Loading',
title: 'Loading data...',
style: { visibility: 'hidden' }
- }, block );
+ });
window.setTimeout(function() { msgDiv.style.visibility = 'visible'; }, 200);
- this.heightUpdate( dojo.position(msgDiv).h, blockIndex );
+ return msgDiv;
},
fillError: function( blockIndex, block ) {
+ dom.empty(block);
var msgDiv = dojo.create(
'div', {
className: 'error',
@@ -324,7 +335,17 @@ return declare( null,
+(this.error ? '
Diagnostic message
'+this.error+'' : '' ),
title: 'An error occurred'
}, block );
- this.heightUpdate( dojo.position(msgDiv).h, blockIndex );
+ this.heightUpdate( dojo.position(msgDiv).h, blockIndex );
+ },
+
+ fillTooManyFeaturesMessage: function( blockIndex, block, scale ) {
+ this.fillMessage(
+ blockIndex,
+ block,
+ 'Too much data to show'
+ + (scale >= this.browser.view.maxPxPerBp ? '': '; zoom in to see detail')
+ + '.'
+ );
},
_showBlock: function(blockIndex, startBase, endBase, scale,
@@ -358,7 +379,37 @@ return declare( null,
containerStart,
containerEnd];
- this.fillBlock.apply( this, args );
+
+ // loadMessage is an opaque mask div that we place over the
+ // block until the fillBlock finishes
+ var loadMessage = this._makeLoadingMessage();
+ blockDiv.appendChild( loadMessage );
+
+ var finish = function() {
+ if( blockDiv && loadMessage.parentNode )
+ blockDiv.removeChild( loadMessage );
+ };
+
+ try {
+ this.fillBlock({
+ blockIndex: blockIndex,
+ block: blockDiv,
+ leftBlock: this.blocks[blockIndex - 1],
+ rightBlock: this.blocks[blockIndex + 1],
+ leftBase: startBase,
+ rightBase: endBase,
+ scale: scale,
+ stripeWidth: this.widthPx,
+ containerStart: containerStart,
+ containerEnd: containerEnd,
+ finishCallback: finish
+ });
+ } catch( e ) {
+ this.error = e;
+ console.error( e, e.stack );
+ this.fillError( blockIndex, blockDiv );
+ finish();
+ }
},
moveBlocks: function(delta) {
@@ -636,12 +687,35 @@ return declare( null,
* @returns {Array} menu options for this track's menu (usually contains save as, etc)
*/
_trackMenuOptions: function() {
+ var that = this;
return [
{ label: 'About this track',
title: 'About track: '+(this.key||this.name),
iconClass: 'jbrowseIconHelp',
action: 'contentDialog',
content: dojo.hitch(this,'_trackDetailsContent')
+ },
+ { label: 'Edit config',
+ title: "edit this track's configuration",
+ iconClass: 'dijitIconConfigure',
+ action: function() {
+ new TrackConfigEditor( that.config )
+ .show( function( result ) {
+ // replace this track's configuration
+ that.browser.publish( '/jbrowse/v1/v/tracks/replace', [result.conf] );
+ });
+ }
+ },
+ { label: 'Delete track',
+ title: "delete this track",
+ iconClass: 'dijitIconDelete',
+ action: function() {
+ new ConfirmDialog({ title: 'Delete track?', message: 'Really delete this track?' })
+ .show( function( confirmed ) {
+ if( confirmed )
+ that.browser.publish( '/jbrowse/v1/v/tracks/delete', [that.config] );
+ });
+ }
}
];
},
@@ -803,6 +877,19 @@ return declare( null,
menu.bindDomNode( this.label );
this.trackMenu = menu;
}
+ },
+
+
+ // display a rendering-timeout message
+ fillTimeout: function( blockIndex, block ) {
+ dom.empty( block );
+ dojo.addClass( block, 'timed_out' );
+ this.fillMessage( blockIndex, block,
+ 'This region took too long'
+ + ' to display, possibly because'
+ + ' it contains too much data.'
+ + ' Try zooming in to show a smaller region.'
+ );
}
});
diff --git a/src/JBrowse/View/Track/Canvas.js b/src/JBrowse/View/Track/Canvas.js
index c08a9de14e..8455dee0cd 100644
--- a/src/JBrowse/View/Track/Canvas.js
+++ b/src/JBrowse/View/Track/Canvas.js
@@ -19,34 +19,55 @@ return declare( BlockBased,
}
},
- fillBlock: function( blockIndex, block,
- leftBlock, rightBlock,
- leftBase, rightBase,
- scale, stripeWidth,
- containerStart, containerEnd) {
+ testCanvasSupport: function( blockIndex, block ) {
+ try {
+ dojo.create('canvas').getContext('2d').fillStyle = 'red';
+ return true;
+ } catch( e ) {
+ this.error = 'This browser does not support HTML canvas elements.';
+ this.fillError( blockIndex, block );
+ return false;
+ }
+ },
+
+ fillBlock: function( args ) {
+ var blockIndex = args.blockIndex;
+ var block = args.block;
+ var leftBase = args.leftBase;
+ var rightBase = args.rightBase;
+ var scale = args.scale;
+
+ if( ! this.testCanvasSupport( blockIndex, block ) )
+ return;
var blockWidth = rightBase - leftBase;
this.heightUpdate( this.height, blockIndex );
- this.renderCanvases( scale, leftBase, rightBase, dojo.hitch(this, function( canvases ) {
- dojo.forEach( canvases, function(c) {
- this.heightUpdate( c.height, blockIndex );
- c.className = 'canvas-track';
- if (!(c.parentNode && c.parentNode.parentNode)) {
- c.style.position = "absolute";
- c.style.left = (100 * ((c.startBase - leftBase) / blockWidth)) + "%";
- switch (this.config.align) {
- case "top":
- c.style.top = "0px";
- break;
- case "bottom":
- default:
- c.style.bottom = this.trackPadding + "px";
- break;
- }
- block.appendChild(c);
- }
- }, this);
- }));
+ this.renderCanvases( scale, leftBase, rightBase, dojo.hitch(this, 'layoutCanvases', args ) );
+ },
+
+ layoutCanvases: function( /**Object*/ args, /**Array[canvas]*/ canvases ) {
+ var block = args.block;
+ var leftBase = args.leftBase;
+ var rightBase = args.rightBase;
+
+ dojo.forEach( canvases, function(c) {
+ this.heightUpdate( c.height, blockIndex );
+ c.className = 'canvas-track';
+ if (!(c.parentNode && c.parentNode.parentNode)) {
+ c.style.position = "absolute";
+ c.style.left = (100 * ((c.startBase - leftBase) / blockWidth)) + "%";
+ switch (this.config.align) {
+ case "top":
+ c.style.top = "0px";
+ break;
+ case "bottom":
+ default:
+ c.style.bottom = this.trackPadding + "px";
+ break;
+ }
+ block.appendChild(c);
+ }
+ }, this);
},
startZoom: function(destScale, destStart, destEnd) {
diff --git a/src/JBrowse/View/Track/CanvasFeatures.js b/src/JBrowse/View/Track/CanvasFeatures.js
new file mode 100644
index 0000000000..15d6d50f18
--- /dev/null
+++ b/src/JBrowse/View/Track/CanvasFeatures.js
@@ -0,0 +1,180 @@
+/**
+ * Feature track that draws features using HTML5 canvas elements.
+ */
+
+define( [
+ 'dojo/_base/declare',
+ 'dojo/dom-construct',
+ 'dojo/_base/array',
+ 'JBrowse/View/GranularRectLayout',
+ 'JBrowse/View/Track/Canvas'
+ ],
+ function( declare, dom, array, Layout, CanvasTrack ) {
+
+return declare( CanvasTrack, {
+
+ constructor: function( args ) {
+ },
+
+ _defaultConfig: function() {
+ return {
+ maxFeatureScreenDensity: 400,
+ style: {
+ bgcolor: 'goldenrod',
+ fgcolor: null,
+ height: 3,
+ marginBottom: 1
+ }
+ };
+ },
+
+ fillBlock: function( args ) {
+ var blockIndex = args.blockIndex;
+ var block = args.block;
+ var leftBase = args.leftBase;
+ var rightBase = args.rightBase;
+ var scale = args.scale;
+
+ if( ! this.testCanvasSupport( blockIndex, block ) )
+ return;
+
+ var region = { ref: this.refSeq.name, start: leftBase, end: rightBase };
+
+ this.store.getRegionStats(
+ region,
+ dojo.hitch( this, function( stats ) {
+
+ var density = stats.featureDensity;
+ var featureScale = this.config.style.featureScale || density / this.config.maxFeatureScreenDensity; // (feat/bp) / ( feat/px ) = px/bp )
+
+ if( scale < featureScale ) {
+ this.fillTooManyFeaturesMessage(
+ blockIndex,
+ block,
+ scale
+ );
+ args.finishCallback();
+ }
+ else {
+ this.fillFeatures( dojo.mixin( {stats: stats}, args ) );
+ }
+ }));
+ },
+
+ _getLayout: function( scale ) {
+ // create the layout if we need to, and if we can
+ if( ( ! this.layout || this.layout.pitchX != 4/scale ) && scale )
+ this.layout = new Layout({pitchX: 4/scale, pitchY: this.config.layoutPitchY || (this.config.style.height + this.config.style.marginBottom) });
+
+ return this.layout;
+ },
+
+ fillFeatures: function( args ) {
+ var track = this;
+
+ var blockIndex = args.blockIndex;
+ var block = args.block;
+ var scale = args.scale;
+ var leftBase = args.leftBase;
+ var rightBase = args.rightBase;
+ var finishCallback = args.finishCallback;
+
+ var timedOut = false;
+ var timeOutError = { toString: function() { return 'Timed out trying to display '+track.name+' block '+blockIndex; } };
+ if( this.config.blockDisplayTimeout )
+ window.setTimeout( function() { timedOut = true; }, this.config.blockDisplayTimeout );
+
+ var fRects = [];
+ var featCallback = dojo.hitch(this,function( feature ) {
+ if( timedOut )
+ throw timeOutError;
+
+ fRects.push( this.layoutFeature( feature, leftBase, scale ) );
+ });
+
+ this.store.getFeatures( { ref: this.refSeq.name,
+ start: leftBase,
+ end: rightBase
+ },
+ featCallback,
+ function () {
+ var totalHeight = track._getLayout(scale).getTotalHeight();
+ var c = dojo.create(
+ 'canvas',
+ { height: totalHeight,
+ width: block.offsetWidth+1,
+ style: { cursor: 'default' },
+ innerHTML: 'Your web browser cannot display this type of track.',
+ className: 'canvas-track'
+ },
+ block
+ );
+ track.renderFeatures( fRects, c );
+
+ track.layoutCanvases([c]);
+ track.heightUpdate( totalHeight,
+ blockIndex );
+ finishCallback();
+ },
+ function( error ) {
+ track.error = error;
+ if( error === timeOutError ) {
+ track.fillTimeout( blockIndex, block );
+ } else {
+ console.error( error, error.stack );
+ track.fillError( blockIndex, block );
+ }
+ finishCallback();
+ }
+ );
+ },
+
+ // calculate the placement of the feature on the canvas for this
+ // block.
+ layoutFeature: function( feature, leftBase, scale ) {
+ var layoutStart = feature.get('start');
+ var layoutEnd = feature.get('end');
+
+ var fHeight = this.config.style.height;
+ var levelHeight = fHeight + this.config.style.marginBottom;
+
+ var uniqueId = feature.id();
+ var top = this._getLayout( scale )
+ .addRect( uniqueId,
+ layoutStart,
+ layoutEnd,
+ levelHeight);
+
+ var fRect = {
+ w: (layoutEnd-layoutStart)*scale,
+ l: (layoutStart-leftBase)*scale,
+ h: fHeight,
+ t: top,
+
+ f: feature
+ };
+ return fRect;
+ },
+
+ // draw the features on the canvas
+ renderFeatures: function( fRects, canvas ) {
+ var context = canvas.getContext('2d');
+ var fgcolor = this.config.style.fgcolor;
+ context.fillStyle = this.config.style.bgcolor;
+ array.forEach( fRects, function( fRect ) {
+ context.fillRect( fRect.l, fRect.t, fRect.w, fRect.h );
+ });
+ if( fgcolor ) {
+ context.lineWidth = 1;
+ context.strokeStyle = fgcolor;
+ array.forEach( fRects, function( fRect ) {
+ // need to stroke a smaller rectangle to remain within
+ // the bounds of the feature's overall height and
+ // width, because of the way stroking is done in
+ // canvas. thus the +0.5 and -1 business.
+ context.strokeRect( fRect.l+0.5, fRect.t+0.5, fRect.w-1, fRect.h-1 );
+ });
+ }
+ }
+});
+});
\ No newline at end of file
diff --git a/src/JBrowse/View/Track/ExportMixin.js b/src/JBrowse/View/Track/ExportMixin.js
index f2638b637c..12c6290257 100644
--- a/src/JBrowse/View/Track/ExportMixin.js
+++ b/src/JBrowse/View/Track/ExportMixin.js
@@ -2,12 +2,14 @@ define( [
'dojo/_base/array',
'dojo/aspect',
'dojo/has',
+ 'dojo/window',
+ 'dojo/dom-construct',
'JBrowse/Util',
'dijit/form/Button',
'dijit/form/RadioButton',
'dijit/Dialog'
],
- function( array, aspect, has, Util, dijitButton, dijitRadioButton, dijitDialog ) {
+ function( array, aspect, has, dojoWindow, dom, Util, dijitButton, dijitRadioButton, dijitDialog ) {
/**
* Mixin for a track that can export its data.
* @lends JBrowse.View.Track.ExportMixin
@@ -50,7 +52,7 @@ return {
region.canExport = this._canExportRegion( region );
},this.track);
- var form = dojo.create('form', { onSubmit: function() { return false; } });
+ var form = dom.create('form', { onSubmit: function() { return false; } });
form.innerHTML = ''
+ '
';
- var actionBar = dojo.create( 'div', {
+ var actionBar = dom.create( 'div', {
className: 'dijitDialogPaneActionBar'
});
@@ -99,6 +104,7 @@ return {
label: 'View',
disabled: ! array.some(possibleRegions,function(r) { return r.canExport; }),
onClick: dojo.hitch( this.track, function() {
+ var track = this;
viewButton.set('disabled',true);
viewButton.set('iconClass','jbrowseIconBusy');
@@ -106,14 +112,14 @@ return {
var format = this._readRadio( form.elements.format );
this.exportRegion( region, format, function(output) {
dialog.hide();
- var text = dojo.create('textarea', {
- rows: 30,
+ var text = dom.create('textarea', {
+ rows: Math.round( dojoWindow.getBox().h / 12 * 0.5 ),
wrap: 'soft',
cols: 80,
readonly: true
});
text.value = output;
- var actionBar = dojo.create( 'div', {
+ var actionBar = dom.create( 'div', {
className: 'dijitDialogPaneActionBar'
});
var exportView = new dijitDialog({
@@ -132,10 +138,10 @@ return {
{
iconClass: 'dijitIconSave',
label: 'Save',
- onClick: dojo.hitch(this, function() {
+ onClick: function() {
exportView.hide();
- window.location.href="data:application/x-"+format.toLowerCase()+","+escape(output);
- })
+ track._fileDownload({ format: format, data: output });
+ }
}).placeAt(actionBar);
}
@@ -160,10 +166,10 @@ return {
var region = this._readRadio( form.elements.region );
dlButton.set('disabled',true);
dlButton.set('iconClass','jbrowseIconBusy');
- this.exportRegion( region, format, function( output ) {
+ this.exportRegion( region, format, dojo.hitch( this, function( output ) {
dialog.hide();
- window.location.href="data:application/x-"+format.toLowerCase()+","+escape(output);
- });
+ this._fileDownload({ format: format, data: output });
+ }));
})})
.placeAt( actionBar );
}
@@ -171,6 +177,17 @@ return {
return [ form, actionBar ];
},
+ _fileDownload: function( args ) {
+ // do the file download by setting the src of a hidden iframe,
+ // because missing with the href of the window messes up
+ // WebApollo long polling
+ var iframe = dom.create( 'iframe', {
+ style: { display: 'none' }
+ },this.div );
+ iframe.src = "data:"+( args.format ? 'application/x-'+args.format.toLowerCase() : 'text/plain' )
+ +","+escape( args.data || '' );
+ },
+
// cross-platform function for (portably) reading the value of a radio control. sigh. *rolls eyes*
_readRadio: function( r ) {
if( r.length ) {
diff --git a/src/JBrowse/View/Track/FeatureCoverage.js b/src/JBrowse/View/Track/FeatureCoverage.js
index 98dd45a47b..458d8bec7e 100644
--- a/src/JBrowse/View/Track/FeatureCoverage.js
+++ b/src/JBrowse/View/Track/FeatureCoverage.js
@@ -21,6 +21,17 @@ var CoverageFeature = Util.fastDeclare(
return declare( Wiggle,
{
+
+ _defaultConfig: function() {
+ return Util.deepUpdate(
+ dojo.clone( this.inherited(arguments) ),
+ {
+ min_score: 0,
+ max_score: 100
+ }
+ );
+ },
+
getGlobalStats: function() {
return {};
},
@@ -28,28 +39,37 @@ return declare( Wiggle,
getFeatures: function( query, featureCallback, finishCallback, errorCallback ) {
var leftBase = query.start;
var rightBase = query.end;
- var coverage = new Array( rightBase-leftBase );
+ var scale = query.scale; // px/bp
+ var widthBp = rightBase-leftBase;
+ var widthPx = widthBp * ( query.scale || 1/query.basesPerSpan);
+
+ var binWidth = Math.ceil( query.basesPerSpan ); // in bp
+
+ var coverageBins = new Array( Math.ceil( widthBp/binWidth ) );
+ var bpToBin = function( bp ) {
+ return Math.floor( (bp-leftBase) / binWidth );
+ };
+
this.store.getFeatures(
query,
dojo.hitch( this, function( feature ) {
- var end = feature.get('end');
- for( var i = feature.get('start')+1; i <= end; i++ ) {
- coverage[i-leftBase] = (coverage[i-leftBase] || 0) + 1;
+ var startBin = bpToBin( feature.get('start') );
+ var endBin = bpToBin( feature.get('end')-1 );
+ for( var i = startBin; i <= endBin; i++ ) {
+ coverageBins[i] = (coverageBins[i] || 0) + 1;
}
}),
function () {
// make fake features from the coverage
- var currFeat;
- array.forEach( coverage, function( c, i ) {
- if( currFeat && c == currFeat.score ) {
- currFeat.end = leftBase+i;
- } else {
- if( currFeat )
- featureCallback( currFeat );
- currFeat = new CoverageFeature({ start: leftBase + i - 1, end: leftBase+i, score: c || 0 });
- }
- });
-
+ for( var i = 0; i < coverageBins.length; i++ ) {
+ var score = coverageBins[i] || 0;
+ var bpOffset = leftBase+binWidth*i;
+ featureCallback( new CoverageFeature({
+ start: bpOffset,
+ end: bpOffset+binWidth,
+ score: score
+ }));
+ }
finishCallback();
}
);
diff --git a/src/JBrowse/View/Track/FixedImage.js b/src/JBrowse/View/Track/FixedImage.js
index d88d081b98..5ef60d5216 100644
--- a/src/JBrowse/View/Track/FixedImage.js
+++ b/src/JBrowse/View/Track/FixedImage.js
@@ -53,11 +53,13 @@ return declare( BlockBased,
},
- fillBlock: function(blockIndex, block,
- leftBlock, rightBlock,
- leftBase, rightBase,
- scale, stripeWidth,
- containerStart, containerEnd) {
+ fillBlock: function( args ) {
+ var blockIndex = args.blockIndex;
+ var block = args.block;
+ var leftBase = args.leftBase;
+ var rightBase = args.rightBase;
+ var scale = args.scale;
+ var finishCallback = args.finishCallback || function() {};
var blockWidth = rightBase - leftBase;
@@ -92,6 +94,7 @@ return declare( BlockBased,
im.onload = loadhandler;
}, this);
+ finishCallback();
}),
dojo.hitch( this, function( error ) {
if( error.status == 404 ) {
@@ -100,6 +103,7 @@ return declare( BlockBased,
this.error = error;
this.fillError( blockIndex, block );
}
+ finishCallback();
})
);
},
diff --git a/src/JBrowse/View/Track/FixedImage/Wiggle.js b/src/JBrowse/View/Track/FixedImage/Wiggle.js
index 676fb39125..fd25945a1e 100644
--- a/src/JBrowse/View/Track/FixedImage/Wiggle.js
+++ b/src/JBrowse/View/Track/FixedImage/Wiggle.js
@@ -42,7 +42,7 @@ var Wiggle = declare( FixedImage,
makeWiggleYScale: function() {
var thisB = this;
this.store.getGlobalStats( function( stats ) {
- if( ! this.yscale )
+ if( ! thisB.yscale )
thisB.makeYScale({ min: stats.scoreMin, max: stats.scoreMax });
});
}
diff --git a/src/JBrowse/View/Track/GridLines.js b/src/JBrowse/View/Track/GridLines.js
index 983c7817fb..158e931e17 100644
--- a/src/JBrowse/View/Track/GridLines.js
+++ b/src/JBrowse/View/Track/GridLines.js
@@ -21,13 +21,10 @@ return dojo.declare( BlockBased,
makeTrackLabel: function() {},
makeTrackMenu: function() {},
- fillBlock: function(blockIndex, block,
- leftBlock, rightBlock,
- leftBase, rightBase, scale,
- padding, stripeWidth) {
-
- this.renderGridlines( block, leftBase, rightBase );
- this.heightUpdate(100, blockIndex);
+ fillBlock: function( args ) {
+ this.renderGridlines( args.block, args.leftBase, args.rightBase );
+ args.finishCallback();
+ this.heightUpdate(100, args.blockIndex);
},
renderGridlines: function(block,leftBase,rightBase) {
diff --git a/src/JBrowse/View/Track/HTMLFeatures.js b/src/JBrowse/View/Track/HTMLFeatures.js
index e70216cbed..78ba734929 100644
--- a/src/JBrowse/View/Track/HTMLFeatures.js
+++ b/src/JBrowse/View/Track/HTMLFeatures.js
@@ -2,6 +2,7 @@ define( [
'dojo/_base/declare',
'dojo/_base/lang',
'dojo/_base/array',
+ 'dojo/dom-construct',
'dojo/dom-geometry',
'dojo/on',
'dojo/has',
@@ -19,6 +20,7 @@ define( [
function( declare,
lang,
array,
+ dom,
domGeom,
on,
has,
@@ -50,12 +52,22 @@ var HTMLFeatures = declare( BlockBased, {
//number of histogram bins per block
this.numBins = 25;
this.histLabel = false;
- this.padding = 5;
+
+ this.defaultPadding = 5;
+ this.padding = this.defaultPadding;
+
+ this.glyphHeightPad = 1;
+ this.levelHeightPad = 2;
+ this.labelPad = 1;
+
+ // if calculated feature % width would be less than minFeatWidth, then set width to minFeatWidth instead
+ this.minFeatWidth = 0.1;
+
this.trackPadding = args.trackPadding;
this.heightCache = {}; // cache for the heights of some
// feature elements, indexed by the
- // complete className of the feature
+ // complete cassName of the feature
// make a default click event handler
if( ! (this.config.events||{}).click ) {
@@ -114,7 +126,7 @@ HTMLFeatures = declare( HTMLFeatures,
description: true,
maxFeatureScreenDensity: 0.5,
- layoutPitchY: 6,
+ blockDisplayTimeout: 5000,
style: {
className: "feature2",
@@ -126,7 +138,8 @@ HTMLFeatures = declare( HTMLFeatures,
minSubfeatureWidth: 6,
maxDescriptionLength: 70,
- showLabels: true
+ showLabels: true,
+ centerChildrenVertically: true // by default use feature child centering
},
hooks: {
create: function(track, feat ) {
@@ -152,10 +165,11 @@ HTMLFeatures = declare( HTMLFeatures,
defaultFeatureDetail: function( /** JBrowse.Track */ track, /** Object */ f, /** HTMLElement */ featDiv, /** HTMLElement */ container ) {
var fmt = dojo.hitch( this, '_fmtDetailField' );
container = container || dojo.create('div', { className: 'detail feature-detail feature-detail-'+track.name, innerHTML: '' } );
- container.innerHTML += fmt( 'Name', f.get('name') );
- container.innerHTML += fmt( 'Type', f.get('type') );
- container.innerHTML += fmt( 'Description', f.get('note') );
- container.innerHTML += fmt(
+ var coreDetails = dojo.create('div', { className: 'core' }, container );
+ coreDetails.innerHTML += fmt( 'Name', f.get('name') );
+ coreDetails.innerHTML += fmt( 'Type', f.get('type') );
+ coreDetails.innerHTML += fmt( 'Description', f.get('note') );
+ coreDetails.innerHTML += fmt(
'Position',
Util.assembleLocString({ start: f.get('start'),
end: f.get('end'),
@@ -163,13 +177,18 @@ HTMLFeatures = declare( HTMLFeatures,
strand: f.get('strand')
})
);
- container.innerHTML += fmt( 'Length', Util.addCommas(f.get('end')-f.get('start'))+' b' );
+ coreDetails.innerHTML += fmt( 'Length', Util.addCommas(f.get('end')-f.get('start'))+' bp' );
// render any additional tags as just key/value
var additionalTags = array.filter( f.tags(), function(t) { return ! {name:1,start:1,end:1,strand:1,note:1,subfeatures:1,type:1}[t.toLowerCase()]; });
- dojo.forEach( additionalTags.sort(), function(t) {
- container.innerHTML += fmt( t, f.get(t) );
- });
+ if( additionalTags.length ) {
+ var at_html = '
Attributes
';
+ dojo.forEach( additionalTags.sort(), function(t) {
+ at_html += fmt( t, f.get(t) );
+ });
+ at_html += '';
+ container.innerHTML += at_html;
+ }
// render the sequence underlying this feature if possible
var field_container = dojo.create('div', { className: 'field_container feature_sequence' }, container );
@@ -186,6 +205,7 @@ HTMLFeatures = declare( HTMLFeatures,
if( refSeqStore ) {
refSeqStore.getFeatures(
{ ref: this.refSeq.name, start: f.get('start'), end: f.get('end')},
+ // feature callback
dojo.hitch( this, function( feature ) {
var seq = feature.get('seq');
valueContainer = dojo.byId(valueContainerID) || valueContainer;
@@ -205,9 +225,17 @@ HTMLFeatures = declare( HTMLFeatures,
f.get('strand') == -1 ? Util.revcom(seq) : seq,
valueContainer
);
- }));
+ }),
+ // end callback
+ function() {},
+ // error callback
+ dojo.hitch( this, function() {
+ valueContainer = dojo.byId(valueContainerID) || valueContainer;
+ valueContainer.innerHTML = '
reference sequence not available';
+ })
+ );
} else {
- valueContainer.innerHTML = '
reference sequences not loaded';
+ valueContainer.innerHTML = '
reference sequence not available';
}
}));
@@ -298,7 +326,12 @@ HTMLFeatures = declare( HTMLFeatures,
};
},
- fillHist: function( blockIndex, block, leftBase, rightBase, stripeWidth ) {
+ fillHist: function( args ) {
+ var blockIndex = args.blockIndex;
+ var block = args.block;
+ var leftBase = args.leftBase;
+ var rightBase = args.rightBase;
+ var stripeWidth = args.stripeWidth;
var dims = this._histDimensions( Math.abs( rightBase - leftBase ) );
@@ -315,7 +348,7 @@ HTMLFeatures = declare( HTMLFeatures,
if (!(typeof hist[bin] == 'number' && isFinite(hist[bin])))
continue;
binDiv = document.createElement("div");
- binDiv.className = "hist "+track.config.style.className + "-hist";
+ binDiv.className = "hist feature-hist "+track.config.style.className + "-hist";
binDiv.style.cssText =
"left: " + ((bin / track.numBins) * 100) + "%; "
+ "height: "
@@ -382,6 +415,8 @@ HTMLFeatures = declare( HTMLFeatures,
this.store.histogram( leftBase, rightBase,
this.numBins, makeHistBlock);
}
+
+ args.finishCallback();
},
endZoom: function(destScale, destBlockBases) {
@@ -436,7 +471,14 @@ HTMLFeatures = declare( HTMLFeatures,
},this);
},
- fillBlock: function( blockIndex, block, leftBlock, rightBlock, leftBase, rightBase, scale, stripeWidth, containerStart, containerEnd ) {
+ fillBlock: function( args ) {
+ var blockIndex = args.blockIndex;
+ var block = args.block;
+ var leftBase = args.leftBase;
+ var rightBase = args.rightBase;
+ var scale = args.scale;
+ var containerStart = args.containerStart;
+ var containerEnd = args.containerEnd;
var region = { ref: this.refSeq.name, start: leftBase, end: rightBase };
@@ -444,8 +486,9 @@ HTMLFeatures = declare( HTMLFeatures,
region,
dojo.hitch( this, function( stats ) {
- var density = stats.featureDensity;
- var histScale = this.config.style.histScale || density * this.config.style._defaultHistScale;
+ var density = stats.featureDensity;
+ var histScale = this.config.style.histScale || density * this.config.style._defaultHistScale;
+ var featureScale = this.config.style.featureScale || density / this.config.maxFeatureScreenDensity; // (feat/bp) / ( feat/px ) = px/bp )
// only update the label once for each block size
var blockBases = Math.abs( leftBase-rightBase );
@@ -462,20 +505,18 @@ HTMLFeatures = declare( HTMLFeatures,
// if we our store offers density histograms, and we are zoomed out far enough, draw them
if( this.store.histograms && scale < histScale ) {
- this.fillHist( blockIndex, block, leftBase, rightBase, stripeWidth,
- containerStart, containerEnd);
+ this.fillHist( args );
}
// if we have no histograms, check the predicted density of
// features on the screen, and display a message if it's
// bigger than maxFeatureScreenDensity
- else if( stats.featureDensity / scale > this.config.maxFeatureScreenDensity ) {
- this.fillMessage(
+ else if( scale < featureScale ) {
+ this.fillTooManyFeaturesMessage(
blockIndex,
block,
- 'Too many features to show'
- + (scale >= this.browser.view.maxPxPerBp ? '': '; zoom in to see detail')
- + '.'
+ scale
);
+ args.finishCallback();
}
else {
// if we have transitioned to viewing features, delete the
@@ -483,9 +524,7 @@ HTMLFeatures = declare( HTMLFeatures,
if( this.yscale ) {
this._removeYScale();
}
- this.fillFeatures(blockIndex, block, leftBlock, rightBlock,
- leftBase, rightBase, scale, stats,
- containerStart, containerEnd);
+ this.fillFeatures( dojo.mixin( {stats: stats}, args ) );
}
}));
},
@@ -564,23 +603,24 @@ HTMLFeatures = declare( HTMLFeatures,
overlaps = overlaps || [];
for (var i = 0; i < overlaps.length; i++) {
- //if the feature overlaps destBlock,
- //move to destBlock & re-position
- sourceSlot = sourceBlock.featureNodes[ overlaps[i] ];
- if (sourceSlot && ("label" in sourceSlot)) {
+ //if the feature overlaps destBlock,
+ //move to destBlock & re-position
+ sourceSlot = sourceBlock.featureNodes[ overlaps[i] ];
+ if (sourceSlot && ("label" in sourceSlot)) {
sourceSlot.label.parentNode.removeChild(sourceSlot.label);
- }
- if (sourceSlot && sourceSlot.feature) {
- if ( sourceSlot.layoutEnd > destLeft
- && sourceSlot.feature.get('start') < destRight ) {
+ }
+ if (sourceSlot && sourceSlot.feature) {
+ if ( sourceSlot.layoutEnd > destLeft
+ && sourceSlot.feature.get('start') < destRight ) {
+
+ sourceSlot.parentNode.removeChild(sourceSlot);
- sourceBlock.removeChild(sourceSlot);
delete sourceBlock.featureNodes[ overlaps[i] ];
- var featDiv =
- this.renderFeature(sourceSlot.feature, overlaps[i],
- destBlock, scale, sourceSlot._labelScale, sourceSlot._descriptionScale,
- containerStart, containerEnd, destBlock );
+ /* feature render, adding to block, centering refactored into addFeatureToBlock() */
+ var featDiv = this.addFeatureToBlock( sourceSlot.feature, overlaps[i],
+ destBlock, scale, sourceSlot._labelScale, sourceSlot._descriptionScale,
+ containerStart, containerEnd );
}
}
}
@@ -588,23 +628,32 @@ HTMLFeatures = declare( HTMLFeatures,
/**
* arguments:
- * @param block div to be filled with info
- * @param leftBlock div to the left of the block to be filled
- * @param rightBlock div to the right of the block to be filled
- * @param leftBase starting base of the block
- * @param rightBase ending base of the block
- * @param scale pixels per base at the current zoom level
- * @param containerStart don't make HTML elements extend further left than this
- * @param containerEnd don't make HTML elements extend further right than this. 0-based.
+ * @param args.block div to be filled with info
+ * @param args.leftBlock div to the left of the block to be filled
+ * @param args.rightBlock div to the right of the block to be filled
+ * @param args.leftBase starting base of the block
+ * @param args.rightBase ending base of the block
+ * @param args.scale pixels per base at the current zoom level
+ * @param args.containerStart don't make HTML elements extend further left than this
+ * @param args.containerEnd don't make HTML elements extend further right than this. 0-based.
*/
- fillFeatures: function(blockIndex, block, leftBlock, rightBlock, leftBase, rightBase, scale, stats, containerStart, containerEnd) {
+ fillFeatures: function(args) {
+ var blockIndex = args.blockIndex;
+ var block = args.block;
+ var leftBase = args.leftBase;
+ var rightBase = args.rightBase;
+ var scale = args.scale;
+ var stats = args.stats;
+ var containerStart = args.containerStart;
+ var containerEnd = args.containerEnd;
+ var finishCallback = args.finishCallback;
this.scale = scale;
block.featureNodes = {};
//determine the glyph height, arrowhead width, label text dimensions, etc.
- if (!this.haveMeasurements) {
+ if( !this.haveMeasurements ) {
this.measureStyles();
this.haveMeasurements = true;
}
@@ -613,17 +662,24 @@ HTMLFeatures = declare( HTMLFeatures,
var descriptionScale = this.config.style.descriptionScale || stats.featureDensity * this.config.style._defaultDescriptionScale;
var curTrack = this;
+
+ var timedOut = false;
+ var timeOutError = { toString: function() { return 'Timed out trying to display '+curTrack.name+' block '+blockIndex; } };
+ if( this.config.blockDisplayTimeout )
+ window.setTimeout( function() { timedOut = true; }, this.config.blockDisplayTimeout );
+
var featCallback = dojo.hitch(this,function( feature ) {
- var uniqueId = feature._uniqueID;
+ if( timedOut )
+ throw timeOutError;
+
+ var uniqueId = feature.id();
if( ! this._featureIsRendered( uniqueId ) ) {
- this.renderFeature( feature, uniqueId, block, scale, labelScale, descriptionScale,
- containerStart, containerEnd, block );
+ /* feature render, adding to block, centering refactored into addFeatureToBlock() */
+ var featDiv = this.addFeatureToBlock( feature, uniqueId, block, scale, labelScale, descriptionScale,
+ containerStart, containerEnd );
}
});
- // var startBase = goLeft ? rightBase : leftBase;
- // var endBase = goLeft ? leftBase : rightBase;
-
this.store.getFeatures( { ref: this.refSeq.name,
start: leftBase,
end: rightBase
@@ -632,14 +688,35 @@ HTMLFeatures = declare( HTMLFeatures,
function () {
curTrack.heightUpdate(curTrack._getLayout(scale).getTotalHeight(),
blockIndex);
+ finishCallback();
},
function( error ) {
curTrack.error = error;
- curTrack.fillError( blockIndex, block );
+ if( error === timeOutError ) {
+ curTrack.fillTimeout( blockIndex, block );
+ } else {
+ console.error( error, error.stack );
+ curTrack.fillError( blockIndex, block );
+ }
+ finishCallback();
}
);
},
+ /**
+ * Creates feature div, adds to block, and centers subfeatures.
+ * Overridable by subclasses that need more control over the substructure.
+ */
+ addFeatureToBlock: function( feature, uniqueId, block, scale, labelScale, descriptionScale,
+ containerStart, containerEnd ) {
+ var featDiv = this.renderFeature( feature, uniqueId, block, scale, labelScale, descriptionScale,
+ containerStart, containerEnd );
+ block.appendChild( featDiv );
+ if( this.config.style.centerChildrenVertically )
+ this._centerChildrenVertically( featDiv );
+ return featDiv;
+ },
+
/**
* Returns true if a feature is visible and rendered someplace in the blocks of this track.
* @private
@@ -679,8 +756,8 @@ HTMLFeatures = declare( HTMLFeatures,
if (Util.is_ie6) heightTest.appendChild(document.createComment("foo"));
document.body.appendChild(heightTest);
glyphBox = domGeom.getMarginBox(heightTest);
- this.glyphHeight = glyphBox.h;
- this.padding += glyphBox.w;
+ this.glyphHeight = Math.round(glyphBox.h);
+ this.padding = this.defaultPadding + glyphBox.w;
document.body.removeChild(heightTest);
//determine the width of the arrowhead, if any
@@ -700,7 +777,28 @@ HTMLFeatures = declare( HTMLFeatures,
}
},
- renderFeature: function( feature, uniqueId, block, scale, labelScale, descriptionScale, containerStart, containerEnd, destBlock ) {
+ getFeatDiv: function( feature ) {
+ var id = this.getId( feature );
+ if( ! id )
+ return null;
+
+ for( var i = 0; i < this.blocks.length; i++ ) {
+ var b = this.blocks[i];
+ if( b && b.featureNodes ) {
+ var f = b.featureNodes[id];
+ if( f )
+ return f;
+ }
+ }
+
+ return null;
+ },
+
+ getId: function( f ) {
+ return f.id();
+ },
+
+ renderFeature: function( feature, uniqueId, block, scale, labelScale, descriptionScale, containerStart, containerEnd ) {
//featureStart and featureEnd indicate how far left or right
//the feature extends in bp space, including labels
//and arrowheads if applicable
@@ -711,8 +809,29 @@ HTMLFeatures = declare( HTMLFeatures,
featureEnd = parseInt(featureEnd);
if( typeof featureStart == 'string' )
featureStart = parseInt(featureStart);
+ // layoutStart: start genome coord (at current scale) of horizontal space need to render feature,
+ // including decorations (arrowhead, label, etc) and padding
+ var layoutStart = featureStart;
+ // layoutEnd: end genome coord (at current scale) of horizontal space need to render feature,
+ // including decorations (arrowhead, label, etc) and padding
+ var layoutEnd = featureEnd;
+
+ // JBrowse now draws arrowheads within feature genome coord bounds
+ // For WebApollo we're keeping arrow outside of feature genome coord bounds,
+ // because otherwise arrow can obscure edge-matching, CDS/UTR transitions, small inton/exons, etc.
+ // Would like to implement arrowhead change in WebApollo plugin, but would need to refactor HTMLFeature more to allow for that
+ if (this.config.style.arrowheadClass) {
+ switch (feature.get('strand')) {
+ case 1:
+ case '+':
+ layoutEnd += (this.plusArrowWidth / scale); break;
+ case -1:
+ case '-':
+ layoutStart -= (this.minusArrowWidth / scale); break;
+ }
+ }
- var levelHeight = this.glyphHeight;
+ var levelHeight = this.glyphHeight + this.glyphHeightPad;
// if the label extends beyond the feature, use the
// label end position as the end position for layout
@@ -725,27 +844,28 @@ HTMLFeatures = declare( HTMLFeatures,
// calculated height of the feature if it will be displayed
if( this.showLabels && scale >= labelScale ) {
if (name) {
- featureEnd = Math.max(featureEnd, featureStart + (''+name).length * this.labelWidth / scale );
- levelHeight += this.labelHeight + 1;
+ layoutEnd = Math.max(layoutEnd, layoutStart + (''+name).length * this.labelWidth / scale );
+ levelHeight += this.labelHeight + this.labelPad;
}
if( description ) {
- featureEnd = Math.max( featureEnd, featureStart + (''+description).length * this.labelWidth / scale );
- levelHeight += this.labelHeight + 1;
+ layoutEnd = Math.max( layoutEnd, layoutStart + (''+description).length * this.labelWidth / scale );
+ levelHeight += this.labelHeight + this.labelPad;
}
}
- featureEnd += Math.max(1, this.padding / scale);
+ layoutEnd += Math.max(1, this.padding / scale);
- var top = this._getLayout( scale ).addRect( uniqueId,
- featureStart,
- featureEnd,
- levelHeight);
+ var top = this._getLayout( scale )
+ .addRect( uniqueId,
+ layoutStart,
+ layoutEnd,
+ levelHeight);
var featDiv = this.config.hooks.create(this, feature );
this._connectFeatDivHandlers( featDiv );
featDiv.track = this;
featDiv.feature = feature;
- featDiv.layoutEnd = featureEnd;
- featDiv.className = (featDiv.className ? featDiv.className + " " : "") + "feature";
+ featDiv.layoutEnd = layoutEnd;
+
// (callbackArgs are the args that will be passed to callbacks
// in this feature's context menu or left-click handlers)
featDiv.callbackArgs = [ this, featDiv.feature, featDiv ];
@@ -759,30 +879,33 @@ HTMLFeatures = declare( HTMLFeatures,
block.featureNodes[uniqueId] = featDiv;
// record whether this feature protrudes beyond the left and/or right side of the block
- if( featureStart < block.startBase ) {
+ if( layoutStart < block.startBase ) {
if( ! block.leftOverlaps ) block.leftOverlaps = [];
block.leftOverlaps.push( uniqueId );
}
- if( featureEnd > block.endBase ) {
+ if( layoutEnd > block.endBase ) {
if( ! block.rightOverlaps ) block.rightOverlaps = [];
block.rightOverlaps.push( uniqueId );
}
+ dojo.addClass(featDiv, "feature");
+ var className = this.config.style.className;
+ if (className == "{type}") { className = feature.get('type'); }
var strand = feature.get('strand');
switch (strand) {
case 1:
case '+':
- featDiv.className = featDiv.className + " " + this.config.style.className + " plus-" + this.config.style.className; break;
+ dojo.addClass(featDiv, "plus-" + className); break;
case -1:
case '-':
- featDiv.className = featDiv.className + " " + this.config.style.className + " minus-" + this.config.style.className; break;
+ dojo.addClass(featDiv, "minus-" + className); break;
default:
- featDiv.className = featDiv.className + " " + this.config.style.className; break;
+ dojo.addClass(featDiv, className);
}
-
var phase = feature.get('phase');
if ((phase !== null) && (phase !== undefined))
- featDiv.className = featDiv.className + " " + featDiv.className + "_phase" + phase;
+// featDiv.className = featDiv.className + " " + featDiv.className + "_phase" + phase;
+ dojo.addClass(featDiv, className + "_phase" + phase);
// Since some browsers don't deal well with the situation where
// the feature goes way, way offscreen, we truncate the feature
@@ -790,10 +913,10 @@ HTMLFeatures = declare( HTMLFeatures,
// To make sure the truncated end of the feature never gets shown,
// we'll destroy and re-create the feature (with updated truncated
// boundaries) in the transfer method.
- var displayStart = Math.max( feature.get('start'), containerStart );
- var displayEnd = Math.min( feature.get('end'), containerEnd );
+ var displayStart = Math.max( featureStart, containerStart );
+ var displayEnd = Math.min( featureEnd, containerEnd );
var blockWidth = block.endBase - block.startBase;
- var featwidth = Math.max( 1, (100 * ((displayEnd - displayStart) / blockWidth)));
+ var featwidth = Math.max( this.minFeatWidth, (100 * ((displayEnd - displayStart) / blockWidth)));
featDiv.style.cssText =
"left:" + (100 * (displayStart - block.startBase) / blockWidth) + "%;"
+ "top:" + top + "px;"
@@ -804,26 +927,18 @@ HTMLFeatures = declare( HTMLFeatures,
var ah = document.createElement("div");
var featwidth_px = featwidth/100*blockWidth*scale;
- // NOTE: arrowheads are hidden until they are centered by
- // _centerFeatureElements, so that they don't jump around
- // on the screen
switch (strand) {
case 1:
case '+':
- if( featwidth_px > this.plusArrowWidth*1.1 ) {
- ah.className = "plus-" + this.config.style.arrowheadClass;
- ah.style.cssText = "visibility: hidden; position: absolute; right: 0px; top: 0px; z-index: 100;";
- featDiv.appendChild(ah);
- }
+ ah.className = "plus-" + this.config.style.arrowheadClass;
+ ah.style.cssText = "left: 100%;"
+ featDiv.appendChild(ah);
break;
case -1:
case '-':
- if( featwidth_px > this.minusArrowWidth*1.1 ) {
- ah.className = "minus-" + this.config.style.arrowheadClass;
- ah.style.cssText =
- "visibility: hidden; position: absolute; left: 0px; top: 0px; z-index: 100;";
- featDiv.appendChild(ah);
- }
+ ah.className = "minus-" + this.config.style.arrowheadClass;
+ ah.style.cssText = "left: " + (-this.minusArrowWidth) + "px;"
+ featDiv.appendChild(ah);
break;
}
}
@@ -835,13 +950,13 @@ HTMLFeatures = declare( HTMLFeatures,
+( description ? '
'+description+'
' : '' ),
style: {
top: (top + this.glyphHeight + 2) + "px",
- left: (100 * (featureStart - block.startBase) / blockWidth)+'%'
+ left: (100 * (layoutStart - block.startBase) / blockWidth)+'%'
}
}, block );
this._connectFeatDivHandlers( labelDiv );
- featDiv.label = labelDiv;
+ featDiv.label = labelDiv;
featDiv.labelDiv = labelDiv;
labelDiv.feature = feature;
@@ -851,74 +966,71 @@ HTMLFeatures = declare( HTMLFeatures,
labelDiv.callbackArgs = [ this, featDiv.feature, featDiv ];
}
- if( destBlock ) {
- destBlock.appendChild(featDiv);
+ if( featwidth > this.config.style.minSubfeatureWidth ) {
+ this.handleSubFeatures(feature, featDiv, displayStart, displayEnd, block);
}
- // defer subfeature rendering and modification hooks into a
- // timeout so that navigation feels faster.
- window.setTimeout( dojo.hitch( this,
- function() {
-
- if( featwidth > this.config.style.minSubfeatureWidth ) {
- var subfeatures = feature.get('subfeatures');
- if( subfeatures ) {
- for (var i = 0; i < subfeatures.length; i++) {
- this.renderSubfeature(feature, featDiv,
- subfeatures[i],
- displayStart, displayEnd);
- }
- }
- }
-
- //ie6 doesn't respect the height style if the div is empty
- if (Util.is_ie6) featDiv.appendChild(document.createComment());
- //TODO: handle event-handler-related IE leaks
+ // render the popup menu if configured
+ if( this.config.menuTemplate ) {
+ window.setTimeout( dojo.hitch( this, '_connectMenus', featDiv ), 50+Math.random()*150 );
+ }
- /* Temi / AP adding right menu click
- AP new schema menuTemplate: an array where everything except
- children, popup and url are passed on as properties to a new
- dijit.Menu object
- */
+ if ( typeof this.config.hooks.modify == 'function' ) {
+ this.config.hooks.modify(this, feature, featDiv);
+ }
- // render the popup menu if configured
- if( this.config.menuTemplate ) {
- this._connectMenus( featDiv );
- }
- if( destBlock )
- this._centerFeatureElements(featDiv);
+ return featDiv;
+ },
- if ( typeof this.config.hooks.modify == 'function' ) {
- this.config.hooks.modify(this, feature, featDiv);
- }
- }),50+Math.random()*50);
+ handleSubFeatures: function( feature, featDiv,
+ displayStart, displayEnd, block ) {
+ var subfeatures = feature.get('subfeatures');
+ if( subfeatures ) {
+ for (var i = 0; i < subfeatures.length; i++) {
+ this.renderSubfeature( feature, featDiv,
+ subfeatures[i],
+ displayStart, displayEnd, block );
+ }
+ }
+ },
- return featDiv;
+ /**
+ * Get the height of a div. Caches div heights based on
+ * classname.
+ */
+ _getHeight: function( theDiv ) {
+ if (this.config.disableHeightCache) {
+ return theDiv.offsetHeight || 0;
+ }
+ else {
+ var c = this.heightCache[ theDiv.className ];
+ if( c )
+ return c;
+ c = theDiv.offsetHeight || 0;
+ this.heightCache[ theDiv.className ] = c;
+ return c;
+ }
},
/**
* Vertically centers all the child elements of a feature div.
* @private
*/
- _centerFeatureElements: function( /**HTMLElement*/ featDiv ) {
- var getHeight = this.config.disableHeightCache
- ? function(child) { return child.offsetHeight || 0; }
- : function( child ) {
- var c = this.heightCache[ child.className ];
- if( c )
- return c;
- c = child.offsetHeight || 0;
- this.heightCache[ child.className ] = c;
- return c;
- };
-
- for( var i = 0; i< featDiv.childNodes.length; i++ ) {
- var child = featDiv.childNodes[i];
- // cache the height of elements, for speed.
- var h = getHeight.call(this,child);
- dojo.style( child, { marginTop: '0', top: ((this.glyphHeight-h)/2) + 'px', visibility: 'visible' });
- }
+ _centerChildrenVertically: function( /**HTMLElement*/ featDiv ) {
+ if( featDiv.childNodes.length > 0 ) {
+ var parentHeight = this._getHeight(featDiv);
+ for( var i = 0; i< featDiv.childNodes.length; i++ ) {
+ var child = featDiv.childNodes[i];
+ // cache the height of elements, for speed.
+ var h = this._getHeight(child);
+ dojo.style( child, { marginTop: '0', top: ((parentHeight-h)/2) + 'px' });
+ // recursively center any descendants
+ if (child.childNodes.length > 0) {
+ this._centerChildrenVertically( child );
+ }
+ }
+ }
},
/**
@@ -942,7 +1054,6 @@ HTMLFeatures = declare( HTMLFeatures,
on( featDiv, 'mouseover', refreshMenu );
if( featDiv.labelDiv )
on( featDiv.labelDiv, 'mouseover', refreshMenu );
- dojo.connect( featDiv.contextMenu, 'onMouseMove', refreshMenu );
},
_refreshMenu: function( featDiv ) {
@@ -987,44 +1098,69 @@ HTMLFeatures = declare( HTMLFeatures,
return menu;
},
- renderSubfeature: function(feature, featDiv, subfeature, displayStart, displayEnd) {
+ renderSubfeature: function( feature, featDiv, subfeature, displayStart, displayEnd, block ) {
var subStart = subfeature.get('start');
var subEnd = subfeature.get('end');
var featLength = displayEnd - displayStart;
-
- var subDiv = document.createElement("div");
-
var type = subfeature.get('type');
- subDiv.className = (this.config.style.subfeatureClasses||{})[type] || this.config.style.className + '-' + type;
- switch ( subfeature.get('strand') ) {
- case 1:
- case '+':
- subDiv.className += " plus-" + subDiv.className; break;
- case -1:
- case '-':
- subDiv.className += " minus-" + subDiv.className; break;
+ var className;
+ if( this.config.style.subfeatureClasses ) {
+ className = this.config.style.subfeatureClasses[type];
+ // if no class mapping specified for type, default to subfeature.get('type')
+ if (className === undefined) { className = type; }
+ // if subfeatureClasses specifies that subfeature type explicitly maps to null className
+ // then don't render the feature
+ else if (className === null) {
+ return null;
+ }
+ }
+ else {
+ // if no config.style.subfeatureClasses to specify subfeature class mapping, default to subfeature.get('type')
+ className = type;
+ }
+ var subDiv = document.createElement("div");
+ dojo.addClass(subDiv, "subfeature");
+ // check for className to avoid adding "null", "plus-null", "minus-null"
+ if (className) {
+ switch ( subfeature.get('strand') ) {
+ case 1:
+ case '+':
+ dojo.addClass(subDiv, "plus-" + className); break;
+ case -1:
+ case '-':
+ dojo.addClass(subDiv, "minus-" + className); break;
+ default:
+ dojo.addClass(subDiv, className);
+ }
}
// if the feature has been truncated to where it doesn't cover
// this subfeature anymore, just skip this subfeature
- if ((subEnd <= displayStart) || (subStart >= displayEnd)) return;
+ if ( subEnd <= displayStart || subStart >= displayEnd )
+ return null;
if (Util.is_ie6) subDiv.appendChild(document.createComment());
- // NOTE: subfeatures are hidden until they are centered by
- // _centerFeatureElements, so that they don't jump around
- // on the screen
- subDiv.style.cssText =
- "visibility: hidden; left: " + (100 * ((subStart - displayStart) / featLength)) + "%;"
- + "top: 0px;"
+ subDiv.style.cssText = "left: " + (100 * ((subStart - displayStart) / featLength)) + "%;"
+ "width: " + (100 * ((subEnd - subStart) / featLength)) + "%;";
featDiv.appendChild(subDiv);
+
+ block.featureNodes[ subfeature.id() ] = subDiv;
+
+ return subDiv;
},
_getLayout: function( scale ) {
+
+ //determine the glyph height, arrowhead width, label text dimensions, etc.
+ if (!this.haveMeasurements) {
+ this.measureStyles();
+ this.haveMeasurements = true;
+ }
+
// create the layout if we need to, and we can
- if( ( ! this.layout || this.layout.pitchX != 4/scale ) && scale )
- this.layout = new Layout({pitchX: 4/scale, pitchY: this.layoutPitchY || this.config.layoutPitchY });
+ if( ( ! this.layout || this.layout.pitchX != 4/scale ) && scale )
+ this.layout = new Layout({pitchX: 4/scale, pitchY: this.config.layoutPitchY || (this.glyphHeight + this.glyphHeightPad) });
return this.layout;
},
@@ -1032,15 +1168,18 @@ HTMLFeatures = declare( HTMLFeatures,
delete this.layout;
},
- // when all the blocks are hidden, we also should recalculate our
- // layout
+ /**
+ * indicates a change to this track has happened that may require a re-layout
+ * clearing layout here, and relying on superclass BlockBased.changed() call and
+ * standard _changedCallback function passed in track constructor to trigger relayout
+ */
changed: function() {
- this.inherited(arguments);
this._clearLayout();
+ this.inherited(arguments);
},
_exportFormats: function() {
- return [ 'GFF3', 'BED' ];
+ return [ 'GFF3', 'BED', { name: 'SequinTable', label: 'Sequin Table' } ];
},
_trackMenuOptions: function() {
diff --git a/src/JBrowse/View/Track/LocationScale.js b/src/JBrowse/View/Track/LocationScale.js
index 8f78d23198..c655f85ff5 100644
--- a/src/JBrowse/View/Track/LocationScale.js
+++ b/src/JBrowse/View/Track/LocationScale.js
@@ -16,17 +16,18 @@ return declare(BlockBased,
this.loaded = true;
this.labelClass = args.labelClass;
this.posHeight = args.posHeight;
- this.height = args.posHeight;
+ this.height = Math.round( args.posHeight * 1.2 );
},
// this track has no track label or track menu, stub them out
makeTrackLabel: function() {},
makeTrackMenu: function() {},
- fillBlock: function(blockIndex, block,
- leftBlock, rightBlock,
- leftBase, rightBase, scale,
- padding, stripeWidth) {
+ fillBlock: function( args ) {
+ var blockIndex = args.blockIndex;
+ var block = args.block;
+ var leftBase = args.leftBase;
+
var posLabel = document.createElement("div");
var numtext = Util.addCommas( leftBase+1 );
posLabel.className = this.labelClass;
@@ -37,7 +38,8 @@ return declare(BlockBased,
posLabel.appendChild( document.createTextNode( numtext ) );
block.appendChild(posLabel);
- this.heightUpdate(this.posHeight, blockIndex);
+ this.heightUpdate( Math.round( this.posHeight*1.2 ), blockIndex);
+ args.finishCallback();
}
});
});
\ No newline at end of file
diff --git a/src/JBrowse/View/Track/Sequence.js b/src/JBrowse/View/Track/Sequence.js
index 96e53e011a..831c0d7c90 100644
--- a/src/JBrowse/View/Track/Sequence.js
+++ b/src/JBrowse/View/Track/Sequence.js
@@ -29,7 +29,10 @@ SequenceTrack.extend(
*/
{
_defaultConfig: function() {
- return { maxExportSpan: 500000 };
+ return {
+ maxExportSpan: 500000,
+ showReverseStrand: true
+ };
},
_exportFormats: function() {
return ['FASTA'];
@@ -48,11 +51,12 @@ SequenceTrack.extend(
nbsp: String.fromCharCode(160),
- fillBlock:function(blockIndex, block,
- leftBlock, rightBlock,
- leftBase, rightBase,
- scale, stripeWidth,
- containerStart, containerEnd) {
+ fillBlock:function( args ) {
+ var blockIndex = args.blockIndex;
+ var block = args.block;
+ var leftBase = args.leftBase;
+ var rightBase = args.rightBase;
+ var scale = args.scale;
var charSize = this.getCharacterMeasurements();
@@ -80,6 +84,8 @@ SequenceTrack.extend(
}, block );
this.heightUpdate( blur.offsetHeight+2*blur.offsetTop, blockIndex );
}
+
+ args.finishCallback();
},
_fillSequenceBlock: function( block, scale, feature ) {
@@ -113,9 +119,11 @@ SequenceTrack.extend(
seqNode.appendChild( this._renderSeqDiv( start, end, seq, scale ));
// and one for the reverse strand
- var comp = this._renderSeqDiv( start, end, Util.complement(seq), scale );
- comp.className = 'revcom';
- seqNode.appendChild( comp );
+ if( this.config.showReverseStrand ) {
+ var comp = this._renderSeqDiv( start, end, Util.complement(seq), scale );
+ comp.className = 'revcom';
+ seqNode.appendChild( comp );
+ }
},
/**
@@ -130,12 +138,16 @@ SequenceTrack.extend(
var container = document.createElement('div');
var charWidth = 100/(end-start)+"%";
var drawChars = scale >= charSize.w;
+ var bigTiles = scale > charSize.w + 4; // whether to add .big styles to the base tiles
for( var i=0; i
';
+ this.applyButton.set('disabled',true);
+ },
+ _clearErrors: function() {
+ dom.empty( this.errorReportArea );
+ this.applyButton.set('disabled',false);
+ },
+
+ _parseNewConfig: function( conf ) {
+ var newconf;
+ try {
+ newconf = JSON.parse( conf, true );
+ this._clearErrors();
+ } catch(e) {
+ this._reportError( e );
+ }
+ if( newconf )
+ newconf.store = this.trackConfig.store;
+ return newconf;
+ }
+
+});
+});
\ No newline at end of file
diff --git a/src/JBrowse/View/TrackList/Faceted.js b/src/JBrowse/View/TrackList/Faceted.js
index feeed2d01d..3c46899157 100644
--- a/src/JBrowse/View/TrackList/Faceted.js
+++ b/src/JBrowse/View/TrackList/Faceted.js
@@ -3,12 +3,12 @@ define(
'dojo/_base/declare',
'dojo/_base/array',
'dijit/layout/AccordionContainer',
- 'dijit/layout/AccordionPane',
+ 'dijit/layout/ContentPane',
'JBrowse/Util',
'dojox/grid/EnhancedGrid',
'dojox/grid/enhanced/plugins/IndirectSelection'
],
- function ( declare, dArray, AccordionContainer, AccordionPane, Util, EnhancedGrid ){
+ function ( declare, dArray, AccordionContainer, ContentPane, Util, EnhancedGrid ){
var dojof = Util.dojof;
return declare( 'JBrowse.View.TrackList.Faceted', null,
@@ -60,6 +60,8 @@ return declare( 'JBrowse.View.TrackList.Faceted', null,
// subscribe to commands coming from the the controller
this.browser.subscribe( '/jbrowse/v1/c/tracks/hide',
dojo.hitch( this, 'setTracksInactive' ));
+ this.browser.subscribe( '/jbrowse/v1/c/tracks/delete',
+ dojo.hitch( this, 'setTracksInactive' ));
this.renderInitial();
@@ -89,10 +91,12 @@ return declare( 'JBrowse.View.TrackList.Faceted', null,
});
});
});
+
this.trackDataStore.onReady( this, '_updateFacetCounts' ); // just once at start
dojo.connect( this.trackDataStore, 'onFetchSuccess', this, '_updateGridSelections' );
dojo.connect( this.trackDataStore, 'onFetchSuccess', this, '_updateMatchCount' );
+
},
/**
@@ -306,6 +310,13 @@ return declare( 'JBrowse.View.TrackList.Faceted', null,
},
renderGrid: function() {
+
+ var displayColumns = dojo.filter(
+ this.displayColumns || this.trackDataStore.getFacetNames(),
+ dojo.hitch(this, '_isDisplayableColumn')
+ );
+ var colWidth = 90/displayColumns.length;
+
var grid = new EnhancedGrid({
id: 'trackSelectGrid',
store: this.trackDataStore,
@@ -314,13 +325,11 @@ return declare( 'JBrowse.View.TrackList.Faceted', null,
noDataMessage: "No tracks match the filtering criteria.",
structure: [
dojo.map(
- dojo.filter( this.displayColumns || this.trackDataStore.getFacetNames(),
- dojo.hitch(this, '_isDisplayableColumn')
- ),
+ displayColumns,
function(facetName) {
// rename name to key to avoid configuration confusion
facetName = {name: 'key'}[facetName.toLowerCase()] || facetName;
- return {'name': this._facetDisplayName(facetName), 'field': facetName.toLowerCase(), 'width': '100px'};
+ return {'name': this._facetDisplayName(facetName), 'field': facetName.toLowerCase(), 'width': colWidth+'%'};
},
this
)
@@ -537,17 +546,17 @@ return declare( 'JBrowse.View.TrackList.Faceted', null,
/**
* Make HTML elements for a single facet selector.
* @private
- * @returns {dijit.layout.AccordionPane}
+ * @returns {dijit.layout.ContentPane}
*/
_renderFacetSelector: function( /**String*/ facetName, /**Array[String]*/ values ) {
- var facetPane = new AccordionPane(
+ var facetPane = new ContentPane(
{
- title: ''
+ this._facetDisplayName(facetName)
+ '
'
- + '
'+feature.get('name')+'
This is some test content!
This message brought to you by the number '+Math.round(Math.random()*100)+'.
';} ",
- "label" : "Popup with content snippet from a function (feature {name})",
- "title" : "function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }"
+ "action" : "contentDialog",
+ "title" : "function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }",
+ "label" : "Popup with content snippet from a function (feature {name})"
},
{
"iconClass" : "dijitIconDatabase",
- "action" : "contentDialog",
"content" : "{name}
This is some test content about {name}, which goes from {start} to {end} on the {strand} strand.
",
- "label" : "Popup with content snippet from string (feature {name})",
- "title" : "function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }"
+ "action" : "contentDialog",
+ "title" : "function(track,feature,div) { return 'Random content snippet '+Math.random()+' title!'; }",
+ "label" : "Popup with content snippet from string (feature {name})"
},
{
"iconClass" : "dijitIconDatabase",
@@ -140,15 +137,18 @@
"label" : "function(track,feature,div) { return 'Run a JS callback '+Math.random()+' title!'; }"
}
],
+ "hooks" : {
+ "modify" : "function( track, feature, div ) { div.style.height = (Math.random()*10+8)+'px'; div.style.backgroundColor = ['green','blue','red','orange','purple'][Math.round(Math.random()*5)];}"
+ },
"key" : "Example alignments",
"feature" : [
"match"
],
"urlTemplate" : "tracks/Alignments/{refseq}/trackData.json",
"compress" : 0,
- "type" : "FeatureTrack",
+ "category" : "Alignments",
"label" : "Alignments",
- "category" : "Alignments"
+ "type" : "FeatureTrack"
},
{
"autocomplete" : "all",
@@ -156,15 +156,15 @@
"style" : {
"className" : "feature5"
},
- "key" : "Protein-coding genes",
"onClick" : "http://www.ncbi.nlm.nih.gov/gquery/?term={name}",
+ "key" : "Protein-coding genes",
"feature" : [
"gene"
],
"urlTemplate" : "tracks/Genes/{refseq}/trackData.json",
"compress" : 0,
- "label" : "Genes",
- "type" : "FeatureTrack"
+ "type" : "FeatureTrack",
+ "label" : "Genes"
},
{
"autocomplete" : "all",
@@ -172,19 +172,19 @@
"style" : {
"className" : "dblhelix"
},
+ "key" : "Frame usage",
"onClick" : {
"url" : "http://www.ncbi.nlm.nih.gov/gquery/?term={name}",
"label" : "search at NCBI"
},
- "key" : "Frame usage",
"feature" : [
"mRNA"
],
"urlTemplate" : "tracks/ReadingFrame/{refseq}/trackData.json",
"compress" : 0,
- "type" : "FeatureTrack",
+ "category" : "Genes",
"label" : "ReadingFrame",
- "category" : "Genes"
+ "type" : "FeatureTrack"
},
{
"autocomplete" : "all",
@@ -202,9 +202,9 @@
"urlTemplate" : "tracks/CDS/{refseq}/trackData.json",
"phase" : 1,
"compress" : 0,
- "category" : "Genes",
+ "type" : "FeatureTrack",
"label" : "CDS",
- "type" : "FeatureTrack"
+ "category" : "Genes"
},
{
"autocomplete" : "all",
@@ -218,16 +218,16 @@
"arrowheadClass" : "transcript-arrowhead"
},
"description" : 1,
- "onClick" : "function() { alert('Ran arbitrary JavaScript!'); };",
"key" : "Exonerate predictions",
+ "onClick" : "function() { alert('This is a user-configurable JavaScript action!'); };",
"feature" : [
"mRNA:exonerate"
],
"urlTemplate" : "tracks/Transcript/{refseq}/trackData.json",
"compress" : 0,
- "type" : "FeatureTrack",
- "label" : "Transcript",
"category" : "Genes",
+ "label" : "Transcript",
+ "type" : "FeatureTrack",
"subfeatures" : true
},
{
@@ -243,8 +243,8 @@
],
"urlTemplate" : "tracks/Clones/{refseq}/trackData.json",
"compress" : 0,
- "label" : "Clones",
- "type" : "FeatureTrack"
+ "type" : "FeatureTrack",
+ "label" : "Clones"
},
{
"autocomplete" : "all",
@@ -264,33 +264,85 @@
{
"storeClass" : "JBrowse/Store/BigWig",
"urlTemplate" : "../../raw/volvox/volvox_microarray.bw",
- "type" : "JBrowse/View/Track/Wiggle",
- "label" : "volvox_microarray.bw",
- "key" : "volvox_microarray.bw"
+ "type" : "JBrowse/View/Track/Wiggle/Density",
+ "label" : "volvox_microarray.bw_density",
+ "bicolor_pivot" : "mean",
+ "key" : "BigWig Density - volvox_microarray"
+ },
+ {
+ "storeClass" : "JBrowse/Store/BigWig",
+ "urlTemplate" : "../../raw/volvox/volvox_microarray.bw",
+ "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+ "label" : "volvox_microarray.bw_xyplot",
+ "variance_band" : "true",
+ "key" : "BigWig XY - volvox_microarray"
+ },
+ {
+ "storeClass" : "JBrowse/Store/BigWig",
+ "urlTemplate" : "../../raw/volvox/volvox_sine.bw",
+ "label" : "volvox_sine_density",
+ "type" : "JBrowse/View/Track/Wiggle/Density",
+ "bicolor_pivot" : "mean",
+ "key" : "BigWig Density - volvox_sine"
+ },
+ {
+ "storeClass" : "JBrowse/Store/BigWig",
+ "urlTemplate" : "../../raw/volvox/volvox_sine.bw",
+ "style" : {
+ "bg_color" : "#ccc"
+ },
+ "label" : "volvox_sine_xyplot",
+ "type" : "JBrowse/View/Track/Wiggle/XYPlot",
+ "key" : "BigWig XY - volvox_sine"
+ },
+ {
+ "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+ "urlTemplate" : "../../raw/volvox/volvox-sorted.bam",
+ "style" : {
+ "className" : "alignment",
+ "arrowheadClass" : "arrowhead",
+ "labelScale" : 100
+ },
+ "label" : "volvox-sorted.bam",
+ "type" : "JBrowse/View/Track/Alignments",
+ "key" : "volvox-sorted.bam"
+ },
+ {
+ "storeClass" : "JBrowse/Store/SeqFeature/BAM",
+ "urlTemplate" : "../../raw/volvox/volvox-sorted.bam",
+ "max_score" : 35,
+ "label" : "volvox-sorted.bam_coverage",
+ "type" : "JBrowse/View/Track/FeatureCoverage",
+ "min_score" : 0,
+ "key" : "volvox-sorted Coverage"
},
{
"urlTemplate" : "tracks/volvox_microarray.wig/{refseq}/trackData.json",
- "compress" : 0,
"style" : {
"className" : "image"
},
- "label" : "volvox_microarray.wig",
+ "compress" : 0,
"type" : "ImageTrack.Wiggle",
+ "label" : "volvox_microarray.wig",
"key" : "volvox_microarray.wig"
},
{
"urlTemplate" : "tracks/bam_simulated/{refseq}/trackData.json",
+ "compress" : 0,
"style" : {
"className" : "basic",
"histScale" : 2,
"featureCss" : "background-color: #66F; height: 8px",
"histCss" : "background-color: #88F"
},
- "compress" : 0,
- "type" : "FeatureTrack",
"label" : "bam_simulated",
+ "type" : "FeatureTrack",
"key" : "Simulated next-gen reads"
}
],
+ "names" : {
+ "url" : "names/",
+ "type" : "Hash"
+ },
"formatVersion" : 1
}
diff --git a/tests/data/volvox_formatted_names/tracks/Alignments/ctgA/names.json b/tests/data/volvox_formatted_names/tracks/Alignments/ctgA/names.json
deleted file mode 100644
index 5d6c0cab49..0000000000
--- a/tests/data/volvox_formatted_names/tracks/Alignments/ctgA/names.json
+++ /dev/null
@@ -1 +0,0 @@
-[[["seg04"],"Alignments","seg04","ctgA",5232,5302,null],[["seg04"],"Alignments","seg04","ctgA",5799,6101,null],[["seg04"],"Alignments","seg04","ctgA",6441,6854,null],[["seg03"],"Alignments","seg03","ctgA",6884,7241,null],[["seg04"],"Alignments","seg04","ctgA",7105,7211,null],[["seg03"],"Alignments","seg03","ctgA",7409,7737,null],[["seg04"],"Alignments","seg04","ctgA",7694,8177,null],[["seg03"],"Alignments","seg03","ctgA",8054,8080,null],[["seg03"],"Alignments","seg03","ctgA",8305,8999,null],[["seg04"],"Alignments","seg04","ctgA",8544,8783,null],[["seg04"],"Alignments","seg04","ctgA",8868,8935,null],[["seg04"],"Alignments","seg04","ctgA",9403,9825,null],[["seg12"],"Alignments","seg12","ctgA",12530,12895,null],[["seg12"],"Alignments","seg12","ctgA",13121,13449,null],[["seg12"],"Alignments","seg12","ctgA",13451,13745,null],[["seg12"],"Alignments","seg12","ctgA",13907,13965,null],[["seg12"],"Alignments","seg12","ctgA",13997,14488,null],[["seg12"],"Alignments","seg12","ctgA",14563,14899,null],[["seg12"],"Alignments","seg12","ctgA",15184,15276,null],[["seg12"],"Alignments","seg12","ctgA",15638,15736,null],[["seg12"],"Alignments","seg12","ctgA",15744,15870,null],[["seg08"],"Alignments","seg08","ctgA",18508,18985,null],[["seg08"],"Alignments","seg08","ctgA",18988,19388,null],[["seg06"],"Alignments","seg06","ctgA",19248,19559,null],[["seg08"],"Alignments","seg08","ctgA",19495,19962,null],[["seg06"],"Alignments","seg06","ctgA",19974,20260,null],[["seg08"],"Alignments","seg08","ctgA",20092,20580,null],[["seg06"],"Alignments","seg06","ctgA",20378,20491,null],[["seg06"],"Alignments","seg06","ctgA",20532,21005,null],[["seg08"],"Alignments","seg08","ctgA",20969,21052,null],[["seg06"],"Alignments","seg06","ctgA",21121,21331,null],[["seg08"],"Alignments","seg08","ctgA",21269,21277,null],[["seg06"],"Alignments","seg06","ctgA",21681,22176,null],[["seg08"],"Alignments","seg08","ctgA",21684,22168,null],[["seg06"],"Alignments","seg06","ctgA",22373,22570,null],[["seg08"],"Alignments","seg08","ctgA",22563,22869,null],[["seg08"],"Alignments","seg08","ctgA",22957,23298,null],[["seg06"],"Alignments","seg06","ctgA",23024,23427,null],[["seg08"],"Alignments","seg08","ctgA",23411,23469,null],[["seg08"],"Alignments","seg08","ctgA",23931,23932,null],[["seg11"],"Alignments","seg11","ctgA",24227,24510,null],[["seg08"],"Alignments","seg08","ctgA",24327,24787,null],[["seg11"],"Alignments","seg11","ctgA",24867,25012,null],[["seg11"],"Alignments","seg11","ctgA",25211,25426,null],[["seg08"],"Alignments","seg08","ctgA",25227,25367,null],[["seg11"],"Alignments","seg11","ctgA",25793,25874,null],[["seg11"],"Alignments","seg11","ctgA",26074,26519,null],[["seg02"],"Alignments","seg02","ctgA",26121,26126,null],[["seg02"],"Alignments","seg02","ctgA",26496,26869,null],[["seg05"],"Alignments","seg05","ctgA",26502,26799,null],[["seg11"],"Alignments","seg11","ctgA",26929,26940,null],[["seg11"],"Alignments","seg11","ctgA",26974,27063,null],[["seg05"],"Alignments","seg05","ctgA",27171,27185,null],[["seg02"],"Alignments","seg02","ctgA",27200,27325,null],[["seg02"],"Alignments","seg02","ctgA",27371,27433,null],[["seg11"],"Alignments","seg11","ctgA",27414,27799,null],[["seg05"],"Alignments","seg05","ctgA",27447,27860,null],[["seg02"],"Alignments","seg02","ctgA",27564,27565,null],[["seg02"],"Alignments","seg02","ctgA",27812,28091,null],[["seg11"],"Alignments","seg11","ctgA",27879,27943,null],[["seg05"],"Alignments","seg05","ctgA",27886,28076,null],[["seg02"],"Alignments","seg02","ctgA",28092,28201,null],[["seg11"],"Alignments","seg11","ctgA",28224,28346,null],[["seg05"],"Alignments","seg05","ctgA",28224,28316,null],[["seg02"],"Alignments","seg02","ctgA",28328,28377,null],[["seg11"],"Alignments","seg11","ctgA",28374,28570,null],[["seg11"],"Alignments","seg11","ctgA",28757,29041,null],[["seg05"],"Alignments","seg05","ctgA",28776,29058,null],[["seg02"],"Alignments","seg02","ctgA",28828,29194,null],[["seg11"],"Alignments","seg11","ctgA",29100,29302,null],[["seg05"],"Alignments","seg05","ctgA",29512,29647,null],[["seg02"],"Alignments","seg02","ctgA",29516,29702,null],[["seg11"],"Alignments","seg11","ctgA",29603,29702,null],[["seg02"],"Alignments","seg02","ctgA",29712,30061,null],[["seg10"],"Alignments","seg10","ctgA",29770,29942,null],[["seg11"],"Alignments","seg11","ctgA",29866,29885,null],[["seg10"],"Alignments","seg10","ctgA",30041,30340,null],[["seg05"],"Alignments","seg05","ctgA",30107,30216,null],[["seg11"],"Alignments","seg11","ctgA",30240,30246,null],[["seg02"],"Alignments","seg02","ctgA",30328,30774,null],[["seg05"],"Alignments","seg05","ctgA",30464,30798,null],[["seg11"],"Alignments","seg11","ctgA",30574,30738,null],[["seg02"],"Alignments","seg02","ctgA",30807,31306,null],[["seg10"],"Alignments","seg10","ctgA",30809,31307,null],[["seg05"],"Alignments","seg05","ctgA",31231,31236,null],[["seg05"],"Alignments","seg05","ctgA",31420,31817,null],[["seg02"],"Alignments","seg02","ctgA",31515,31729,null],[["seg02"],"Alignments","seg02","ctgA",31752,32154,null],[["seg10"],"Alignments","seg10","ctgA",31760,31984,null],[["seg05"],"Alignments","seg05","ctgA",32009,32057,null],[["seg05"],"Alignments","seg05","ctgA",32207,32680,null],[["seg01"],"Alignments","seg01","ctgA",32328,32359,null],[["seg10"],"Alignments","seg10","ctgA",32373,32937,null],[["seg02"],"Alignments","seg02","ctgA",32594,32696,null],[["seg02"],"Alignments","seg02","ctgA",32891,32901,null],[["seg05"],"Alignments","seg05","ctgA",33052,33325,null],[["seg02"],"Alignments","seg02","ctgA",33126,33388,null],[["seg05"],"Alignments","seg05","ctgA",33437,33868,null],[["seg02"],"Alignments","seg02","ctgA",33438,33443,null],[["seg02"],"Alignments","seg02","ctgA",33758,34209,null],[["seg05"],"Alignments","seg05","ctgA",34243,34313,null],[["seg02"],"Alignments","seg02","ctgA",34400,34466,null],[["seg05"],"Alignments","seg05","ctgA",34604,34983,null],[["seg05"],"Alignments","seg05","ctgA",35332,35507,null],[["seg05"],"Alignments","seg05","ctgA",35641,35904,null],[["seg09"],"Alignments","seg09","ctgA",36615,37057,null],[["seg09"],"Alignments","seg09","ctgA",37207,37227,null],[["seg15"],"Alignments","seg15","ctgA",39264,39361,null],[["seg15"],"Alignments","seg15","ctgA",39752,40034,null],[["seg15"],"Alignments","seg15","ctgA",40514,40954,null],[["seg14"],"Alignments","seg14","ctgA",41136,41318,null],[["seg15"],"Alignments","seg15","ctgA",41251,41365,null],[["seg15"],"Alignments","seg15","ctgA",41491,41504,null],[["seg14"],"Alignments","seg14","ctgA",41753,41948,null],[["seg15"],"Alignments","seg15","ctgA",41940,42377,null],[["seg14"],"Alignments","seg14","ctgA",42056,42474,null],[["seg15"],"Alignments","seg15","ctgA",42747,42954,null],[["seg14"],"Alignments","seg14","ctgA",42889,43270,null],[["seg14"],"Alignments","seg14","ctgA",43394,43811,null],[["seg15"],"Alignments","seg15","ctgA",43400,43897,null],[["seg15"],"Alignments","seg15","ctgA",44042,44113,null],[["seg14"],"Alignments","seg14","ctgA",44064,44556,null],[["seg07"],"Alignments","seg07","ctgA",44190,44514,null],[["seg15"],"Alignments","seg15","ctgA",44398,44888,null],[["seg07"],"Alignments","seg07","ctgA",44551,45043,null],[["seg14"],"Alignments","seg14","ctgA",44762,45030,null],[["seg14"],"Alignments","seg14","ctgA",45230,45488,null],[["seg15"],"Alignments","seg15","ctgA",45280,45375,null],[["seg07"],"Alignments","seg07","ctgA",45372,45600,null],[["seg15"],"Alignments","seg15","ctgA",45710,46041,null],[["seg14"],"Alignments","seg14","ctgA",45789,46022,null],[["seg07"],"Alignments","seg07","ctgA",45896,46315,null],[["seg14"],"Alignments","seg14","ctgA",46091,46318,null],[["seg15"],"Alignments","seg15","ctgA",46424,46564,null],[["seg07"],"Alignments","seg07","ctgA",46490,46890,null],[["seg15"],"Alignments","seg15","ctgA",46737,47087,null],[["seg14"],"Alignments","seg14","ctgA",46815,46992,null],[["seg07"],"Alignments","seg07","ctgA",47125,47297,null],[["seg15"],"Alignments","seg15","ctgA",47328,47595,null],[["seg14"],"Alignments","seg14","ctgA",47448,47829,null],[["seg07"],"Alignments","seg07","ctgA",47734,47983,null],[["seg15"],"Alignments","seg15","ctgA",47857,47979,null],[["seg15"],"Alignments","seg15","ctgA",48168,48453,null],[["seg07"],"Alignments","seg07","ctgA",48446,48709,null],[["seg07"],"Alignments","seg07","ctgA",48930,49186,null],[["seg13"],"Alignments","seg13","ctgA",49405,49476,null],[["seg07"],"Alignments","seg07","ctgA",49471,49699,null],[["seg13"],"Alignments","seg13","ctgA",49761,50000,null],[["seg07"],"Alignments","seg07","ctgA",49956,50000,null]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_names/tracks/Alignments/ctgA/names.txt b/tests/data/volvox_formatted_names/tracks/Alignments/ctgA/names.txt
new file mode 100644
index 0000000000..ef50af29ac
--- /dev/null
+++ b/tests/data/volvox_formatted_names/tracks/Alignments/ctgA/names.txt
@@ -0,0 +1,149 @@
+[["seg04"],"Alignments","seg04","ctgA",5232,5302]
+[["seg04"],"Alignments","seg04","ctgA",5799,6101]
+[["seg04"],"Alignments","seg04","ctgA",6441,6854]
+[["seg03"],"Alignments","seg03","ctgA",6884,7241]
+[["seg04"],"Alignments","seg04","ctgA",7105,7211]
+[["seg03"],"Alignments","seg03","ctgA",7409,7737]
+[["seg04"],"Alignments","seg04","ctgA",7694,8177]
+[["seg03"],"Alignments","seg03","ctgA",8054,8080]
+[["seg03"],"Alignments","seg03","ctgA",8305,8999]
+[["seg04"],"Alignments","seg04","ctgA",8544,8783]
+[["seg04"],"Alignments","seg04","ctgA",8868,8935]
+[["seg04"],"Alignments","seg04","ctgA",9403,9825]
+[["seg12"],"Alignments","seg12","ctgA",12530,12895]
+[["seg12"],"Alignments","seg12","ctgA",13121,13449]
+[["seg12"],"Alignments","seg12","ctgA",13451,13745]
+[["seg12"],"Alignments","seg12","ctgA",13907,13965]
+[["seg12"],"Alignments","seg12","ctgA",13997,14488]
+[["seg12"],"Alignments","seg12","ctgA",14563,14899]
+[["seg12"],"Alignments","seg12","ctgA",15184,15276]
+[["seg12"],"Alignments","seg12","ctgA",15638,15736]
+[["seg12"],"Alignments","seg12","ctgA",15744,15870]
+[["seg08"],"Alignments","seg08","ctgA",18508,18985]
+[["seg08"],"Alignments","seg08","ctgA",18988,19388]
+[["seg06"],"Alignments","seg06","ctgA",19248,19559]
+[["seg08"],"Alignments","seg08","ctgA",19495,19962]
+[["seg06"],"Alignments","seg06","ctgA",19974,20260]
+[["seg08"],"Alignments","seg08","ctgA",20092,20580]
+[["seg06"],"Alignments","seg06","ctgA",20378,20491]
+[["seg06"],"Alignments","seg06","ctgA",20532,21005]
+[["seg08"],"Alignments","seg08","ctgA",20969,21052]
+[["seg06"],"Alignments","seg06","ctgA",21121,21331]
+[["seg08"],"Alignments","seg08","ctgA",21269,21277]
+[["seg06"],"Alignments","seg06","ctgA",21681,22176]
+[["seg08"],"Alignments","seg08","ctgA",21684,22168]
+[["seg06"],"Alignments","seg06","ctgA",22373,22570]
+[["seg08"],"Alignments","seg08","ctgA",22563,22869]
+[["seg08"],"Alignments","seg08","ctgA",22957,23298]
+[["seg06"],"Alignments","seg06","ctgA",23024,23427]
+[["seg08"],"Alignments","seg08","ctgA",23411,23469]
+[["seg08"],"Alignments","seg08","ctgA",23931,23932]
+[["seg11"],"Alignments","seg11","ctgA",24227,24510]
+[["seg08"],"Alignments","seg08","ctgA",24327,24787]
+[["seg11"],"Alignments","seg11","ctgA",24867,25012]
+[["seg11"],"Alignments","seg11","ctgA",25211,25426]
+[["seg08"],"Alignments","seg08","ctgA",25227,25367]
+[["seg11"],"Alignments","seg11","ctgA",25793,25874]
+[["seg11"],"Alignments","seg11","ctgA",26074,26519]
+[["seg02"],"Alignments","seg02","ctgA",26121,26126]
+[["seg02"],"Alignments","seg02","ctgA",26496,26869]
+[["seg05"],"Alignments","seg05","ctgA",26502,26799]
+[["seg11"],"Alignments","seg11","ctgA",26929,26940]
+[["seg11"],"Alignments","seg11","ctgA",26974,27063]
+[["seg05"],"Alignments","seg05","ctgA",27171,27185]
+[["seg02"],"Alignments","seg02","ctgA",27200,27325]
+[["seg02"],"Alignments","seg02","ctgA",27371,27433]
+[["seg11"],"Alignments","seg11","ctgA",27414,27799]
+[["seg05"],"Alignments","seg05","ctgA",27447,27860]
+[["seg02"],"Alignments","seg02","ctgA",27564,27565]
+[["seg02"],"Alignments","seg02","ctgA",27812,28091]
+[["seg11"],"Alignments","seg11","ctgA",27879,27943]
+[["seg05"],"Alignments","seg05","ctgA",27886,28076]
+[["seg02"],"Alignments","seg02","ctgA",28092,28201]
+[["seg11"],"Alignments","seg11","ctgA",28224,28346]
+[["seg05"],"Alignments","seg05","ctgA",28224,28316]
+[["seg02"],"Alignments","seg02","ctgA",28328,28377]
+[["seg11"],"Alignments","seg11","ctgA",28374,28570]
+[["seg11"],"Alignments","seg11","ctgA",28757,29041]
+[["seg05"],"Alignments","seg05","ctgA",28776,29058]
+[["seg02"],"Alignments","seg02","ctgA",28828,29194]
+[["seg11"],"Alignments","seg11","ctgA",29100,29302]
+[["seg05"],"Alignments","seg05","ctgA",29512,29647]
+[["seg02"],"Alignments","seg02","ctgA",29516,29702]
+[["seg11"],"Alignments","seg11","ctgA",29603,29702]
+[["seg02"],"Alignments","seg02","ctgA",29712,30061]
+[["seg10"],"Alignments","seg10","ctgA",29770,29942]
+[["seg11"],"Alignments","seg11","ctgA",29866,29885]
+[["seg10"],"Alignments","seg10","ctgA",30041,30340]
+[["seg05"],"Alignments","seg05","ctgA",30107,30216]
+[["seg11"],"Alignments","seg11","ctgA",30240,30246]
+[["seg02"],"Alignments","seg02","ctgA",30328,30774]
+[["seg05"],"Alignments","seg05","ctgA",30464,30798]
+[["seg11"],"Alignments","seg11","ctgA",30574,30738]
+[["seg02"],"Alignments","seg02","ctgA",30807,31306]
+[["seg10"],"Alignments","seg10","ctgA",30809,31307]
+[["seg05"],"Alignments","seg05","ctgA",31231,31236]
+[["seg05"],"Alignments","seg05","ctgA",31420,31817]
+[["seg02"],"Alignments","seg02","ctgA",31515,31729]
+[["seg02"],"Alignments","seg02","ctgA",31752,32154]
+[["seg10"],"Alignments","seg10","ctgA",31760,31984]
+[["seg05"],"Alignments","seg05","ctgA",32009,32057]
+[["seg05"],"Alignments","seg05","ctgA",32207,32680]
+[["seg01"],"Alignments","seg01","ctgA",32328,32359]
+[["seg10"],"Alignments","seg10","ctgA",32373,32937]
+[["seg02"],"Alignments","seg02","ctgA",32594,32696]
+[["seg02"],"Alignments","seg02","ctgA",32891,32901]
+[["seg05"],"Alignments","seg05","ctgA",33052,33325]
+[["seg02"],"Alignments","seg02","ctgA",33126,33388]
+[["seg05"],"Alignments","seg05","ctgA",33437,33868]
+[["seg02"],"Alignments","seg02","ctgA",33438,33443]
+[["seg02"],"Alignments","seg02","ctgA",33758,34209]
+[["seg05"],"Alignments","seg05","ctgA",34243,34313]
+[["seg02"],"Alignments","seg02","ctgA",34400,34466]
+[["seg05"],"Alignments","seg05","ctgA",34604,34983]
+[["seg05"],"Alignments","seg05","ctgA",35332,35507]
+[["seg05"],"Alignments","seg05","ctgA",35641,35904]
+[["seg09"],"Alignments","seg09","ctgA",36615,37057]
+[["seg09"],"Alignments","seg09","ctgA",37207,37227]
+[["seg15"],"Alignments","seg15","ctgA",39264,39361]
+[["seg15"],"Alignments","seg15","ctgA",39752,40034]
+[["seg15"],"Alignments","seg15","ctgA",40514,40954]
+[["seg14"],"Alignments","seg14","ctgA",41136,41318]
+[["seg15"],"Alignments","seg15","ctgA",41251,41365]
+[["seg15"],"Alignments","seg15","ctgA",41491,41504]
+[["seg14"],"Alignments","seg14","ctgA",41753,41948]
+[["seg15"],"Alignments","seg15","ctgA",41940,42377]
+[["seg14"],"Alignments","seg14","ctgA",42056,42474]
+[["seg15"],"Alignments","seg15","ctgA",42747,42954]
+[["seg14"],"Alignments","seg14","ctgA",42889,43270]
+[["seg14"],"Alignments","seg14","ctgA",43394,43811]
+[["seg15"],"Alignments","seg15","ctgA",43400,43897]
+[["seg15"],"Alignments","seg15","ctgA",44042,44113]
+[["seg14"],"Alignments","seg14","ctgA",44064,44556]
+[["seg07"],"Alignments","seg07","ctgA",44190,44514]
+[["seg15"],"Alignments","seg15","ctgA",44398,44888]
+[["seg07"],"Alignments","seg07","ctgA",44551,45043]
+[["seg14"],"Alignments","seg14","ctgA",44762,45030]
+[["seg14"],"Alignments","seg14","ctgA",45230,45488]
+[["seg15"],"Alignments","seg15","ctgA",45280,45375]
+[["seg07"],"Alignments","seg07","ctgA",45372,45600]
+[["seg15"],"Alignments","seg15","ctgA",45710,46041]
+[["seg14"],"Alignments","seg14","ctgA",45789,46022]
+[["seg07"],"Alignments","seg07","ctgA",45896,46315]
+[["seg14"],"Alignments","seg14","ctgA",46091,46318]
+[["seg15"],"Alignments","seg15","ctgA",46424,46564]
+[["seg07"],"Alignments","seg07","ctgA",46490,46890]
+[["seg15"],"Alignments","seg15","ctgA",46737,47087]
+[["seg14"],"Alignments","seg14","ctgA",46815,46992]
+[["seg07"],"Alignments","seg07","ctgA",47125,47297]
+[["seg15"],"Alignments","seg15","ctgA",47328,47595]
+[["seg14"],"Alignments","seg14","ctgA",47448,47829]
+[["seg07"],"Alignments","seg07","ctgA",47734,47983]
+[["seg15"],"Alignments","seg15","ctgA",47857,47979]
+[["seg15"],"Alignments","seg15","ctgA",48168,48453]
+[["seg07"],"Alignments","seg07","ctgA",48446,48709]
+[["seg07"],"Alignments","seg07","ctgA",48930,49186]
+[["seg13"],"Alignments","seg13","ctgA",49405,49476]
+[["seg07"],"Alignments","seg07","ctgA",49471,49699]
+[["seg13"],"Alignments","seg13","ctgA",49761,50000]
+[["seg07"],"Alignments","seg07","ctgA",49956,50000]
diff --git a/tests/data/volvox_formatted_names/tracks/CDS/ctgA/names.json b/tests/data/volvox_formatted_names/tracks/CDS/ctgA/names.json
deleted file mode 100644
index f23a9c1dbf..0000000000
--- a/tests/data/volvox_formatted_names/tracks/CDS/ctgA/names.json
+++ /dev/null
@@ -1 +0,0 @@
-[[["Apple1"],"CDS","Apple1","ctgA",9999,11500,null],[["Apple2"],"CDS","Apple2","ctgA",12999,17200,null],[[],"CDS",null,"ctgA",12999,13800,null],[[],"CDS",null,"ctgA",14999,15500,null],[[],"CDS",null,"ctgA",16999,17200,null],[["Apple3"],"CDS","Apple3","ctgA",17399,23000,null]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_names/tracks/CDS/ctgA/names.txt b/tests/data/volvox_formatted_names/tracks/CDS/ctgA/names.txt
new file mode 100644
index 0000000000..45698915be
--- /dev/null
+++ b/tests/data/volvox_formatted_names/tracks/CDS/ctgA/names.txt
@@ -0,0 +1,6 @@
+[["Apple1"],"CDS","Apple1","ctgA",9999,11500]
+[["Apple2"],"CDS","Apple2","ctgA",12999,17200]
+[[],"CDS",null,"ctgA",12999,13800]
+[[],"CDS",null,"ctgA",14999,15500]
+[[],"CDS",null,"ctgA",16999,17200]
+[["Apple3"],"CDS","Apple3","ctgA",17399,23000]
diff --git a/tests/data/volvox_formatted_names/tracks/Clones/ctgA/names.json b/tests/data/volvox_formatted_names/tracks/Clones/ctgA/names.json
deleted file mode 100644
index f6eac1d15f..0000000000
--- a/tests/data/volvox_formatted_names/tracks/Clones/ctgA/names.json
+++ /dev/null
@@ -1 +0,0 @@
-[[["b101.2"],"Clones","b101.2","ctgA",999,20000,null]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_names/tracks/Clones/ctgA/names.txt b/tests/data/volvox_formatted_names/tracks/Clones/ctgA/names.txt
new file mode 100644
index 0000000000..50d0014aad
--- /dev/null
+++ b/tests/data/volvox_formatted_names/tracks/Clones/ctgA/names.txt
@@ -0,0 +1 @@
+[["b101.2"],"Clones","b101.2","ctgA",999,20000]
diff --git a/tests/data/volvox_formatted_names/tracks/EST/ctgA/names.json b/tests/data/volvox_formatted_names/tracks/EST/ctgA/names.json
deleted file mode 100644
index be061bc90a..0000000000
--- a/tests/data/volvox_formatted_names/tracks/EST/ctgA/names.json
+++ /dev/null
@@ -1 +0,0 @@
-[[["agt221.5"],"EST","agt221.5","ctgA",1049,7300,null],[["agt830.5"],"EST","agt830.5","ctgA",1049,3202,null],[["agt767.5"],"EST","agt767.5","ctgA",1149,7200,null],[["agt830.3"],"EST","agt830.3","ctgA",5409,7503,null],[["agt221.3"],"EST","agt221.3","ctgA",7499,8000,null],[["agt767.3"],"EST","agt767.3","ctgA",7999,9000,null]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_names/tracks/EST/ctgA/names.txt b/tests/data/volvox_formatted_names/tracks/EST/ctgA/names.txt
new file mode 100644
index 0000000000..06786fe56b
--- /dev/null
+++ b/tests/data/volvox_formatted_names/tracks/EST/ctgA/names.txt
@@ -0,0 +1,6 @@
+[["agt221.5"],"EST","agt221.5","ctgA",1049,7300]
+[["agt830.5"],"EST","agt830.5","ctgA",1049,3202]
+[["agt767.5"],"EST","agt767.5","ctgA",1149,7200]
+[["agt830.3"],"EST","agt830.3","ctgA",5409,7503]
+[["agt221.3"],"EST","agt221.3","ctgA",7499,8000]
+[["agt767.3"],"EST","agt767.3","ctgA",7999,9000]
diff --git a/tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgA/names.json b/tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgA/names.json
deleted file mode 100644
index a894630e03..0000000000
--- a/tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgA/names.json
+++ /dev/null
@@ -1 +0,0 @@
-[[["Remark:hga","hga"],"ExampleFeatures","Remark:hga","ctgA",999,2000,null],[["f07"],"ExampleFeatures","f07","ctgA",1658,1984,null],[["f06"],"ExampleFeatures","f06","ctgA",3013,6130,null],[["f05"],"ExampleFeatures","f05","ctgA",4714,5968,null],[["f08"],"ExampleFeatures","f08","ctgA",13279,16394,null],[["f10"],"ExampleFeatures","f10","ctgA",15328,15533,null],[["f13"],"ExampleFeatures","f13","ctgA",19156,22915,null],[["f15"],"ExampleFeatures","f15","ctgA",22131,24633,null],[["f14"],"ExampleFeatures","f14","ctgA",23071,23185,null],[["f02"],"ExampleFeatures","f02","ctgA",24561,28338,null],[["f09"],"ExampleFeatures","f09","ctgA",36033,38167,null],[["f03"],"ExampleFeatures","f03","ctgA",36648,40440,null],[["f04"],"ExampleFeatures","f04","ctgA",37241,38653,null],[["f01"],"ExampleFeatures","f01","ctgA",44704,47713,null],[["f11"],"ExampleFeatures","f11","ctgA",46989,48410,null],[["f12"],"ExampleFeatures","f12","ctgA",49757,50000,null]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgA/names.txt b/tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgA/names.txt
new file mode 100644
index 0000000000..ef5afac54a
--- /dev/null
+++ b/tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgA/names.txt
@@ -0,0 +1,16 @@
+[["Remark:hga","hga"],"ExampleFeatures","Remark:hga","ctgA",999,2000]
+[["f07"],"ExampleFeatures","f07","ctgA",1658,1984]
+[["f06"],"ExampleFeatures","f06","ctgA",3013,6130]
+[["f05"],"ExampleFeatures","f05","ctgA",4714,5968]
+[["f08"],"ExampleFeatures","f08","ctgA",13279,16394]
+[["f10"],"ExampleFeatures","f10","ctgA",15328,15533]
+[["f13"],"ExampleFeatures","f13","ctgA",19156,22915]
+[["f15"],"ExampleFeatures","f15","ctgA",22131,24633]
+[["f14"],"ExampleFeatures","f14","ctgA",23071,23185]
+[["f02"],"ExampleFeatures","f02","ctgA",24561,28338]
+[["f09"],"ExampleFeatures","f09","ctgA",36033,38167]
+[["f03"],"ExampleFeatures","f03","ctgA",36648,40440]
+[["f04"],"ExampleFeatures","f04","ctgA",37241,38653]
+[["f01"],"ExampleFeatures","f01","ctgA",44704,47713]
+[["f11"],"ExampleFeatures","f11","ctgA",46989,48410]
+[["f12"],"ExampleFeatures","f12","ctgA",49757,50000]
diff --git a/tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgB/names.json b/tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgB/names.json
deleted file mode 100644
index cfcc1d26fa..0000000000
--- a/tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgB/names.json
+++ /dev/null
@@ -1 +0,0 @@
-[[["f07"],"ExampleFeatures","f07","ctgB",1658,1984,null],[["f06"],"ExampleFeatures","f06","ctgB",3013,6130,null],[["f05"],"ExampleFeatures","f05","ctgB",4714,5968,null]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgB/names.txt b/tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgB/names.txt
new file mode 100644
index 0000000000..33caf6fae4
--- /dev/null
+++ b/tests/data/volvox_formatted_names/tracks/ExampleFeatures/ctgB/names.txt
@@ -0,0 +1,3 @@
+[["f07"],"ExampleFeatures","f07","ctgB",1658,1984]
+[["f06"],"ExampleFeatures","f06","ctgB",3013,6130]
+[["f05"],"ExampleFeatures","f05","ctgB",4714,5968]
diff --git a/tests/data/volvox_formatted_names/tracks/Genes/ctgA/names.json b/tests/data/volvox_formatted_names/tracks/Genes/ctgA/names.json
deleted file mode 100644
index 4d71184db7..0000000000
--- a/tests/data/volvox_formatted_names/tracks/Genes/ctgA/names.json
+++ /dev/null
@@ -1 +0,0 @@
-[[["EDEN"],"Genes","EDEN","ctgA",1049,9000,null]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_names/tracks/Genes/ctgA/names.txt b/tests/data/volvox_formatted_names/tracks/Genes/ctgA/names.txt
new file mode 100644
index 0000000000..0ef799b5f7
--- /dev/null
+++ b/tests/data/volvox_formatted_names/tracks/Genes/ctgA/names.txt
@@ -0,0 +1 @@
+[["EDEN"],"Genes","EDEN","ctgA",1049,9000]
diff --git a/tests/data/volvox_formatted_names/tracks/Motifs/ctgA/names.json b/tests/data/volvox_formatted_names/tracks/Motifs/ctgA/names.json
deleted file mode 100644
index 86425bc804..0000000000
--- a/tests/data/volvox_formatted_names/tracks/Motifs/ctgA/names.json
+++ /dev/null
@@ -1 +0,0 @@
-[[["m11"],"Motifs","m11","ctgA",11910,15561,null],[["m05"],"Motifs","m05","ctgA",13800,14007,null],[["m14"],"Motifs","m14","ctgA",14730,17239,null],[["m03"],"Motifs","m03","ctgA",15395,16159,null],[["m08"],"Motifs","m08","ctgA",17022,17675,null],[["m13"],"Motifs","m13","ctgA",17666,17690,null],[["m07"],"Motifs","m07","ctgA",18047,18552,null],[["m12"],"Motifs","m12","ctgA",21747,25612,null],[["m02"],"Motifs","m02","ctgA",28331,30033,null],[["m10"],"Motifs","m10","ctgA",28341,28447,null],[["m06"],"Motifs","m06","ctgA",30577,31748,null],[["m04"],"Motifs","m04","ctgA",33324,35791,null],[["m15"],"Motifs","m15","ctgA",37496,40559,null],[["m09"],"Motifs","m09","ctgA",46011,48851,null],[["m01"],"Motifs","m01","ctgA",48252,48366,null]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_names/tracks/Motifs/ctgA/names.txt b/tests/data/volvox_formatted_names/tracks/Motifs/ctgA/names.txt
new file mode 100644
index 0000000000..a8adbb70c4
--- /dev/null
+++ b/tests/data/volvox_formatted_names/tracks/Motifs/ctgA/names.txt
@@ -0,0 +1,15 @@
+[["m11"],"Motifs","m11","ctgA",11910,15561]
+[["m05"],"Motifs","m05","ctgA",13800,14007]
+[["m14"],"Motifs","m14","ctgA",14730,17239]
+[["m03"],"Motifs","m03","ctgA",15395,16159]
+[["m08"],"Motifs","m08","ctgA",17022,17675]
+[["m13"],"Motifs","m13","ctgA",17666,17690]
+[["m07"],"Motifs","m07","ctgA",18047,18552]
+[["m12"],"Motifs","m12","ctgA",21747,25612]
+[["m02"],"Motifs","m02","ctgA",28331,30033]
+[["m10"],"Motifs","m10","ctgA",28341,28447]
+[["m06"],"Motifs","m06","ctgA",30577,31748]
+[["m04"],"Motifs","m04","ctgA",33324,35791]
+[["m15"],"Motifs","m15","ctgA",37496,40559]
+[["m09"],"Motifs","m09","ctgA",46011,48851]
+[["m01"],"Motifs","m01","ctgA",48252,48366]
diff --git a/tests/data/volvox_formatted_names/tracks/NameTest/ctgA/names.json b/tests/data/volvox_formatted_names/tracks/NameTest/ctgA/names.json
deleted file mode 100644
index 77bcf1fe0c..0000000000
--- a/tests/data/volvox_formatted_names/tracks/NameTest/ctgA/names.json
+++ /dev/null
@@ -1 +0,0 @@
-[[["Gene:hga","hga"],"NameTest","Gene:hga","ctgA",1099,2000,null],[["Protein:HGA","hga"],"NameTest","Protein:HGA","ctgA",1199,1900,null],[["Gene:hgb","hgb"],"NameTest","Gene:hgb","ctgA",1599,3000,null],[["Protein:HGB","hgb"],"NameTest","Protein:HGB","ctgA",1799,2900,null]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_names/tracks/NameTest/ctgA/names.txt b/tests/data/volvox_formatted_names/tracks/NameTest/ctgA/names.txt
new file mode 100644
index 0000000000..0f3974403b
--- /dev/null
+++ b/tests/data/volvox_formatted_names/tracks/NameTest/ctgA/names.txt
@@ -0,0 +1,4 @@
+[["Gene:hga","hga"],"NameTest","Gene:hga","ctgA",1099,2000]
+[["Protein:HGA","hga"],"NameTest","Protein:HGA","ctgA",1199,1900]
+[["Gene:hgb","hgb"],"NameTest","Gene:hgb","ctgA",1599,3000]
+[["Protein:HGB","hgb"],"NameTest","Protein:HGB","ctgA",1799,2900]
diff --git a/tests/data/volvox_formatted_names/tracks/ReadingFrame/ctgA/names.json b/tests/data/volvox_formatted_names/tracks/ReadingFrame/ctgA/names.json
deleted file mode 100644
index 7472ba8fed..0000000000
--- a/tests/data/volvox_formatted_names/tracks/ReadingFrame/ctgA/names.json
+++ /dev/null
@@ -1 +0,0 @@
-[[["EDEN.2"],"ReadingFrame","EDEN.2","ctgA",1049,9000,null],[["EDEN.1"],"ReadingFrame","EDEN.1","ctgA",1049,9000,null],[["EDEN.3"],"ReadingFrame","EDEN.3","ctgA",1299,9000,null],[["Apple2"],"ReadingFrame","Apple2","ctgA",12999,17200,null],[["Apple3"],"ReadingFrame","Apple3","ctgA",17399,23000,null]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_names/tracks/ReadingFrame/ctgA/names.txt b/tests/data/volvox_formatted_names/tracks/ReadingFrame/ctgA/names.txt
new file mode 100644
index 0000000000..0ef7e0eaa5
--- /dev/null
+++ b/tests/data/volvox_formatted_names/tracks/ReadingFrame/ctgA/names.txt
@@ -0,0 +1,5 @@
+[["EDEN.2"],"ReadingFrame","EDEN.2","ctgA",1049,9000]
+[["EDEN.1"],"ReadingFrame","EDEN.1","ctgA",1049,9000]
+[["EDEN.3"],"ReadingFrame","EDEN.3","ctgA",1299,9000]
+[["Apple2"],"ReadingFrame","Apple2","ctgA",12999,17200]
+[["Apple3"],"ReadingFrame","Apple3","ctgA",17399,23000]
diff --git a/tests/data/volvox_formatted_names/tracks/Transcript/ctgA/names.json b/tests/data/volvox_formatted_names/tracks/Transcript/ctgA/names.json
deleted file mode 100644
index 9cee801812..0000000000
--- a/tests/data/volvox_formatted_names/tracks/Transcript/ctgA/names.json
+++ /dev/null
@@ -1 +0,0 @@
-[[["Apple3"],"Transcript","Apple3","ctgA",17399,23000,null]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_names/tracks/Transcript/ctgA/names.txt b/tests/data/volvox_formatted_names/tracks/Transcript/ctgA/names.txt
new file mode 100644
index 0000000000..3816bbd057
--- /dev/null
+++ b/tests/data/volvox_formatted_names/tracks/Transcript/ctgA/names.txt
@@ -0,0 +1 @@
+[["Apple3"],"Transcript","Apple3","ctgA",17399,23000]
diff --git a/tests/data/volvox_formatted_names/tracks/snps/ctgA/names.json b/tests/data/volvox_formatted_names/tracks/snps/ctgA/names.json
deleted file mode 100644
index e78d32f0aa..0000000000
--- a/tests/data/volvox_formatted_names/tracks/snps/ctgA/names.json
+++ /dev/null
@@ -1 +0,0 @@
-[[["FakeSNP"],"snps","FakeSNP","ctgA",999,1000,null]]
\ No newline at end of file
diff --git a/tests/data/volvox_formatted_names/tracks/snps/ctgA/names.txt b/tests/data/volvox_formatted_names/tracks/snps/ctgA/names.txt
new file mode 100644
index 0000000000..7cd8600f1b
--- /dev/null
+++ b/tests/data/volvox_formatted_names/tracks/snps/ctgA/names.txt
@@ -0,0 +1 @@
+[["FakeSNP"],"snps","FakeSNP","ctgA",999,1000]
diff --git a/tests/data/volvox_formatted_refseqs/seq/refSeqs.json b/tests/data/volvox_formatted_refseqs/seq/refSeqs.json
index f877745c20..cc1b002d6e 100644
--- a/tests/data/volvox_formatted_refseqs/seq/refSeqs.json
+++ b/tests/data/volvox_formatted_refseqs/seq/refSeqs.json
@@ -1,16 +1,16 @@
[
{
- "length" : 6079,
- "name" : "ctgB",
+ "length" : 50001,
+ "name" : "ctgA",
"seqChunkSize" : 20000,
- "end" : 6079,
+ "end" : 50001,
"start" : 0
},
{
- "length" : 50001,
- "name" : "ctgA",
+ "length" : 6079,
+ "name" : "ctgB",
"seqChunkSize" : 20000,
- "end" : 50001,
+ "end" : 6079,
"start" : 0
}
]
diff --git a/tests/install_selenium.sh b/tests/install_selenium.sh
new file mode 100755
index 0000000000..f4a0d6ebfe
--- /dev/null
+++ b/tests/install_selenium.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+set -e;
+
+# try to install pip if we don't have it
+if ! ( which pip >/dev/null 2>&1 ); then
+ if ( which apt-get ); then
+ sudo apt-get install python-pip
+ else if ( which easy_install >/dev/null 2>&1 ); then
+ easy_install pip
+ fi;
+ fi;
+fi;
+
+# install selenium and nose with pip
+pip install selenium nose
diff --git a/tests/js_tests/index.html b/tests/js_tests/index.html
index 4e5173e093..baa97ac67a 100644
--- a/tests/js_tests/index.html
+++ b/tests/js_tests/index.html
@@ -1,7 +1,8 @@
-
+
Jasmine Spec Runner
@@ -20,6 +21,12 @@
+
+
+
+
+
+