[galaxy-commits] galaxy-dist commit 2ac11399c20e: trackster: Overview track, viz cloning, "Go-to" specific location, UI fixes

8 Sep 2010

# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User Kanwei Li <kanwei@gmail.com>
# Date 1282839152 14400
# Node ID 2ac11399c20ed6b844f563b77de089b9ddff657e
# Parent  291183d3896bcedef4d632a91fe7169d07bd8154
trackster: Overview track, viz cloning, "Go-to" specific location, UI fixes
- Each track now has an Overview checkbox that will set the initial chromosome-wide view of that track to become the overview
- Visualizations that users own or are shared with can now be cloned
- Go-to feature lets users go directly to a certain chrom (eg "chr1"), or chrom and position ("chr1:1-100,000,000")
- Fix double flushing when creating converter
- Line tracks display mode is now inline
- Use smaller font for tracks
- Fix web-kit bug where using scrollbar would also trigger viewport dragging
- Fix Line tracks jumping around when changing position
- Made default Line track height 80px from 100px
- Fix drag-zoom overlay appearing at top of header instead of Label track

- Minor grid refactoring

--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -115,7 +115,7 @@
         // To adjust the size of the viewport to fit the fixed-height footer
         var refresh = function() {
             if (view !== undefined) {
-                view.viewport_container.height( $("#center").height() - 110 );
+                view.viewport_container.height( $("#center").height() - $(".nav-container").height() - 40 );
                 view.nav_container.width( $("#center").width() );
                 view.redraw();
             }

--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -204,12 +204,6 @@ class UsesVisualization( SharableItemSec
             latest_revision = visualization.latest_revision
             tracks = []
 
-            # Set dbkey.
-            try:
-                dbkey = latest_revision.dbkey
-            except KeyError:
-                dbkey = None
-        
             # Set tracks.
             if 'tracks' in latest_revision.config:
                 hda_query = trans.sa_session.query( trans.model.HistoryDatasetAssociation )
@@ -227,12 +221,9 @@ class UsesVisualization( SharableItemSec
                         "dataset_id": dataset.id,
                         "prefs": simplejson.dumps(prefs),
                     } )
-                    if dbkey is None: dbkey = dataset.dbkey # Hack for backward compat
             
-            
-            ## TODO: chrom needs to be able to be set; right now it's empty.
             config = { "title": visualization.title, "vis_id": trans.security.encode_id( visualization.id ), 
-                        "tracks": tracks, "chrom": "", "dbkey": dbkey }
+                        "tracks": tracks, "chrom": "", "dbkey": visualization.dbkey }
             
         return config
         

Binary file static/images/fugue/navigation.png has changed

--- a/static/scripts/packed/trackster.js
+++ b/static/scripts/packed/trackster.js
@@ -1,1 +1,1 @@
-var DENSITY=200,FEATURE_LEVELS=10,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...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONT
 EXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};var Cache=function(a){this.num_elements=a;this.clear()};$.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,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;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();this.reset()};$.extend(
 View.prototype,{init:function(){var b=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(b);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(b);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide().appendTo(b);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.viewport=$("<div/>").addClass("viewport").appendTo(this.viewport_container);this.nav_container=$("<div/>").addClass("nav-container").appendTo(b);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overvi
 ew_viewport);this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);this.low_input=$("<input/>").addClass("low").css("width","10em").appendTo(this.chrom_form);$("<span/>").text(" - ").appendTo(this.chrom_form);this.high_input=$("<input/>").addClass("high").css("width","10em").appendTo(this.chrom_form);if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);this.zo_link=$("<a/>").click(function(){a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.pn
 g" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(c){if(c.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=c.chrom_info;var f='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var e=a.chrom_data[i]["chrom"];f+='<option value="'+e+'">'+e+"</option>"}a.chrom_select.html(f);var d=function(){if(a.chrom_select.val()===""){a.intro_div.show();a.content_div.hide()}else{a.intro_div.hide();a.content_div.show()}a.chrom=a.chrom_select.val();var h=$.grep(a.chrom_data,function(k,l){return k.chrom===a.chrom})[0];a.max_high=(h!==undefined?h.len:0);a.reset();a.redraw(true);for(var j in a.tracks){var g=a.tracks[j];if(g.init){g.init()}}a.redraw()};a.chrom_select.bind("change",d);d()},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(c){a.zoom_in(c.pageX,this.viewport_container)});thi
 s.overview_box.bind("dragstart",function(c){this.current_x=c.offsetX}).bind("drag",function(c){var f=c.offsetX-this.current_x;this.current_x=c.offsetX;var d=Math.round(f/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-d)});this.viewport_container.bind("dragstart",function(c){this.original_low=a.low;this.current_height=c.clientY;this.current_x=c.offsetX}).bind("drag",function(f){var c=$(this);var h=f.offsetX-this.current_x;var d=c.scrollTop()-(f.clientY-this.current_height);c.scrollTop(d);this.current_height=f.clientY;this.current_x=f.offsetX;var g=Math.round(h/a.viewport_container.width()*(a.high-a.low));a.move_delta(g)});this.top_labeltrack.bind("dragstart",function(c){this.drag_origin_x=c.clientX;this.drag_origin_pos=c.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.viewport_container.height(),top:"0px",position:"absolute","background-color":"#cfc",border:"1px solid #6a6",opacity:0.5,"z-index":1000}).app
 endTo($(this))}).bind("drag",function(h){var d=Math.min(h.clientX,this.drag_origin_x)-a.container.offset().left,c=Math.max(h.clientX,this.drag_origin_x)-a.container.offset().left,g=(a.high-a.low),f=a.viewport_container.width();a.low_input.val(commatize(Math.round(d/f*g)+a.low));a.high_input.val(commatize(Math.round(c/f*g)+a.low));this.drag_div.css({left:d+"px",width:(c-d)+"px"})}).bind("dragend",function(j){var d=Math.min(j.clientX,this.drag_origin_x),c=Math.max(j.clientX,this.drag_origin_x),g=(a.high-a.low),f=a.viewport_container.width(),h=a.low;a.low=Math.round(d/f*g)+h;a.high=Math.round(c/f*g)+h;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))},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_tra
 ck: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(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];this.viewport.append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(f){var d=this.high-this.low,b=this.low,e=this.high;if(b<this.max_low){b=this.max_low}if(e>this.max_high){e=this.max_high}if(this.high!==0&&
 d<this.min_separation){e=b+this.min_separation}this.low=Math.floor(b);this.high=Math.ceil(e);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));this.overview_box.css({left:(this.low/(this.max_high-this.max_low))*this.overview_viewport.width(),width:Math.max(12,(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())}).show();this.low_input.val(commatize(this.low));this.high_input.val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(b,c){if(this.max_high===0||this.high-this.low<this.min_separation){return}var d=this.high-this.low,e=d/2+this.low,a=(d/this.zoom_factor)/2;if(b){e=b/this.viewport_container.width()*(
 this.high-this.low)+this.low}this.low=Math.round(e-a);this.high=Math.round(e+a);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var b=this.high-this.low,c=b/2+this.low,a=(b*this.zoom_factor)/2;this.low=Math.round(c-a);this.high=Math.round(c+a);this.redraw()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div />").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","auto");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(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=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+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()},5000)}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)}}});var TiledTrack=function(){this.left_offset=200};$.extend(TiledT
 rack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=functio
 n(a,b){Track.call(this,null,a,b);this.track_type="LabelTrack";this.hidden=true;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($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.hidden=true;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");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,j){console.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){if(this.data_cache.get(j)===undefined){this.get_data(f,b);return}var m=this.data_cache.get(j);if(m===null){this.content_div.css("height","0px");return}e.get(0).width=Math.ceil(d*o+this.left_offset);e.get(0).height=this.height_px;e.css({position:"absolute",top:0,left:(g-this.view.low)*o-this.left_offset});for(var h=0,l=m.length;h<l;h++){var a=Math.round(h*o);n.fillText(m[h],a+this.left_offset,10)}k.append(e);return e}this.content_div.css("he
 ight","0px")}});var LineTrack=function(d,b,a,c){this.track_type="LineTrack";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}if(c.mode!==undefined){this.prefs.mode=c.mode}};$.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");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").va
 l(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.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;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e
 ){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e+this.left_offset);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.ro
 und(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(o){var a=$("<div />").addClass("form-row");var h="track_"+o+"_minval",m=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),n=$("<input></input>").attr("id",h).val(b),l="track_"+o+"_maxval",g=$("<label></label>").attr("for",l).text("Max value:"),k=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",l).val(k),e="track_"+o+"_mode",d=$("<label></label>").attr("for",e).text("Display mode:"),j=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mo
 de_"+j).attr("selected","selected");return a.append(m).append(n).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!==this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=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(d,b,a,c){this.track_type="FeatureTrack";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.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.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.prefs={block_color:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var b=this,c=b.view.max_low+"_"+b.view.max_high;if(b.mode_div===undefined){b.mode_div=$("<div class='right-float menubutton popup' />").text("Display Mode").appendTo(b.header_div);b.mode="Auto";var a=function(d){b.mode_div.text(d);b.mode=d;b.tile_cache.clear();b.draw()};make_popupmenu(b.mode_div,{Auto:function(){a("Auto")},Dense:function(){a("Dense")},Squish:function(){a("Squish")},Pack:function(){a("Pack")}})}else{b.mode_div.hide()}this.init_each({low:b.view.max_low,high
 :b.view.max_high,dataset_id:b.dataset_id,chrom:b.view.chrom,resolution:this.view.resolution},function(d){b.mode_div.show();b.data_cache.set(c,d);b.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(thi
 s.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u++){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_
 color;n.fillRect(k,h+4,e,3)}},draw_tile:function(X,h,n,ak){var E=h*DENSITY*X,ad=(h+1)*DENSITY*X,D=DENSITY*X;var ae=E+"_"+ad;var z=this.data_cache.get(ae);if(z===undefined){this.data_queue[[E,ad]]=true;this.get_data(E,ad);return}var a=Math.ceil(D*ak),L=$("<canvas class='tile'></canvas>"),Z=this.prefs.label_color,f=this.prefs.block_color,m=this.mode,V=(m==="Squish")||(m==="Dense")&&(m!=="Pack")||(m==="Auto"&&(z.extra_info==="no_detail")),P=this.left_offset,aj,s,al;if(z.dataset_type==="summary_tree"){s=30}else{if(m==="Dense"){s=15;al=10}else{al=(V?this.vertical_nodetail_px:this.vertical_detail_px);s=this.incremental_slots(this.view.zoom_res,z.data,V,m)*al+15;aj=this.inc_slots[this.view.zoom_res]}}L.css({position:"absolute",top:0,left:(E-this.view.low)*ak-P});L.get(0).width=a+P;L.get(0).height=s;n.parent().css("height",Math.max(this.height_px,s)+"px");var A=L.get(0).getContext("2d");A.fillStyle=f;A.font=this.default_font;A.textAlign="right";if(z.dataset_type=="summary_tree"){var
  K,H=55,ac=255-H,g=ac*2/3,R=z.data,C=z.max,l=z.avg,b=Math.ceil(z.delta*ak);for(var ag=0,w=R.length;ag<w;ag++){var T=Math.floor((R[ag][0]-E)*ak);var S=R[ag][1];if(!S){continue}K=Math.floor(ac-(S/C)*ac);A.fillStyle="rgb("+K+","+K+","+K+")";A.fillRect(T+P,0,b,20);if(this.prefs.show_counts&&A.measureText(S).width<b){if(K>g){A.fillStyle="black"}else{A.fillStyle="#ddd"}A.textAlign="center";A.fillText(S,T+P+(b/2),12)}}n.append(L);return L}var ai=z.data;var af=0;for(var ag=0,w=ai.length;ag<w;ag++){var M=ai[ag],J=M[0],ah=M[1],U=M[2],F=M[3];if(ah<=ad&&U>=E){var W=Math.floor(Math.max(0,(ah-E)*ak)),B=Math.ceil(Math.min(a,Math.max(0,(U-E)*ak))),Q=(m==="Dense"?0:aj[J]*al);if(z.dataset_type==="bai"){A.fillStyle=f;if(M[4] instanceof Array){var t=Math.floor(Math.max(0,(M[4][0]-E)*ak)),I=Math.ceil(Math.min(a,Math.max(0,(M[4][1]-E)*ak))),r=Math.floor(Math.max(0,(M[5][0]-E)*ak)),p=Math.ceil(Math.min(a,Math.max(0,(M[5][1]-E)*ak)));if(M[4][1]>=E&&M[4][0]<=ad){this.rect_or_text(A,ak,E,ad,M[4][0],M
 [4][2],t+P,I-t,Q)}if(M[5][1]>=E&&M[5][0]<=ad){this.rect_or_text(A,ak,E,ad,M[5][0],M[5][2],r+P,p-r,Q)}if(r>I){A.fillStyle="#999";A.fillRect(I+P,Q+5,r-I,1)}}else{A.fillStyle=f;this.rect_or_text(A,ak,E,ad,ah,F,W+P,B-W,Q)}if(m!=="Dense"&&!V&&ah>E){A.fillStyle=this.prefs.label_color;if(h===0&&W-A.measureText(F).width<0){A.textAlign="left";A.fillText(J,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(J,W-2+P,Q+8)}A.fillStyle=f}}else{if(z.dataset_type==="interval_index"){if(V){A.fillRect(W+P,Q+5,B-W,1)}else{var v=M[4],O=M[5],Y=M[6],e=M[7];var u,aa,G=null,am=null;if(O&&Y){G=Math.floor(Math.max(0,(O-E)*ak));am=Math.ceil(Math.min(a,Math.max(0,(Y-E)*ak)))}if(m!=="Dense"&&F!==undefined&&ah>E){A.fillStyle=Z;if(h===0&&W-A.measureText(F).width<0){A.textAlign="left";A.fillText(F,B+2+P,Q+8)}else{A.textAlign="right";A.fillText(F,W-2+P,Q+8)}A.fillStyle=f}if(e){if(v){if(v=="+"){A.fillStyle=RIGHT_STRAND}else{if(v=="-"){A.fillStyle=LEFT_STRAND}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=f}for(var ae=0,d=
 e.length;ae<d;ae++){var o=e[ae],c=Math.floor(Math.max(0,(o[0]-E)*ak)),N=Math.ceil(Math.min(a,Math.max((o[1]-E)*ak)));if(c>N){continue}u=5;aa=3;A.fillRect(c+P,Q+aa,N-c,u);if(G!==undefined&&!(c>am||N<G)){u=9;aa=1;var ab=Math.max(c,G),q=Math.min(N,am);A.fillRect(ab+P,Q+aa,q-ab,u)}}}else{u=9;aa=1;A.fillRect(W+P,Q+aa,B-W,u);if(M.strand){if(M.strand=="+"){A.fillStyle=RIGHT_STRAND_INV}else{if(M.strand=="-"){A.fillStyle=LEFT_STRAND_INV}}A.fillRect(W+P,Q,B-W,10);A.fillStyle=prefs.block_color}}}}}af++}}n.append(L);return L},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<label />").attr("for",f).text("Show summary counts"),b=$('<inpu
 t type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div />").append(b).append(c);return a.append(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e+"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});
+var DENSITY=200,FEATURE_LEVELS=10,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...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),PX_PER_CHAR=CONTEXT.measureText("A").width,RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src=image_path+"/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src=image_path+"/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src=image_path+"/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONT
 EXT.createPattern(right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src=image_path+"/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function round_1000(a){return Math.round(a*1000)/1000}var Cache=function(a){this.num_elements=a;this.clear()};$.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,c,e,d,b){this.container=a;this.vis_id=d;this.dbkey=b;this.title=e;this.chrom=c;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();this.reset()};$.extend(View.prototype,{init:function(){var b=this.container,a=this;this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(b);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(b);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide().appendTo(b);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.nav_container=$("<div/>").addClass("nav-container").appendTo(b);this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.nav);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_o
 verview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_form=$("<form/>").attr("action",function(){void (0)}).appendTo(this.nav_controls);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.chrom_form);this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keypress",function(c){if((c.keyCode||c.which)===13){a.go_to($(this).val());$(this).hide();return false}}).appendTo(this.chrom_form);this.location_span=$("<span/>").addClass("location").appendTo(this.chrom_form);if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.chrom_form)}this.goto_link=$("<a/>").click(function(){a.nav_input.toggle();a.nav_input.focus()}).html('<img src="'+image_path+'/fugue/navigation.png" />').appendTo(this.chrom_form);this.zo_link=$("<a/>").click(function()
 {a.zoom_out();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);this.zi_link=$("<a/>").click(function(){a.zoom_in();a.redraw()}).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);$.ajax({url:chrom_url,data:(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}),dataType:"json",success:function(c){if(c.reference){a.add_label_track(new ReferenceTrack(a))}a.chrom_data=c.chrom_info;var e='<option value="">Select Chrom/Contig</option>';for(i in a.chrom_data){var d=a.chrom_data[i]["chrom"];e+='<option value="'+d+'">'+d+"</option>"}a.chrom_select.html(e);a.intro_div.show();a.content_div.hide();a.chrom_select.bind("change",function(){a.change_chrom(a.chrom_select.val())})},error:function(){alert("Could not load chroms for this dbkey:",a.dbkey)}});this.content_div.bind("dblclick",function(c){a.zoom_in(c.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(c){
 this.current_x=c.offsetX}).bind("drag",function(c){var f=c.offsetX-this.current_x;this.current_x=c.offsetX;var d=Math.round(f/a.viewport_container.width()*(a.max_high-a.max_low));a.move_delta(-d)});this.viewport_container.bind("dragstart",function(c){this.original_low=a.low;this.current_height=c.clientY;this.current_x=c.offsetX;this.active=(c.clientX<a.viewport_container.width()-16)?true:false}).bind("drag",function(f){if(!this.active){return}var c=$(this);var h=f.offsetX-this.current_x;var d=c.scrollTop()-(f.clientY-this.current_height);c.scrollTop(d);this.current_height=f.clientY;this.current_x=f.offsetX;var g=Math.round(h/a.viewport_container.width()*(a.high-a.low));a.move_delta(g)});this.top_labeltrack.bind("dragstart",function(c){this.drag_origin_x=c.clientX;this.drag_origin_pos=c.clientX/a.viewport_container.width()*(a.high-a.low)+a.low;this.drag_div=$("<div />").css({height:a.content_div.height(),top:"0px",position:"absolute","background-color":"#cfc",border:"1px soli
 d #6a6",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(h){var d=Math.min(h.clientX,this.drag_origin_x)-a.container.offset().left,c=Math.max(h.clientX,this.drag_origin_x)-a.container.offset().left,g=(a.high-a.low),f=a.viewport_container.width();a.update_location(Math.round(d/f*g)+a.low,Math.round(c/f*g)+a.low);this.drag_div.css({left:d+"px",width:(c-d)+"px"})}).bind("dragend",function(j){var d=Math.min(j.clientX,this.drag_origin_x),c=Math.max(j.clientX,this.drag_origin_x),g=(a.high-a.low),f=a.viewport_container.width(),h=a.low;a.low=Math.round(d/f*g)+h;a.high=Math.round(c/f*g)+h;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))},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(d,a,f){var c=this;var e=$.grep(c.chrom_data
 ,function(h,j){return h.chrom===d})[0];if(e===undefined){return}c.chrom=d;if(c.chrom===""){c.intro_div.show();c.content_div.hide()}else{c.intro_div.hide();c.content_div.show()}c.chrom_select.val(c.chrom);c.max_high=e.len;c.reset();c.redraw(true);for(var g in c.tracks){var b=c.tracks[g];if(b.init){b.init()}}if(a!==undefined&&f!==undefined){c.low=Math.max(a,0);c.high=Math.min(f,c.max_high)}c.overview_viewport.find("canvas").remove();c.redraw()},go_to:function(f){var k=this,b=f.split(":"),h=b[0],j=b[1];if(j!==undefined){try{var g=j.split("-"),a=parseInt(g[0].replace(/,/g,"")),d=parseInt(g[1].replace(/,/g,""))}catch(c){return false}}k.change_chrom(h,a,d)},move_delta:function(c){var a=this;var b=a.high-a.low;if(a.low-c<a.max_low){a.low=a.max_low;a.high=a.max_low+b}else{if(a.high-c>a.max_high){a.high=a.max_high;a.low=a.max_high-b}else{a.high-=c;a.low-=c}}a.redraw()},add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.contain
 er_div.attr("id","track_"+a.track_id);this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){this.has_changes=true;a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)];this.num_tracks-=1},update_options:function(){this.has_changes=true;var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];this.viewport.append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(f){var d=this.high-this.low,b=this.low,e=this.high;if(b<this.max_low){b=this.max_low}if(e>this.max_high){e=this.max_high}if(this.high!==0&&d<this.min_separation){e=b+this.min_separation}this.low=Math.floor(b);this.high=Math.ceil(e);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))));this.overview_box.css({left:(this.low/(this.max_high-this.max_low))*this.overview_viewport.width(),width:Math.max(12,(this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())}).show();this.update_location(this.low,this.high);if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;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()}});var Track=function(b,a,c){this.name=b;this.parent_element=c;this.view=a;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div />").addClass("track").append(this.header_div).append(this.content_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.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.vie
 w.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){var c=this,b=c.view;if(c.display_modes!==undefined){if(c.mode_div===undefined){c.mode_div=$("<div class='right-float menubutton popup' />").appendTo(c.header_di
 v);var g=c.display_modes[0];c.mode=g;c.mode_div.text(g);var a=function(h){c.mode_div.text(h);c.mode=h;c.tile_cache.clear();c.draw()};var e={};for(var d in c.display_modes){var f=c.display_modes[d];e[f]=function(h){return function(){a(h)}}(f)}make_popupmenu(c.mode_div,e)}else{c.mode_div.hide()}}if(c.overview_check_div===undefined){c.overview_check_div=$("<div class='right-float' />").css("margin-top","-3px").appendTo(c.header_div);c.overview_check=$("<input type='checkbox' class='overview_check' />").appendTo(c.overview_check_div);c.overview_check.bind("click",function(){var h=this;b.overview_viewport.find("canvas").remove();c.set_overview();$(".overview_check").each(function(){if(this!==h){$(this).attr("checked",false)}})});c.overview_check_div.append($("<label />").text("Overview"))}};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var j=this.view.low,e=this.view.high,f=e-j,d=this.view.resolution;var l=$("<div style='position: relative;'></div>"),m=this.conte
 nt_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(l),this.max_height=0;var a=Math.floor(j/d/DENSITY);while((a*DENSITY*d)<e){var k=this.content_div.width()+"_"+m+"_"+a;var c=this.tile_cache.get(k);if(c){var g=a*DENSITY*d;var b=(g-j)*m;if(this.left_offset){b-=this.left_offset}c.css({left:b});l.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,k,j,e,a,d,l,m)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){if(!c.initial_canvas){c.initial_canvas=$(tile_element).clone();var l=tile_element.get(0).getContext("2d");var j=c.initial_canvas.get(0).getContext("2d");var k=l.getImageData(0,0,l.canvas.width,l.canvas.height);j.putImageData(k,0,0);c.set_overview()}c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.cont
 ent_div.css("height",c.max_height+"px")}}},50)},set_overview:function(){var a=this.view;a.overview_viewport.height(a.default_overview_height);a.overview_box.height(a.default_overview_height);if(this.overview_check.is(":checked")){a.overview_viewport.append(this.initial_canvas);a.overview_viewport.height(this.initial_canvas.height());a.overview_box.height(this.initial_canvas.height())}$(window).trigger("resize")}});var LabelTrack=function(a,b){Track.call(this,null,a,b);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.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.chil
 dren(":first").remove();this.content_div.append(b)}});var ReferenceTrack=function(a){this.track_type="ReferenceTrack";Track.call(this,null,a,a.top_labeltrack);TiledTrack.call(this);this.hidden=true;this.height_px=12;this.container_div.addClass("reference-track");this.dummy_canvas=$("<canvas></canvas>").get(0).getContext("2d");this.data_queue={};this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE)};$.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;$.ajax({url:reference_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dbkey:this.view.dbkey},success:function(g){c.data_cache.set(e,g);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(f,b,k,o){var g=b*DENSITY*f,d=DENSITY*f,e=$("<canvas class='tile'></canvas>"),n=e.get(0).getContext("2d"),j=f+"_"+b;if(o>PX_PER_CHAR){if(t
 his.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);n.fillText(m[h],a+this.left_offset,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=["Line","Filled","Intensity"];this.mode="Line";Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=80;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(c.min_value!==undefined){this.prefs.min_value=c.min_value}if(c.max_value!==undefined){this.prefs.max_value=c.max_value}};$.extend(LineTrack.prototype,Tiled
 Track.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(round_1000(a.prefs.min_value));var d=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(round_1000(a.prefs.max_value));d.css({position:"relative",top:"32px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a
 .height_px+32+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url: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){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,j){console.log(h,g,j)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,
 m=this.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(k){var a=$("<div />").addClass("form-row");var e="track_"+k+"_minval",h=$("<label></label>").attr("for",e).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),j=$("<input></input>").attr("id",e).val(b),g="track_"+k+"_maxval",d=$("<label></label>").attr("for",g).text("Max value:"
 ),f=(this.prefs.max_value===undefined?"":this.prefs.max_value),c=$("<input></input>").attr("id",g).val(f);return a.append(h).append(j).append(d).append(c)},update_options:function(c){var a=$("#track_"+c+"_minval").val(),b=$("#track_"+c+"_maxval").val();if(a!==this.prefs.min_value||b!==this.prefs.max_value){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(b);this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+c+"_minval").text(this.prefs.min_value);$("#linetrack_"+c+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(d,b,a,c){this.track_type="FeatureTrack";this.display_modes=["Auto","Dense","Squish","Pack"];Track.call(this,d,b,b.viewport_container);TiledTrack.call(this);this.height_px=0;this.container_div.addClass("feature-track");this.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=2;this.su
 mmary_draw_height=20;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:"black",label_color:"black",show_counts:true};if(c.block_color!==undefined){this.prefs.block_color=c.block_color}if(c.label_color!==undefined){this.prefs.label_color=c.label_color}if(c.show_counts!==undefined){this.prefs.show_counts=c.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b="initial";this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.mode_div.show();a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolutio
 n,mode:this.mode},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,h,c,r){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.inc_slots[a].mode=r;this.s_e_by_tile[a]={}}var n=this.inc_slots[a].w_scale,z=[],l=0,b=$("<canvas></canvas>").get(0).getContext("2d"),o=this.view.max_low;var B=[];if(this.inc_slots[a].mode!==r){delete this.inc_slots[a];this.inc_slots[a]={mode:r,w_scale:n};delete this.s_e_by_tile[a];this.s_e_by_tile[a]={}}for(var w=0,x=h.length;w<x;w++){var g=h[w],m=g[0];if(this.inc_slots[a][m]!==undefined){l=Math.max(l,this.inc_slots[a][m]);B.push(this.inc_slots[a][m])}else{z.push(w)}}for(var w=0,x=z.length;w<x;w++){var g=h[z[w]],m=g[0],s=g[1],d=g[2],q=g[3],e=Math.floor((s-o)*n),f=Math.ceil((d-o)*n);if(q!==undefined&&!c){var t=b.measureText(q).width;if(e-t<0){f+=t}else{e-=t}}var v=0;while(true){var p=true;if(this.s_e_by_tile[a][v]!==undefined){for(var u=0,A=this.s_e_by_tile[a][v].length;u<A;u+
 +){var y=this.s_e_by_tile[a][v][u];if(f>y[0]&&e<y[1]){p=false;break}}}if(p){if(this.s_e_by_tile[a][v]===undefined){this.s_e_by_tile[a][v]=[]}this.s_e_by_tile[a][v].push([e,f]);this.inc_slots[a][m]=v;l=Math.max(l,v);break}v++}}return l},rect_or_text:function(n,o,f,m,b,d,k,e,h){n.textAlign="center";var j=Math.round(o/2);if((this.mode==="Pack"||this.mode==="Auto")&&d!==undefined&&o>PX_PER_CHAR){n.fillStyle=this.prefs.block_color;n.fillRect(k,h+1,e,9);n.fillStyle="#eee";for(var g=0,l=d.length;g<l;g++){if(b+g>=f&&b+g<=m){var a=Math.floor(Math.max(0,(b+g-f)*o));n.fillText(d[g],a+this.left_offset+j,h+9)}}}else{n.fillStyle=this.prefs.block_color;n.fillRect(k,h+4,e,3)}},draw_tile:function(Y,l,o,al){var F=l*DENSITY*Y,ae=(l+1)*DENSITY*Y,E=ae-F;var af=(!this.initial_canvas?"initial":F+"_"+ae);var A=this.data_cache.get(af);var d;if(A===undefined){this.data_queue[[F,ae]]=true;this.get_data(F,ae);return}var a=Math.ceil(E*al),M=$("<canvas class='tile'></canvas>"),aa=this.prefs.label_color,g
 =this.prefs.block_color,n=this.mode,W=(n==="Squish")||(n==="Dense")&&(n!=="Pack")||(n==="Auto"&&(A.extra_info==="no_detail")),Q=this.left_offset,ak,t,am;if(A.dataset_type==="summary_tree"){t=this.summary_draw_height}else{if(n==="Dense"){t=15;am=10}else{am=(W?this.vertical_nodetail_px:this.vertical_detail_px);t=this.incremental_slots(this.view.zoom_res,A.data,W,n)*am+15;ak=this.inc_slots[this.view.zoom_res]}}M.css({position:"absolute",top:0,left:(F-this.view.low)*al-Q});M.get(0).width=a+Q;M.get(0).height=t;o.parent().css("height",Math.max(this.height_px,t)+"px");var B=M.get(0).getContext("2d");B.fillStyle=g;B.font=this.default_font;B.textAlign="right";if(A.dataset_type=="summary_tree"){var L,I=55,ad=255-I,h=ad*2/3,S=A.data,D=A.max,m=A.avg,b=Math.ceil(A.delta*al);for(var ah=0,z=S.length;ah<z;ah++){var U=Math.floor((S[ah][0]-F)*al);var T=S[ah][1];if(!T){continue}L=Math.floor(ad-(T/D)*ad);B.fillStyle="rgb("+L+","+L+","+L+")";B.fillRect(U+Q,0,b,this.summary_draw_height);if(this.p
 refs.show_counts&&B.measureText(T).width<b){if(L>h){B.fillStyle="black"}else{B.fillStyle="#ddd"}B.textAlign="center";B.fillText(T,U+Q+(b/2),12)}}d="Summary";o.append(M);return M}var aj=A.data;var ag=0;for(var ah=0,z=aj.length;ah<z;ah++){var N=aj[ah],K=N[0],ai=N[1],V=N[2],G=N[3];if(ai<=ae&&V>=F){var X=Math.floor(Math.max(0,(ai-F)*al)),C=Math.ceil(Math.min(a,Math.max(0,(V-F)*al))),R=(n==="Dense"?0:ak[K]*am);if(A.dataset_type==="bai"){B.fillStyle=g;if(N[4] instanceof Array){var u=Math.floor(Math.max(0,(N[4][0]-F)*al)),J=Math.ceil(Math.min(a,Math.max(0,(N[4][1]-F)*al))),s=Math.floor(Math.max(0,(N[5][0]-F)*al)),q=Math.ceil(Math.min(a,Math.max(0,(N[5][1]-F)*al)));if(N[4][1]>=F&&N[4][0]<=ae){this.rect_or_text(B,al,F,ae,N[4][0],N[4][2],u+Q,J-u,R)}if(N[5][1]>=F&&N[5][0]<=ae){this.rect_or_text(B,al,F,ae,N[5][0],N[5][2],s+Q,q-s,R)}if(s>J){B.fillStyle="#999";B.fillRect(J+Q,R+5,s-J,1)}}else{B.fillStyle=g;this.rect_or_text(B,al,F,ae,ai,G,X+Q,C-X,R)}if(n!=="Dense"&&!W&&ai>F){B.fillStyle=th
 is.prefs.label_color;if(l===0&&X-B.measureText(G).width<0){B.textAlign="left";B.fillText(K,C+2+Q,R+8)}else{B.textAlign="right";B.fillText(K,X-2+Q,R+8)}B.fillStyle=g}}else{if(A.dataset_type==="interval_index"){if(W){B.fillRect(X+Q,R+5,C-X,1)}else{var w=N[4],P=N[5],Z=N[6],f=N[7];var v,ab,H=null,an=null;if(P&&Z){H=Math.floor(Math.max(0,(P-F)*al));an=Math.ceil(Math.min(a,Math.max(0,(Z-F)*al)))}if(n!=="Dense"&&G!==undefined&&ai>F){B.fillStyle=aa;if(l===0&&X-B.measureText(G).width<0){B.textAlign="left";B.fillText(G,C+2+Q,R+8)}else{B.textAlign="right";B.fillText(G,X-2+Q,R+8)}B.fillStyle=g}if(f){if(w){if(w=="+"){B.fillStyle=RIGHT_STRAND}else{if(w=="-"){B.fillStyle=LEFT_STRAND}}B.fillRect(X+Q,R,C-X,10);B.fillStyle=g}for(var af=0,e=f.length;af<e;af++){var p=f[af],c=Math.floor(Math.max(0,(p[0]-F)*al)),O=Math.ceil(Math.min(a,Math.max((p[1]-F)*al)));if(c>O){continue}v=5;ab=3;B.fillRect(c+Q,R+ab,O-c,v);if(H!==undefined&&!(c>an||O<H)){v=9;ab=1;var ac=Math.max(c,H),r=Math.min(O,an);B.fillRe
 ct(ac+Q,R+ab,r-ac,v)}}}else{v=9;ab=1;B.fillRect(X+Q,R+ab,C-X,v);if(N.strand){if(N.strand=="+"){B.fillStyle=RIGHT_STRAND_INV}else{if(N.strand=="-"){B.fillStyle=LEFT_STRAND_INV}}B.fillRect(X+Q,R,C-X,10);B.fillStyle=prefs.block_color}}}}}ag++}}o.append(M);return M},gen_options:function(j){var a=$("<div />").addClass("form-row");var e="track_"+j+"_block_color",l=$("<label />").attr("for",e).text("Block color:"),m=$("<input />").attr("id",e).attr("name",e).val(this.prefs.block_color),k="track_"+j+"_label_color",g=$("<label />").attr("for",k).text("Text color:"),h=$("<input />").attr("id",k).attr("name",k).val(this.prefs.label_color),f="track_"+j+"_show_count",c=$("<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(l).append(m).append(g).append(h).append(d)},update_options:function(e){var b=$("#track_"+e
 +"_block_color").val(),d=$("#track_"+e+"_label_color").val(),c=$("#track_"+e+"_mode option:selected").val(),a=$("#track_"+e+"_show_count").attr("checked");if(b!==this.prefs.block_color||d!==this.prefs.label_color||a!==this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=d;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(d,b,a,c){FeatureTrack.call(this,d,b,a,c);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{});

--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -37,6 +37,10 @@ left_img_inv.onload = function() {
     LEFT_STRAND_INV = CONTEXT.createPattern(left_img_inv, "repeat");
 };
 
+function round_1000(num) {
+    return Math.round(num * 1000) / 1000;    
+}
+    
 var Cache = function( num_elements ) {
     this.num_elements = num_elements;
     this.clear();
@@ -96,7 +100,6 @@ var View = function( container, chrom, t
         this.content_div = $("<div/>").addClass("content").css("position", "relative").appendTo(parent_element);
         this.intro_div = $("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide().appendTo(parent_element);
         this.viewport_container = $("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);
-        this.viewport = $("<div/>").addClass("viewport").appendTo(this.viewport_container);
         
         this.nav_container = $("<div/>").addClass("nav-container").appendTo(parent_element);
         this.nav_labeltrack = $("<div/>").addClass("nav-labeltrack").appendTo(this.nav_container);
@@ -104,18 +107,26 @@ var View = function( container, chrom, t
         this.overview = $("<div/>").addClass("overview").appendTo(this.nav);
         this.overview_viewport = $("<div/>").addClass("overview-viewport").appendTo(this.overview);
         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() { void(0); } ).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);
-        this.low_input = $("<input/>").addClass("low").css("width", "10em").appendTo(this.chrom_form);
-        $("<span/>").text(" - ").appendTo(this.chrom_form);
-        this.high_input = $("<input/>").addClass("high").css("width", "10em").appendTo(this.chrom_form);
+        this.nav_input = $("<input/>").addClass("nav-input").hide().bind("keypress", function(e) {
+            if ((e.keyCode || e.which) === 13) {
+                view.go_to( $(this).val() );
+                $(this).hide();
+                return false;
+            }
+            
+        }).appendTo(this.chrom_form);
+        this.location_span = $("<span/>").addClass("location").appendTo(this.chrom_form);
         if (this.vis_id !== undefined) {
             this.hidden_input = $("<input/>").attr("type", "hidden").val(this.vis_id).appendTo(this.chrom_form);
         }
-        this.zi_link = $("<a/>").click(function() { view.zoom_in(); view.redraw() }).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);
-        this.zo_link = $("<a/>").click(function() { view.zoom_out(); view.redraw() }).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);;
+        this.goto_link = $("<a/>").click(function() { view.nav_input.toggle(); view.nav_input.focus(); }).html('<img src="'+image_path+'/fugue/navigation.png" />').appendTo(this.chrom_form);
+        this.zo_link = $("<a/>").click(function() { view.zoom_out(); view.redraw() }).html('<img src="'+image_path+'/fugue/magnifier-zoom-out.png" />').appendTo(this.chrom_form);
+        this.zi_link = $("<a/>").click(function() { view.zoom_in(); view.redraw() }).html('<img src="'+image_path+'/fugue/magnifier-zoom.png" />').appendTo(this.chrom_form);        
         
         $.ajax({
             url: chrom_url, 
@@ -132,34 +143,11 @@ var View = function( container, chrom, t
                     chrom_options += '<option value="' + chrom + '">' + chrom + '</option>';
                 }
                 view.chrom_select.html(chrom_options);
-                
-                var change_chrom = function () {
-                    if (view.chrom_select.val() === "") {
-                        // No chrom selected
-                        view.intro_div.show();
-                        view.content_div.hide();
-                    } else {
-                        view.intro_div.hide();
-                        view.content_div.show();
-                    }
-                    view.chrom = view.chrom_select.val();
-                    var found = $.grep(view.chrom_data, function(v, i) {
-                        return v.chrom === view.chrom;
-                    })[0];
-                    view.max_high = (found !== undefined ? found.len : 0);
-                    view.reset();
-                    view.redraw(true);
-                
-                    for (var track_id in view.tracks) {
-                        var track = view.tracks[track_id];
-                        if (track.init) {
-                            track.init();
-                        }
-                    }
-                    view.redraw();
-                };
-                view.chrom_select.bind( "change", change_chrom );
-                change_chrom();
+                view.intro_div.show();
+                view.content_div.hide();
+                view.chrom_select.bind("change", function() {
+                    view.change_chrom(view.chrom_select.val());
+                });
             },
             error: function() {
                 alert( "Could not load chroms for this dbkey:", view.dbkey );
@@ -199,13 +187,13 @@ var View = function( container, chrom, t
             this.original_low = view.low;
             this.current_height = e.clientY;
             this.current_x = e.offsetX;
+            this.active = (e.clientX < view.viewport_container.width() - 16) ? true : false; // Fix webkit scrollbar
         }).bind( "drag", function( e ) {
+            if (!this.active) { return; }
             var container = $(this);
             var delta = e.offsetX - this.current_x;
             var new_scroll = container.scrollTop() - (e.clientY - this.current_height);
-            // if ( new_scroll < container.get(0).scrollHeight - container.height() ) {
-                container.scrollTop(new_scroll);
-            // }
+            container.scrollTop(new_scroll);
             this.current_height = e.clientY;
             this.current_x = e.offsetX;
 
@@ -217,7 +205,7 @@ var View = function( container, chrom, t
             this.drag_origin_x = e.clientX;
             this.drag_origin_pos = e.clientX / view.viewport_container.width() * (view.high - view.low) + view.low;
             this.drag_div = $("<div />").css( { 
-                "height": view.viewport_container.height(), "top": "0px", "position": "absolute", 
+                "height": view.content_div.height(), "top": "0px", "position": "absolute", 
                 "background-color": "#cfc", "border": "1px solid #6a6", "opacity": 0.5, "z-index": 1000
             } ).appendTo( $(this) );
         }).bind( "drag", function(e) {
@@ -226,8 +214,7 @@ var View = function( container, chrom, t
                 span = (view.high - view.low),
                 width = view.viewport_container.width();
             
-            view.low_input.val(commatize(Math.round(min / width * span) + view.low));
-            view.high_input.val(commatize(Math.round(max / width * span) + view.low));
+            view.update_location(Math.round(min / width * span) + view.low, Math.round(max / width * span) + view.low);
             this.drag_div.css( { "left": min + "px", "width": (max - min) + "px" } );
         }).bind( "dragend", function(e) {
             var min = Math.min(e.clientX, this.drag_origin_x),
@@ -245,6 +232,64 @@ var View = function( container, chrom, t
         this.add_label_track( new LabelTrack( this, this.top_labeltrack ) );
         this.add_label_track( new LabelTrack( this, this.nav_labeltrack ) );
     },
+    update_location: function(low, high) {
+        this.location_span.text( commatize(low) + ' - ' + commatize(high) );
+        this.nav_input.val( this.chrom + ':' + commatize(low) + '-' + commatize(high) );
+    },
+    change_chrom: function(chrom, low, high) {
+        var view = this;
+        var found = $.grep(view.chrom_data, function(v, i) {
+            return v.chrom === chrom;
+        })[0];
+        if (found === undefined) {
+            // Invalid chrom
+            return;
+        }
+        view.chrom = chrom;
+        if (view.chrom === "") {
+            // No chrom selected
+            view.intro_div.show();
+            view.content_div.hide();
+        } else {
+            view.intro_div.hide();
+            view.content_div.show();
+        }
+        view.chrom_select.val(view.chrom);
+        view.max_high = found.len;
+        view.reset();
+        view.redraw(true);
+    
+        for (var track_id in view.tracks) {
+            var track = view.tracks[track_id];
+            if (track.init) {
+                track.init();
+            }
+        }
+        if (low !== undefined && high !== undefined) {
+            view.low = Math.max(low, 0);
+            view.high = Math.min(high, view.max_high);
+        }
+        view.overview_viewport.find("canvas").remove();
+        view.redraw();
+        
+    },
+    go_to: function(str) {
+        var view = this,
+            chrom_pos = str.split(":"),
+            chrom = chrom_pos[0],
+            pos = chrom_pos[1];
+        
+        if (pos !== undefined) {
+            try {
+                var pos_split   = pos.split("-"),
+                    new_low     = parseInt(pos_split[0].replace(/,/g, "")),
+                    new_high    = parseInt(pos_split[1].replace(/,/g, ""));
+            } catch (e) {
+                return false;
+            }
+        }
+        view.change_chrom(chrom, new_low, new_high);
+    },
     move_delta: function(delta_chrom) {
         var view = this;
         var current_chrom_span = view.high - view.low;
@@ -327,8 +372,7 @@ var View = function( container, chrom, t
             // Minimum width for usability
             width: Math.max( 12, (this.high - this.low)/(this.max_high - this.max_low) * this.overview_viewport.width() )
         }).show();
-        this.low_input.val( commatize(this.low) );
-        this.high_input.val( commatize(this.high) );
+        this.update_location(this.low, this.high);
         if (!nodraw) {
             for (var i = 0, len = this.tracks.length; i < len; i++) {
                 if (this.tracks[i] && this.tracks[i].enabled) {
@@ -386,6 +430,7 @@ var Track = function (name, view, parent
         track.data_queue = {};
         track.tile_cache.clear();
         track.data_cache.clear();
+        track.initial_canvas = undefined;
         track.content_div.css( "height", "auto" );
         if (!track.content_div.text()) {
             track.content_div.text(DATA_LOADING);
@@ -432,7 +477,49 @@ var Track = function (name, view, parent
 });
 
 var TiledTrack = function() {
-    this.left_offset = 200;
+    var track = this,
+        view = track.view;
+    
+    if (track.display_modes !== undefined) {
+        if (track.mode_div === undefined) {
+            track.mode_div = $("<div class='right-float menubutton popup' />").appendTo(track.header_div);
+            var init_mode = track.display_modes[0];
+            track.mode = init_mode;
+            track.mode_div.text(init_mode);
+        
+            var change_mode = function(name) {
+                track.mode_div.text(name);
+                track.mode = name;
+                track.tile_cache.clear();
+                track.draw();
+            };
+            var mode_mapping = {};
+            for (var i in track.display_modes) {
+                var mode = track.display_modes[i];
+                mode_mapping[mode] = function(mode) {
+                    return function() { change_mode(mode); }
+                }(mode);
+            }
+            make_popupmenu(track.mode_div, mode_mapping);
+        } else {
+            track.mode_div.hide();
+        }
+    }
+    if (track.overview_check_div === undefined) {
+        track.overview_check_div = $("<div class='right-float' />").css("margin-top", "-3px").appendTo(track.header_div);
+        track.overview_check = $("<input type='checkbox' class='overview_check' />").appendTo(track.overview_check_div);
+        track.overview_check.bind("click", function() {
+            var curr = this;
+            view.overview_viewport.find("canvas").remove();
+            track.set_overview();
+            $(".overview_check").each(function() {
+                if (this !== curr) {
+                    $(this).attr("checked", false);
+                }
+            });
+        });
+        track.overview_check_div.append( $("<label />").text("Overview") );
+    }
 };
 $.extend( TiledTrack.prototype, Track.prototype, {
     draw: function() {
@@ -476,13 +563,33 @@ var TiledTrack = function() {
         setTimeout(function() {
             if ( !(low > track.view.high || high < track.view.low) ) {
                 tile_element = track.draw_tile( resolution, tile_index, parent_element, w_scale );
-                if ( tile_element ) {
+                if (tile_element) {
+                    // Store initial canvas in we need to use it for overview
+                    if (!track.initial_canvas) {
+                        track.initial_canvas = $(tile_element).clone();
+                        var src_ctx = tile_element.get(0).getContext("2d");
+                        var tgt_ctx = track.initial_canvas.get(0).getContext("2d");
+                        var data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height);
+                        tgt_ctx.putImageData(data, 0, 0);
+                        track.set_overview();
+                    }
                     track.tile_cache.set(key, tile_element);
                     track.max_height = Math.max( track.max_height, tile_element.height() );
                     track.content_div.css("height", track.max_height + "px");
                 }
             }
         }, 50);
+    }, set_overview: function() {
+        var view = this.view;
+        view.overview_viewport.height(view.default_overview_height);
+        view.overview_box.height(view.default_overview_height);
+        
+        if (this.initial_canvas && this.overview_check.is(":checked")) {
+            view.overview_viewport.append(this.initial_canvas);
+            view.overview_viewport.height(this.initial_canvas.height());
+            view.overview_box.height(this.initial_canvas.height());
+        }
+        $(window).trigger("resize");
     }
 });
 
@@ -580,7 +687,7 @@ var ReferenceTrack = function (view) {
                 var c_start = Math.round(c * w_scale);
                 ctx.fillText(seq[c], c_start + this.left_offset, 10);
             }
-            parent_element.append( canvas );
+            parent_element.append(canvas);
             return canvas;
         }
         this.content_div.css("height", "0px");
@@ -589,17 +696,18 @@ var ReferenceTrack = function (view) {
 
 var LineTrack = function ( name, view, dataset_id, prefs ) {
     this.track_type = "LineTrack";
+    this.display_modes = ["Line", "Filled", "Intensity"];
+    this.mode = "Line";
     Track.call( this, name, view, view.viewport_container );
     TiledTrack.call( this );
     
-    this.height_px = 100;
+    this.height_px = 80;
     this.dataset_id = dataset_id;
     this.data_cache = new Cache(CACHED_DATA);
     this.tile_cache = new Cache(CACHED_TILES_LINE);
     this.prefs = { 'min_value': undefined, 'max_value': undefined, 'mode': 'Line' };
     if (prefs.min_value !== undefined) { this.prefs.min_value = prefs.min_value; }
     if (prefs.max_value !== undefined) { this.prefs.max_value = prefs.max_value; }
-    if (prefs.mode !== undefined) { this.prefs.mode = prefs.mode; }
 };
 $.extend( LineTrack.prototype, TiledTrack.prototype, {
     init: function() {
@@ -626,13 +734,13 @@ var LineTrack = function ( name, view, d
             $('#linetrack_' + track_id + '_minval').remove();
             $('#linetrack_' + track_id + '_maxval').remove();
             
-            var min_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(track.prefs.min_value);
-            var max_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(track.prefs.max_value);
+            var min_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(round_1000(track.prefs.min_value));
+            var max_label = $("<div />").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(round_1000(track.prefs.max_value));
             
-            max_label.css({ position: "relative", top: "25px", left: "10px" });
+            max_label.css({ position: "relative", top: "32px", left: "10px" });
             max_label.prependTo(track.container_div);
     
-            min_label.css({ position: "relative", top: track.height_px + 55 + "px", left: "10px" });
+            min_label.css({ position: "relative", top: track.height_px + 32 + "px", left: "10px" });
             min_label.prependTo(track.container_div);
         });
     },
@@ -689,7 +797,7 @@ var LineTrack = function ( name, view, d
             left: ( tile_low - this.view.low ) * w_scale
         });
         
-        canvas.get(0).width = Math.ceil( tile_length * w_scale + this.left_offset);
+        canvas.get(0).width = Math.ceil( tile_length * w_scale );
         canvas.get(0).height = this.height_px;
         var ctx = canvas.get(0).getContext("2d"),
             in_path = false,
@@ -698,7 +806,7 @@ var LineTrack = function ( name, view, d
             vertical_range = this.vertical_range,
             total_frequency = this.total_frequency,
             height_px = this.height_px,
-            mode = this.prefs.mode;
+            mode = this.mode;
             
         ctx.beginPath();
         
@@ -768,7 +876,7 @@ var LineTrack = function ( name, view, d
         } else {
             ctx.stroke();
         }
-        parent_element.append( canvas );
+        parent_element.append(canvas);
         return canvas;
     }, gen_options: function(track_id) {
         var container = $("<div />").addClass("form-row");
@@ -780,23 +888,15 @@ var LineTrack = function ( name, view, d
             maxval = 'track_' + track_id + '_maxval',
             max_label = $('<label></label>').attr("for", maxval).text("Max value:"),
             max_val = (this.prefs.max_value === undefined ? "" : this.prefs.max_value),
-            max_input = $('<input></input>').attr("id", maxval).val(max_val),
-            mode = 'track_' + track_id + '_mode',
-            mode_label = $('<label></label>').attr("for", mode).text("Display mode:"),
-            mode_val = (this.prefs.mode === undefined ? "Line" : this.prefs.mode),
-            mode_input = $('<select id="' +mode+ '"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');
-            
-            mode_input.children("#mode_"+mode_val).attr('selected', 'selected');
-            
-        return container.append(min_label).append(min_input).append(max_label).append(max_input).append(mode_label).append(mode_input);
+            max_input = $('<input></input>').attr("id", maxval).val(max_val);
+
+        return container.append(min_label).append(min_input).append(max_label).append(max_input);
     }, update_options: function(track_id) {
         var min_value = $('#track_' + track_id + '_minval').val(),
-            max_value = $('#track_' + track_id + '_maxval').val(),
-            mode = $('#track_' + track_id + '_mode option:selected').val();
-        if ( min_value !== this.prefs.min_value || max_value !== this.prefs.max_value || mode !== this.prefs.mode ) {
+            max_value = $('#track_' + track_id + '_maxval').val();
+        if ( min_value !== this.prefs.min_value || max_value !== this.prefs.max_value ) {
             this.prefs.min_value = parseFloat(min_value);
             this.prefs.max_value = parseFloat(max_value);
-            this.prefs.mode = mode;
             this.vertical_range = this.prefs.max_value - this.prefs.min_value;
             // Update the y-axis
             $('#linetrack_' + track_id + '_minval').text(this.prefs.min_value);
@@ -809,6 +909,7 @@ var LineTrack = function ( name, view, d
 
 var FeatureTrack = function ( name, view, dataset_id, prefs ) {
     this.track_type = "FeatureTrack";
+    this.display_modes = ["Auto", "Dense", "Squish", "Pack"];
     Track.call( this, name, view, view.viewport_container );
     TiledTrack.call( this );
     
@@ -819,13 +920,15 @@ var FeatureTrack = function ( name, view
     this.show_labels_scale = 0.001;
     this.showing_details = false;
     this.vertical_detail_px = 10;
-    this.vertical_nodetail_px = 3;
+    this.vertical_nodetail_px = 2;
+    this.summary_draw_height = 20;
     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': 'black', 'label_color': 'black', 'show_counts': true };
     if (prefs.block_color !== undefined) { this.prefs.block_color = prefs.block_color; }
@@ -835,39 +938,11 @@ var FeatureTrack = function ( name, view
 $.extend( FeatureTrack.prototype, TiledTrack.prototype, {
     init: function() {
         var track = this,
-            key = track.view.max_low + '_' + track.view.max_high;
-            if (track.mode_div === undefined) {
-                track.mode_div = $("<div class='right-float menubutton popup' />").text("Display Mode").appendTo(track.header_div);
-                track.mode = "Auto";
-                
-                var change_mode = function(name) {
-                    track.mode_div.text(name);
-                    track.mode = name;
-                    track.tile_cache.clear();
-                    track.draw();
-                };
-                make_popupmenu(track.mode_div, {
-                    "Auto": function() {
-                        change_mode("Auto");
-                    },
-                    "Dense": function() {
-                        change_mode("Dense");
-                    },
-                    "Squish": function() {
-                        change_mode("Squish");
-                    },
-                    "Pack": function() {
-                        change_mode("Pack");
-                    }
-                });
-            } else {
-                track.mode_div.hide();
-            }
+            key = "initial";
             
-            this.init_each({  low: track.view.max_low, 
-                                    high: track.view.max_high, dataset_id: track.dataset_id,
-                                    chrom: track.view.chrom, resolution: this.view.resolution }, function (result) {
-            
+        this.init_each({    low: track.view.max_low, 
+                            high: track.view.max_high, dataset_id: track.dataset_id,
+                            chrom: track.view.chrom, resolution: this.view.resolution }, function (result) {    
             track.mode_div.show();
             track.data_cache.set(key, result);
             track.draw();
@@ -993,8 +1068,8 @@ var FeatureTrack = function ( name, view
     draw_tile: function( resolution, tile_index, parent_element, w_scale ) {
         var tile_low = tile_index * DENSITY * resolution,
             tile_high = ( tile_index + 1 ) * DENSITY * resolution,
-            tile_span = DENSITY * resolution;
-        // console.log("drawing " + tile_index);
+            tile_span = tile_high - tile_low;
+        // console.log("drawing " + tile_low + " to " + tile_high);
 
         /*for (var k in this.data_cache.obj_cache) {
             var k_split = k.split("_"), k_low = k_split[0], k_high = k_split[1];
@@ -1004,9 +1079,9 @@ var FeatureTrack = function ( name, view
             }
         }*/
         
-        // var k = this.view.low + '_' + this.view.high;
-        var k = tile_low + '_' + tile_high;
+        var k = (!this.initial_canvas ? "initial" : tile_low + '_' + tile_high);
         var result = this.data_cache.get(k);
+        var cur_mode;
         
         if (result === undefined) {
             this.data_queue[ [tile_low, tile_high] ] = true;
@@ -1024,7 +1099,7 @@ var FeatureTrack = function ( name, view
             slots, required_height, y_scale;
         
         if (result.dataset_type === "summary_tree") {
-            required_height = 30;
+            required_height = this.summary_draw_height;
         } else if (mode === "Dense") {
             required_height = 15;
             y_scale = 10;
@@ -1066,7 +1141,7 @@ var FeatureTrack = function ( name, view
                 if (!y) { continue; }
                 color = Math.floor( color_span - (y / max) * color_span );
                 ctx.fillStyle = "rgb(" +color+ "," +color+ "," +color+ ")";
-                ctx.fillRect(x + left_offset, 0, delta_x_px, 20);
+                ctx.fillRect(x + left_offset, 0, delta_x_px, this.summary_draw_height);
 
                 if (this.prefs.show_counts && ctx.measureText(y).width < delta_x_px) {
                     if (color > color_cutoff) {
@@ -1078,7 +1153,7 @@ var FeatureTrack = function ( name, view
                     ctx.fillText(y, x + left_offset + (delta_x_px/2), 12);
                 }
             }
-            
+            cur_mode = "Summary";
             parent_element.append( new_canvas );
             return new_canvas;
         }

--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -661,11 +661,11 @@ class DatasetInstance( object ):
         new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps ).values()[0]
         new_dataset.hid = self.hid
         new_dataset.name = self.name
-        trans.sa_session.add( new_dataset )
-        trans.sa_session.flush()
+        session = trans.sa_session
+        session.add( new_dataset )
         assoc.dataset = new_dataset
-        trans.sa_session.add( assoc )
-        trans.sa_session.flush()
+        session.add( assoc )
+        session.flush()
         return None
     def clear_associated_files( self, metadata_safe = False, purge = False ):
         raise 'Unimplemented'

--- a/lib/galaxy/web/controllers/visualization.py
+++ b/lib/galaxy/web/controllers/visualization.py
@@ -30,8 +30,9 @@ class VisualizationListGrid( grids.Grid 
         grids.GridAction( "Create new visualization", dict( action='create' ) )
     ]
     operations = [
-        grids.GridOperation( "View", allow_multiple=False, url_args=dict( controller='tracks', action='browser' ) ),
+        grids.GridOperation( "View/Edit", allow_multiple=False, url_args=dict( controller='tracks', action='browser' ) ),
         grids.GridOperation( "Edit Attributes", allow_multiple=False, url_args=dict( action='edit') ),
+        grids.GridOperation( "Clone", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False, url_args=dict( action='clone') ),
         grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
         grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True, confirm="Are you sure you want to delete this visualization?" ),
     ]
@@ -86,6 +87,34 @@ class VisualizationController( BaseContr
         return self.list( trans, args, kwargs )
     
     @web.expose
+    @web.require_login()
+    def clone(self, trans, id, *args, **kwargs):
+        viz = self.get_visualization( trans, id, check_ownership=False )
+        user = trans.get_user()
+        if viz.user == user:
+            owner = True
+        else:
+            if trans.sa_session.query( model.VisualizationUserShareAssociation ) \
+                    .filter_by( user=user, visualization=viz ).count() == 0:
+                error( "Visualization is not owned by or shared with current user" )
+            owner = False
+        new_viz = model.Visualization()
+        new_viz.title = "Clone of '%s'" % viz.title
+        new_viz.dbkey = viz.dbkey
+        new_viz.type = viz.type
+        new_viz.latest_revision = viz.latest_revision
+        if not owner:
+            new_viz.title += " shared by '%s'" % viz.user.email
+        new_viz.user = user
+        # Persist
+        session = trans.sa_session
+        session.add( new_viz )
+        session.flush()
+        # Display the management page
+        trans.set_message( 'Clone created with name "%s"' % new_viz.title )
+        return self.list( trans )
+        
+    @web.expose
     @web.require_login( "use Galaxy visualizations", use_panels=True )
     def list( self, trans, *args, **kwargs ):
         # Handle operation

--- a/static/june_2007_style/blue/trackster.css
+++ b/static/june_2007_style/blue/trackster.css
@@ -1,13 +1,15 @@
 .viewport-container{overflow-x:hidden;overflow-y:auto;}
 .nav{padding:0 0;color:#333;font-weight:bold;}
-.nav-controls{text-align:center;background:#cccccc;background-image:url(panel_header_bg.png);background-position:top center;background-repeat:repeat-x;padding:2px 0;}
+.content{font:9px verdana;}
+.nav-controls{text-align:center;position:relative;background:#cccccc;background-image:url(panel_header_bg.png);background-position:top center;background-repeat:repeat-x;padding:2px 0;}
 .nav-controls input{margin:0 5px;}
 .nav-controls a{padding:0 0.4em;}
+.nav-input{font-size:12px;position:absolute;right:0px;bottom:25px;width:20em;z-index:1000;}
+.location{display:inline-block;width:15em;margin:0px 10px;}
 .intro{position:absolute;top:50%;left:30%;color:#555;font-size:16px;}
 .overview{width:100%;margin:0px;color:white;}
 .overview-viewport{position:relative;height:14px;background:white;border-bottom:solid gray 1px;margin:0;}
-.overview-box{position:absolute;margin-top:0px;height:14px;background:#ddd url(../images/visualization/draggable_horizontal.png) center center no-repeat;}
-.viewport{background-color:#fff;}
+.overview-box{opacity:0.5;z-index:100;position:absolute;margin-top:0px;height:14px;background:#cfc url(../images/visualization/draggable_horizontal.png) center center no-repeat;border-style:solid;border-color:#6a6;border-width:0px 2px;}
 .viewport-canvas{width:100%;height:100px;}
 .yaxislabel{color:#777;}
 .line-track .track-content{border-top:1px solid #ddd;border-bottom:1px solid #ddd;}
@@ -20,5 +22,5 @@
 .label-track{}
 .label-track .label{border-left:solid #999 1px;padding:1px;display:inline-block;}
 .right-float{float:right;margin-left:5px;}
-.top-labeltrack{border-bottom:solid #999 1px;}
+.top-labeltrack{position:relative;border-bottom:solid #999 1px;}
 .nav-labeltrack{border-top:solid #999 1px;border-bottom:solid #999 1px;}

--- a/static/june_2007_style/trackster.css.tmpl
+++ b/static/june_2007_style/trackster.css.tmpl
@@ -2,17 +2,16 @@
     overflow-x: hidden;
     overflow-y: auto;
 }
-
-/*canvas{ 
-    border-left: 1px solid green;
-    border-right: 1px solid red; } /* debugging */
 .nav {
     padding: 0 0;
     color:#333;font-weight:bold;
 }
-
+.content {
+    font: 9px verdana;
+}
 .nav-controls {
     text-align: center;
+    position: relative;
     background:#cccccc;
     background-image:url(panel_header_bg.png);
     background-position:top center;
@@ -25,7 +24,20 @@
 .nav-controls a {
     padding: 0 0.4em;
 }
-.intro{
+.nav-input {
+    font-size: 12px;
+    position: absolute;
+    right: 0px;
+    bottom: 25px;
+    width: 20em;
+    z-index: 1000;
+}
+.location {
+    display: inline-block;
+    width: 15em;
+    margin: 0px 10px;
+}
+.intro {
     position: absolute;
     top: 50%;
     left: 30%;
@@ -37,7 +49,6 @@
     margin: 0px;
     color: white;
 }
-
 .overview-viewport {
     position: relative;
     height: 14px;
@@ -48,20 +59,16 @@
     margin: 0;
 }
 .overview-box {
+    opacity: 0.5;
+    z-index: 100;
     position: absolute;
     margin-top: 0px;
     height: 14px;
-    background: #ddd url(../images/visualization/draggable_horizontal.png) center center no-repeat;
-    /*border-style: outset;*/
+    background: #cfc url(../images/visualization/draggable_horizontal.png) center center no-repeat;
+    border-style: solid;
+    border-color: #6a6;
+    border-width: 0px 2px;
 }
-
-.viewport {
-/*    overflow-x: hidden;*/
-    background-color: #fff;
-/*    overflow: scroll;*/
-/*    border-bottom: 2px solid black;*/
-}
-
 .viewport-canvas {
     width: 100%;
     height: 100px;
@@ -121,6 +128,7 @@
 }
 
 .top-labeltrack {
+    position: relative;
     border-bottom: solid #999 1px;
 }
 

--- a/templates/visualization/display.mako
+++ b/templates/visualization/display.mako
@@ -10,7 +10,7 @@
         // To adjust the size of the viewport to fit the fixed-height footer
         var refresh = function( e ) {
             if (view !== undefined) {
-                view.viewport_container.height( $(window).height() - 100 );
+                view.viewport_container.height( $("#center").height() - $(".nav-container").height() - 40 );
                 view.nav_container.width( $("#center").width() );
                 view.redraw();
             }

--- a/static/june_2007_style/process_css.py
+++ b/static/june_2007_style/process_css.py
@@ -84,7 +84,7 @@ def build_stylesheet_parser():
     #   Just match anything that looks like a selector, including element, class,
     #   id, attribute, and pseudoclass. Attributes are not handled properly (spaces,
     #   and even newlines in the quoted string are legal).
-    simple_selector = Word( alphanums + ".#*:()[]|=\"'_-" )
+    simple_selector = Word( alphanums + "@.#*:()[]|=\"'_-" )
     combinator = Literal( ">" ) | Literal( "+" )
     selector = Group( simple_selector + ZeroOrMore( Optional( combinator ) + simple_selector ) )
     selectors = Group( delimitedList( selector ) )

--- a/tools/regVariation/compute_q_values.xml
+++ b/tools/regVariation/compute_q_values.xml
@@ -46,7 +46,7 @@
 
 **What it does**
 
-This program computes the q-values based on the p-values of multiple simultaneous tests. The q-valules are computed using a specific R package, created by John Storey and Alan Dabney, called "qvalue". The program takes five inputs:
+This program computes the q-values based on the p-values of multiple simultaneous tests. The q-values are computed using a specific R package, created by John Storey and Alan Dabney, called "qvalue". The program takes five inputs:
  
 - The first input is a TABULAR format file consisting of one column only that represents the p-values of multiple simultaneous tests, one line for every p-value. 
 - The second input is the lambda parameter. The user can choose either the default: seq(0, 0.95, 0.05) or a decimal number between 0.0 and 1.0.
@@ -103,7 +103,7 @@ Let us have the first input file of p-va
 	0.904129283
 	0.031152635
 
-Runnig the program will give the following output::
+Running the program will give the following output::
 
 	pi0: 0.140311054	
 

--- a/templates/grid_base.mako
+++ b/templates/grid_base.mako
@@ -97,10 +97,8 @@
         
         // Operations that are async (AJAX) compatible.
         var async_ops = {};
-        %for operation in grid.operations:
-            %if operation.async_compatible:
-                async_ops['${operation.label.lower()}'] = "True";
-            %endif
+        %for operation in [op for op in grid.operations if op.async_compatible]:
+            async_ops['${operation.label.lower()}'] = "True";
         %endfor
         
         // Initialize grid controls
@@ -108,15 +106,13 @@
             // Initialize operation buttons.
             $('input[name=operation]:submit').each(function() {
                 $(this).click( function() {
-                   // Get the webapp
                    var webapp = $("input[name=webapp]").attr("value");
-                   // Get operation name.
-                   var operation_name = $(this).attr("value");
+                   var operation_name = $(this).val();
                    // For some reason, $('input[name=id]:checked').val() does not return all ids for checked boxes.
                    // The code below performs this function.
                    var item_ids = [];
                    $('input[name=id]:checked').each(function() {
-                       item_ids[item_ids.length] = $(this).val();
+                       item_ids.push( $(this).val() );
                    });
                    do_operation(webapp, operation_name, item_ids); 
                 });
@@ -133,28 +129,24 @@
                 $(this).mouseup( function() {
                    $(this).removeClass('gray-background'); 
                 });
-                
             });
             
             // Initialize sort links.
             $('.sort-link').each( function() {
-                var sort_key = $(this).attr('sort_key');
                 $(this).click( function() {
-                   set_sort_condition(sort_key);
-                   return false; 
+                   set_sort_condition( $(this).attr('sort_key') );
+                   return false;
                 });
-                
             });
             
             // Initialize page links.
             $('.page-link > a').each( function() {
-                var page_num = $(this).attr('page_num');
                 $(this).click( function() {
-                   set_page(page_num);
-                   return false; 
+                   set_page( $(this).attr('page_num') );
+                   return false;
                 });
-                
             });
+            
             $('#show-all-link').click( function() {
                 set_page('all');
                 return false;
@@ -163,9 +155,7 @@
             // Initialize categorical filters.
             $('.categorical-filter > a').each( function() {
                 $(this).click( function() {
-                    var filter_key = $(this).attr('filter_key');
-                    var filter_val = $(this).attr('filter_val');
-                    set_categorical_filter(filter_key, filter_val);
+                    set_categorical_filter( $(this).attr('filter_key'), $(this).attr('filter_val') );
                     return false;
                 });
             });
@@ -179,15 +169,15 @@
                     text_input_obj.val('');
                     add_filter_condition(column_key, text_input, true);
                     return false;
-                });                
+                });
             });
-                                        
+            
             // Initialize autocomplete for text inputs in search UI.
             var t = $("#input-tags-filter");
             if (t.length) {
                 t.autocomplete(  "${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='History' )}", 
                                  { selectFirst: false, autoFill: false, highlight: false, mustMatch: false });
-            }      
+            }
  
             var t2 = $("#input-name-filter");
             if (t2.length) {
@@ -209,14 +199,15 @@
             // Initialize grid selection checkboxes.
             $(".grid").each( function() {
                 var checkboxes = $(this).find("input.grid-row-select-checkbox");
-                var update = $(this).find( "span.grid-selected-count" );
-                update.text("");
+                var check_count = $(this).find("span.grid-selected-count");
+                var update_checked = function() {
+                    check_count.text( $(checkboxes).filter(":checked").length );
+                };
+                
                 $(checkboxes).each( function() {
-                    $(this).change( function() {
-                        var n = $(checkboxes).filter("[checked]").size();
-                        update.text( n );
-                    });
+                    $(this).change(update_checked);
                 });
+                update_checked();
             });
             
             // Initialize item labels.

    

[galaxy-commits] galaxy-dist commit 2ac11399c20e: trackster: Overview track, viz cloning, "Go-to" specific location, UI fixes

commits-noreply＠bitbucket.org