e.content_div.text("Converting input data so that it can be easily reused.");setTimeout(a,2000)}else{e.dataset_id=f.dataset_id;e.content_div.text("Running job.");e.init()}}})};a()},tool_region_and_parameters_str:function(c,a,d){var b=this,e=(c!==undefined&&a!==undefined&&d!=undefined?c+":"+a+"-"+d:"all");return" - region=["+e+"], parameters=["+b.tool.get_param_values().join(", ")+"]"}});var LabelTrack=function(a,b){this.track_type="LabelTrack";this.hidden=true;Track.call(this,null,a,b);this.container_div.addClass("label-track")};$.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.content_div.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);this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.extend(ReferenceTrack.prototype,TiledTrack.prototype,{get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,j=f+"_"+b;var e=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(e)}e=$(e);var n=e.get(0).getContext("2d");if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o),i=Math.round(o/2);n.fillText(m[h],a+this.left_offset+i,10)}k.append(e);return e}this.content_div.css("height","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.original_dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={color:"black",min_value:undefined,max_value:undefined,mode:this.mode};this.restore_prefs(c)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,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",top:a.height_px+12+"px",left:"10px"});f.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:this.data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){var h=g.data;c.data_cache.set(e,h);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*o,a=DENSITY*o,w=o+"_"+r;var b=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(b)}b=$(b);if(this.data_cache.get(w)===undefined){this.get_data(o,r);return}var v=this.data_cache.get(w);if(!v){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),j=false,k=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,t=this.total_frequency,d=this.height_px,l=this.mode;n.beginPath();n.fillStyle=this.prefs.color;var u,h,f;if(v.length>1){f=Math.ceil((v[1][0]-v[0][0])*e)}else{f=10}for(var p=0,q=v.length;p<q;p++){u=Math.round((v[p][0]-s)*e);h=v[p][1];if(h===null){if(j&&l==="Filled"){n.lineTo(u,d)}j=false;continue}if(h<k){h=k}else{if(h>g){h=g}}if(l==="Histogram"){h=Math.round(d-(h-k)/m*d);n.fillRect(u,h,f,d-h)}else{if(l==="Intensity"){h=255-Math.floor((h-k)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(u,0,f,d)}else{h=Math.round(d-(h-k)/m*d);if(j){n.lineTo(u,h)}else{j=true;if(l==="Filled"){n.moveTo(u,d);n.lineTo(u,h)}else{n.moveTo(u,h)}}}}}if(l==="Filled"){if(j){n.lineTo(u,d)}n.fill()}else{n.stroke()}c.append(b);return b},gen_options:function(m){var a=$("<div />").addClass("form-row");var e="track_"+m+"_color",b=$("<label />").attr("for",e).text("Color:"),c=$("<input />").attr("id",e).attr("name",e).val(this.prefs.color),h="track_"+m+"_minval",l=$("<label></label>").attr("for",h).text("Min value:"),d=(this.prefs.min_value===undefined?"":this.prefs.min_value),k=$("<input></input>").attr("id",h).val(d),j="track_"+m+"_maxval",g=$("<label></label>").attr("for",j).text("Max value:"),i=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",j).val(i);return a.append(l).append(k).append(g).append(f).append(b).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_color").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.color){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.color=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(f,c,a,e,g,d,b){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,f,c,c.viewport_container);TiledTrack.call(this,g,d,b);this.height_px=0;this.container_div.addClass("feature-track");this.dataset_id=a;this.original_dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.summary_draw_height=30;this.default_font="9px Monaco, Lucida Console, monospace";this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.left_offset=200;this.prefs={block_color:"#444",label_color:"black",show_counts:true};this.restore_prefs(e)};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution,mode:a.mode},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(b.data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,b,p){var r=this.inc_slots[a];if(!r||(r.mode!==p)){r={};r.w_scale=a;r.mode=p;this.inc_slots[a]=r;this.s_e_by_tile[a]={}}var l=r.w_scale,x=[],y=[],j=0,n=this.view.max_low;for(var v=0,w=h.length;v<w;v++){var g=h[v],k=g[0];if(r[k]!==undefined){j=Math.max(j,r[k]);y.push(r[k])}else{x.push(v)}}var q=this.s_e_by_tile[a];var m=function(D,E){var C;for(var B=0,F=undefined;B<=MAX_FEATURE_DEPTH;B++){C=true;F=q[B];if(F!==undefined){for(var z=0,A=F.length;z<A;z++){var i=F[z];if(E>i[0]&&D<i[1]){C=false;break}}}if(C){break}}if(C){return B}else{return -1}};for(var v=0,w=x.length;v<w;v++){var g=h[x[v]],k=g[0],t=g[1],c=g[2],o=g[3],d=Math.floor((t-n)*l),f=Math.ceil((c-n)*l),u=CONTEXT.measureText(o).width,e;if(o!==undefined&&!b){if(d-u<0){f+=u;e="left"}else{d-=u;e="right"}}var s=m(d,f);if(s<0){}if(s>=0){slot=q[s];if(slot===undefined){slot=q[s]=[]}slot.push([d,f]);r[k]=s;j=Math.max(j,s)}else{console.log("WARNING: not displaying feature")}}return j},rect_or_text:function(r,l,t,b,q,i,f,e){r.textAlign="center";var k=0,p=Math.round(l/2);for(var m=0,s=i.length;m<s;m++){var j=i[m],d="MIDNSHP"[j[0]],n=j[1];if(d==="H"||d==="S"){k-=n}var g=q+k,w=Math.floor(Math.max(0,(g-t)*l)),h=Math.floor(Math.max(0,(g+n-t)*l));switch(d){case"S":case"H":case"M":var o=f.slice(k,n);if((this.mode==="Pack"||this.mode==="Auto")&&f!==undefined&&l>PX_PER_CHAR){r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+1,h-w,9);r.fillStyle=CONNECTOR_COLOR;for(var u=0,a=o.length;u<a;u++){if(g+u>=t&&g+u<=b){var v=Math.floor(Math.max(0,(g+u-t)*l));r.fillText(o[u],v+this.left_offset+p,e+9)}}}else{r.fillStyle=this.prefs.block_color;r.fillRect(w+this.left_offset,e+(this.mode!="Dense"?4:5),h-w,(this.mode!="Dense"?3:1))}break;case"N":r.fillStyle=CONNECTOR_COLOR;r.fillRect(w+this.left_offset,e+5,h-w,1);break;case"D":r.fillStyle="red";r.fillRect(w+this.left_offset,e+4,h-w,3);break;case"P":case"I":break}k+=n}},draw_tile:function(ae,o,s,at){var M=o*DENSITY*ae,aj=(o+1)*DENSITY*ae,L=aj-M;var al=(!this.initial_canvas?"initial":M+"_"+aj);var H=this.data_cache.get(al);var e;if(H===undefined||H==="pending"||(this.mode!=="Auto"&&H.dataset_type==="summary_tree")){this.data_queue[[M,aj]]=true;this.get_data(M,aj);return}var a=Math.ceil(L*at),ag=this.prefs.label_color,l=this.prefs.block_color,r=this.mode,w=25,ac=(r==="Squish")||(r==="Dense")&&(r!=="Pack")||(r==="Auto"&&(H.extra_info==="no_detail")),V=this.left_offset,ar,C,au;var q=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(q)}q=$(q);if(H.dataset_type==="summary_tree"){C=this.summary_draw_height}else{if(r==="Dense"){C=w;au=10}else{au=(ac?this.vertical_nodetail_px:this.vertical_detail_px);var z=(at<0.0001?1/this.view.zoom_res:at);C=this.incremental_slots(z,H.data,ac,r)*au+w;ar=this.inc_slots[z]}}q.css({position:"absolute",top:0,left:(M-this.view.low)*at-V});q.get(0).width=a+V;q.get(0).height=C;s.parent().css("height",Math.max(this.height_px,C)+"px");var I=q.get(0).getContext("2d");I.fillStyle=l;I.font=this.default_font;I.textAlign="right";this.container_div.find(".yaxislabel").remove();if(H.dataset_type=="summary_tree"){var X=H.data,K=H.max,b=Math.ceil(H.delta*at);var p=$("<div />").addClass("yaxislabel").text(K);p.css({position:"absolute",top:"22px",left:"10px"});p.prependTo(this.container_div);for(var an=0,G=X.length;an<G;an++){var Z=Math.floor((X[an][0]-M)*at);var Y=X[an][1];if(!Y){continue}var ak=Y/K*this.summary_draw_height;I.fillStyle="black";I.fillRect(Z+V,this.summary_draw_height-ak,b,ak);if(this.prefs.show_counts&&I.measureText(Y).width<b){I.fillStyle="#bbb";I.textAlign="center";I.fillText(Y,Z+V+(b/2),this.summary_draw_height-5)}}e="Summary";s.append(q);return q}if(H.message){q.css({border:"solid red","border-width":"2px 2px 2px 0px"});I.fillStyle="red";I.textAlign="left";I.fillText(H.message,100+V,au);return q}for(var ap=0;ap<this.filters.length;ap++){if(this.filters[ap].applies_to(H.data[0])){q.addClass(FILTERABLE_CLASS);break}}var aq=H.data;var am=0;for(var an=0,G=aq.length;an<G;an++){var R=aq[an],Q=R[0],ao=R[1],ab=R[2],N=R[3];if(this.mode!="Dense"&&ar[Q]===undefined){continue}var aa=false;var T;for(var ap=0;ap<this.filters.length;ap++){T=this.filters[ap];T.update_attrs(R);if(!T.keep(R)){aa=true;break}}if(aa){continue}if(ao<=aj&&ab>=M){var ad=Math.floor(Math.max(0,(ao-M)*at)),J=Math.ceil(Math.min(a,Math.max(0,(ab-M)*at))),W=(r==="Dense"?1:(1+ar[Q]))*au;var F,ah,O=null,av=null;if(H.dataset_type==="bai"){I.fillStyle=l;if(R[5] instanceof Array){var D=Math.floor(Math.max(0,(R[4][0]-M)*at)),P=Math.ceil(Math.min(a,Math.max(0,(R[4][1]-M)*at))),B=Math.floor(Math.max(0,(R[5][0]-M)*at)),v=Math.ceil(Math.min(a,Math.max(0,(R[5][1]-M)*at)));if(R[4][1]>=M&&R[4][0]<=aj){this.rect_or_text(I,at,M,aj,R[4][0],R[4][2],R[4][3],W)}if(R[5][1]>=M&&R[5][0]<=aj){this.rect_or_text(I,at,M,aj,R[5][0],R[5][2],R[5][3],W)}if(B>P){I.fillStyle=CONNECTOR_COLOR;I.fillRect(P+V,W+5,B-P,1)}}else{I.fillStyle=l;this.rect_or_text(I,at,M,aj,ao,R[4],R[5],W)}if(r!=="Dense"&&!ac&&ao>M){I.fillStyle=this.prefs.label_color;if(o===0&&ad-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+V,W+8)}else{I.textAlign="right";I.fillText(N,ad-2+V,W+8)}I.fillStyle=l}}else{if(H.dataset_type==="interval_index"){if(ac){I.fillStyle=l;I.fillRect(ad+V,W+5,J-ad,1)}else{var E=R[4],U=R[5],af=R[6],h=R[7];if(U&&af){O=Math.floor(Math.max(0,(U-M)*at));av=Math.ceil(Math.min(a,Math.max(0,(af-M)*at)))}if(r!=="Dense"&&N!==undefined&&ao>M){I.fillStyle=ag;if(o===0&&ad-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+V,W+8)}else{I.textAlign="right";I.fillText(N,ad-2+V,W+8)}I.fillStyle=l}if(h){if(E){if(E=="+"){I.fillStyle=RIGHT_STRAND}else{if(E=="-"){I.fillStyle=LEFT_STRAND}}I.fillRect(ad+V,W,J-ad,10);I.fillStyle=l}for(var al=0,g=h.length;al<g;al++){var u=h[al],d=Math.floor(Math.max(0,(u[0]-M)*at)),S=Math.ceil(Math.min(a,Math.max((u[1]-M)*at)));if(d>S){continue}F=5;ah=3;I.fillRect(d+V,W+ah,S-d,F);if(O!==undefined&&!(d>av||S<O)){F=9;ah=1;var ai=Math.max(d,O),A=Math.min(S,av);I.fillRect(ai+V,W+ah,A-ai,F)}}}else{F=9;ah=1;I.fillRect(ad+V,W+ah,J-ad,F);if(R.strand){if(R.strand=="+"){I.fillStyle=RIGHT_STRAND_INV}else{if(R.strand=="-"){I.fillStyle=LEFT_STRAND_INV}}I.fillRect(ad+V,W,J-ad,10);I.fillStyle=l}}}}else{if(H.dataset_type==="vcf"){if(ac){I.fillStyle=l;I.fillRect(ad+V,W+5,J-ad,1)}else{var t=R[4],n=R[5],c=R[6];F=9;ah=1;I.fillRect(ad+V,W,J-ad,F);if(r!=="Dense"&&N!==undefined&&ao>M){I.fillStyle=ag;if(o===0&&ad-I.measureText(N).width<0){I.textAlign="left";I.fillText(N,J+2+V,W+8)}else{I.textAlign="right";I.fillText(N,ad-2+V,W+8)}I.fillStyle=l}var m=t+" / "+n;if(ao>M&&I.measureText(m).width<(J-ad)){I.fillStyle="white";I.textAlign="center";I.fillText(m,V+ad+(J-ad)/2,W+8);I.fillStyle=l}}}}}am++}}return q},gen_options:function(i){var a=$("<div />").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label />").attr("for",e).text("Block color:"),l=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label />").attr("for",j).text("Text color:"),h=$("<input />").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c,e){FeatureTrack.call(this,d,b,a,c,e);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});var ToolDataFeatureTrack=function(d,b,a,c,e){FeatureTrack.call(this,d,b,a,c,e);this.track_type="ToolDataFeatureTrack"};$.extend(ToolDataFeatureTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{init:function(){var b=this,c="initial";b.data_url=raw_data_url;b.data_query_wait=1000;var a={low:b.view.max_low,high:b.view.max_high,dataset_id:b.dataset_id,chrom:b.view.chrom,resolution:this.view.resolution,mode:b.mode};this.init_each(a,function(d){b.mode_div.show();b.data_cache.set(c,d);b.draw();var e=function(){if(b.data_cache.num_elements==0){setTimeout(e,300)}else{b.data_url=default_data_url}};e()})}});
\ No newline at end of file
diff --git a/static/scripts/trackster.js b/static/scripts/trackster.js
index d8b647982ff..a5b6c0a1ac0 100644
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -8,7 +8,7 @@
 var 
     DENSITY = 200,
     FEATURE_LEVELS = 10,
-    MAX_FEATURE_DEPTH = 50,
+    MAX_FEATURE_DEPTH = 100,
     DEFAULT_DATA_QUERY_WAIT = 5000,
     CONNECTOR_COLOR = "#ccc",
     DATA_ERROR = "There was an error in indexing this dataset.",
@@ -1600,68 +1600,65 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
             });
         }
     },
-    incremental_slots: function( level, features, no_detail, mode ) {
-        if (!this.inc_slots[level]) {
-            this.inc_slots[level] = {};
-            this.inc_slots[level].w_scale = level;
-            this.inc_slots[level].mode = mode;
+    //
+    // Place features in slots for drawing (i.e. pack features).
+    // this.inc_slots[level] is created in this method. this.inc_slots[level]
+    // is a dictionary of slotted features; key is feature uid, value is a dictionary
+    // with keys 'slot' and 'text'.
+    // Returns the number of slots used to pack features.
+    //
+    incremental_slots: function(level, features, no_detail, mode) {
+        //
+        // Get/create incremental slots for level. If display mode changed,
+        // need to create new slots.
+        //
+        var inc_slots = this.inc_slots[level];
+        if (!inc_slots || (inc_slots.mode !== mode)) {
+            inc_slots = {};
+            inc_slots.w_scale = level;
+            inc_slots.mode = mode;
+            this.inc_slots[level] = inc_slots;
             this.s_e_by_tile[level] = {};
         }
+        
+        //
+        // If feature already exists in slots (from previously seen tiles), use the same slot,
+        // otherwise if not seen, add to "undone" list for slot calculation.
+        //
+        var w_scale = inc_slots.w_scale,
+            undone = [], slotted = [],
+            highest_slot = 0, // To measure how big to draw canvas
+            max_low = this.view.max_low;
         // TODO: Should calculate zoom tile index, which will improve performance
         // by only having to look at a smaller subset
         // if (this.s_e_by_tile[0] === undefined) { this.s_e_by_tile[0] = []; }
-        var w_scale = this.inc_slots[level].w_scale,
-            undone = [],
-            highest_slot = 0, // To measure how big to draw canvas
-            max_low = this.view.max_low;
-            
-        var slotted = [];
-        // Reset packing when we change display mode
-        if (this.inc_slots[level].mode !== mode) {
-            delete this.inc_slots[level];
-            this.inc_slots[level] = { "mode": mode, "w_scale": w_scale };
-            delete this.s_e_by_tile[level];
-            this.s_e_by_tile[level] = {};
-        }
-        // If feature already exists in slots (from previously seen tiles), use the same slot,
-        // otherwise if not seen, add to "undone" list for slot calculation
         for (var i = 0, len = features.length; i < len; i++) {
             var feature = features[i],
                 feature_uid = feature[0];
-            if (this.inc_slots[level][feature_uid] !== undefined) {
-                highest_slot = Math.max(highest_slot, this.inc_slots[level][feature_uid]);
-                slotted.push(this.inc_slots[level][feature_uid]);
+            if (inc_slots[feature_uid] !== undefined) {
+                highest_slot = Math.max(highest_slot, inc_slots[feature_uid]);
+                slotted.push(inc_slots[feature_uid]);
             } else {
                 undone.push(i);
             }
         }
         
-        // console.log("Slotted: ", features.length - undone.length, "/", features.length, slotted);
-        for (var i = 0, len = undone.length; i < len; i++) {
-            var feature = features[undone[i]],
-                feature_uid = feature[0],
-                feature_start = feature[1],
-                feature_end = feature[2],
-                feature_name = feature[3],
-                f_start = Math.floor( (feature_start - max_low) * w_scale ),
-                f_end = Math.ceil( (feature_end - max_low) * w_scale );
-                        
-            if (feature_name !== undefined && !no_detail) {
-                var text_len = CONTEXT.measureText(feature_name).width;
-                if (f_start - text_len < 0) {
-                    f_end += text_len;
-                } else {
-                    f_start -= text_len;
-                }
-            }
-            
-            var j = 0;
-            // Try to fit the feature to the first slot that doesn't overlap any other features in that slot
-            while (j <= MAX_FEATURE_DEPTH) {
-                var found = true;
-                if (this.s_e_by_tile[level][j] !== undefined) {
-                    for (var k = 0, k_len = this.s_e_by_tile[level][j].length; k < k_len; k++) {
-                        var s_e = this.s_e_by_tile[level][j][k];
+        //
+        // Slot unslotted features.
+        //
+        var s_e_by_tile = this.s_e_by_tile[level];
+        
+        // Find the first slot s/t current feature doesn't overlap any other features in that slot.
+        // Returns -1 if no slot was found.
+        var find_slot = function(f_start, f_end) {
+            var found;
+            for (var slot_num = 0, slot = undefined; slot_num <= MAX_FEATURE_DEPTH; slot_num++) {
+                found = true;
+                slot = s_e_by_tile[slot_num];
+                if (slot !== undefined) {
+                    // Iterate through features already in slot to see if current feature will fit.
+                    for (var k = 0, k_len = slot.length; k < k_len; k++) {
+                        var s_e = slot[k];
                         if (f_end > s_e[0] && f_start < s_e[1]) {
                             found = false;
                             break;
@@ -1669,20 +1666,99 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
                     }
                 }
                 if (found) {
-                    if (this.s_e_by_tile[level][j] === undefined) { this.s_e_by_tile[level][j] = []; }
-                    this.s_e_by_tile[level][j].push([f_start, f_end]);
-                    this.inc_slots[level][feature_uid] = j;
-                    highest_slot = Math.max(highest_slot, j);
                     break;
                 }
-                j++;
+            }
+            
+            if (found) {
+                return slot_num;
+            }
+            else {
+                return -1;
+            }
+        };
+        
+        // Do slotting.
+        for (var i = 0, len = undone.length; i < len; i++) {
+            var feature = features[undone[i]],
+                feature_uid = feature[0],
+                feature_start = feature[1],
+                feature_end = feature[2],
+                feature_name = feature[3],
+                // Where to start, end drawing on screen.
+                f_start = Math.floor( (feature_start - max_low) * w_scale ),
+                f_end = Math.ceil( (feature_end - max_low) * w_scale ),
+                text_len = CONTEXT.measureText(feature_name).width,
+                text_align;
+            
+            // Update start, end drawing locations to include feature name.
+            // Try to put the name on the left, if not, put on right.
+            if (feature_name !== undefined && !no_detail) {
+                if (f_start - text_len < 0) {
+                    f_end += text_len;
+                    text_align = "left";
+                } else {
+                    f_start -= text_len;
+                    text_align = "right";
+                }
+            }
+                        
+            // Find slot.
+            var slot_num = find_slot(f_start, f_end);
+            if (slot_num < 0) {
+                /*
+                TODO: this is not yet working --
+                console.log(feature_uid, "looking for slot with text on the right");
+                // Slot not found. If text was on left, try on right and see
+                // if slot can be found.
+                // TODO: are there any checks we need to do to ensure that text
+                // will fit on tile?
+                if (text_align == "left") {
+                    f_start -= text_len;
+                    f_end -= text_len;
+                    text_align = "right";
+                    slot_num = find_slot(f_start, f_end);
+                }
+                if (slot_num >= 0) {
+                    console.log(feature_uid, "found slot with text on the right");
+                }
+                */
+            }
+            
+            // Do slotting.
+            if (slot_num >= 0) {
+                // Add current feature to slot.
+                slot = s_e_by_tile[slot_num];
+                if (slot === undefined) { 
+                    slot = s_e_by_tile[slot_num] = [];
+                }
+                slot.push([f_start, f_end]);
+                inc_slots[feature_uid] = slot_num;
+                highest_slot = Math.max(highest_slot, slot_num);
+            }
+            else {
+                // TODO: remove this warning when skipped features are handled.
+                // Show warning for skipped feature.
+                console.log("WARNING: not displaying feature"); // , feature_uid, f_start, f_end);
             }
         }
-        return highest_slot;
         
+        // Debugging: view slots data.
+        /*
+        for (var i = 0; i < MAX_FEATURE_DEPTH; i++) {
+            var slot = s_e_by_tile[i];
+            if (slot !== undefined) {
+                console.log(i, "*************");
+                for (var k = 0, k_len = slot.length; k < k_len; k++) {
+                    console.log("\t", slot[k][0], slot[k][1]);
+                }
+            }
+        }
+        */
+        return highest_slot;
     },
     // Right now this function is used only for rendering BAM reads.
-    rect_or_text: function( ctx, w_scale, tile_low, tile_high, feature_start, orig_seq, cigar, y_center ) {
+    rect_or_text: function( ctx, w_scale, tile_low, tile_high, feature_start, cigar, orig_seq, y_center ) {
         ctx.textAlign = "center";
         var cur_offset = 0,
             gap = Math.round(w_scale / 2);
@@ -1895,28 +1971,26 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
                 // All features need a start, end, and vertical center.
                 var f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
                     f_end   = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
-                    y_center = (mode === "Dense" ? 1 : (1 + slots[feature_uid])) * y_scale;
-                
+                    y_center = (mode === "Dense" ? 1 : (1 + slots[feature_uid])) * y_scale;                
                 var thickness, y_start, thick_start = null, thick_end = null;
                 
                 // BAM/read drawing.
                 if (result.dataset_type === "bai") {
-                    var cigar = feature[4];
                     ctx.fillStyle = block_color;
                     if (feature[5] instanceof Array) {
                         // Read is paired.
-                        var b1_start = Math.floor( Math.max(0, (feature[5][0] - tile_low) * w_scale) ),
-                            b1_end   = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) ),
-                            b2_start = Math.floor( Math.max(0, (feature[6][0] - tile_low) * w_scale) ),
-                            b2_end   = Math.ceil( Math.min(width, Math.max(0, (feature[6][1] - tile_low) * w_scale)) );
-                        
+                        var b1_start = Math.floor( Math.max(0, (feature[4][0] - tile_low) * w_scale) ),
+                            b1_end   = Math.ceil( Math.min(width, Math.max(0, (feature[4][1] - tile_low) * w_scale)) ),
+                            b2_start = Math.floor( Math.max(0, (feature[5][0] - tile_low) * w_scale) ),
+                            b2_end   = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) );
+
                         // Draw left/forward read.
-                        if (feature[5][1] >= tile_low && feature[5][0] <= tile_high) {
-                            this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], cigar, y_center);
+                        if (feature[4][1] >= tile_low && feature[4][0] <= tile_high) {
+                                this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], y_center);
                         }
                         // Draw right/reverse read.
-                        if (feature[6][1] >= tile_low && feature[6][0] <= tile_high) {
-                            this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[6][0], feature[6][2], cigar, y_center);
+                        if (feature[5][1] >= tile_low && feature[5][0] <= tile_high) {
+                            this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], y_center);
                         }
                         // Draw connector.
                         if (b2_start > b1_end) {
@@ -1926,21 +2000,20 @@ $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
                     } else {
                         // Read is single.
                         ctx.fillStyle = block_color;
-                        this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature_start, feature_name, cigar, y_center);
+                        this.rect_or_text(ctx, w_scale, tile_low, tile_high, feature_start, feature[4], feature[5], y_center);
                     }
                     if (mode !== "Dense" && !no_detail && feature_start > tile_low) {
-                        // Draw label
+                        // Draw label.
                         ctx.fillStyle = this.prefs.label_color;
                         if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) {
                             ctx.textAlign = "left";
-                            ctx.fillText(feature_uid, f_end + 2 + left_offset, y_center + 8);
+                            ctx.fillText(feature_name, f_end + 2 + left_offset, y_center + 8);
                         } else {
                             ctx.textAlign = "right";
-                            ctx.fillText(feature_uid, f_start - 2 + left_offset, y_center + 8);
+                            ctx.fillText(feature_name, f_start - 2 + left_offset, y_center + 8);
                         }
                         ctx.fillStyle = block_color;
                     }
-                        
                 }
                 // Interval index drawing.
                 else if (result.dataset_type === "interval_index") {