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added boolean support for subfeatures
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@jsmirob
jsmirob committed Mar 7, 2013
1 parent 7661cfd commit 64974b0
Showing 1 changed file with 54 additions and 24 deletions.
78 changes: 54 additions & 24 deletions src/JBrowse/View/Track/HTMLFeatures.js
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Original file line number Diff line number Diff line change
Expand Up @@ -464,23 +464,36 @@ var HTMLFeatures = declare( [ BlockBased, YScaleMixin, ExportMixin, FeatureDetai
containerStart, containerEnd );
// if there are boolean coverage divs, modify feature accordingly.
if ( sourceSlot.booleanCovs ) {
console.log('called!');
var subfeatures = [];
//remove subfeatures
// remove subfeatures
while ( featDiv.firstChild ) {
subfeatures.push( featDiv.firstChild );
featDiv.removeChild( featDiv.firstChild );
}
var s = Math.max( featDiv.feature.get('start'), containerStart );
var e = Math.min( featDiv.feature.get('end'), containerEnd );
var s = featDiv.featureEdges.s;
var e = featDiv.featureEdges.e;
for ( var key in sourceSlot.booleanCovs ) {
if ( sourceSlot.booleanCovs.hasOwnProperty(key) ) {
// dynamically resize the coverage divs.
var start = sourceSlot.booleanCovs[key].span.s;
var end = sourceSlot.booleanCovs[key].span.e;
if ( end < containerStart || start > containerEnd) continue; // note: we should also remove it from booleanCovs at some point.
sourceSlot.booleanCovs[key].style.left = 100*(start-s)/(e-s)+'%';
sourceSlot.booleanCovs[key].style.width = 100*(end-start)/(e-s)+'%';
featDiv.appendChild( sourceSlot.booleanCovs[key] );
}}
// add the processed subfeatures, if in frame.
dojo.query( '.basicSubfeature', sourceSlot ).forEach(
function(node, idx, arr) {
var start = node.subfeatureEdges.s;
var end = node.subfeatureEdges.e;
if ( end < containerStart || start > containerEnd ) return;
node.style.left = 100*(start-s)/(e-s)+'%';
node.style.width = 100*(end-start)/(e-s)+'%';
featDiv.appendChild(node);
}
)
featDiv.className = 'basic';
featDiv.oldClassName = sourceSlot.oldClassName;
featDiv.booleanCovs = sourceSlot.booleanCovs;
Expand Down Expand Up @@ -569,7 +582,7 @@ var HTMLFeatures = declare( [ BlockBased, YScaleMixin, ExportMixin, FeatureDetai
invSpan.splice(i,1); }
if (invSpan[0].end <= invSpan[0].start) {
invSpan.splice(0,1); }
curTrack.maskBySpans( invSpan, args.spans, containerStart, containerEnd );
curTrack.maskBySpans( invSpan, args.spans );
}
finishCallback();
},
Expand Down Expand Up @@ -615,7 +628,7 @@ var HTMLFeatures = declare( [ BlockBased, YScaleMixin, ExportMixin, FeatureDetai
/**
* If spans are passed to the track (i.e. if it is a boolean track), mask features accordingly.
*/
maskBySpans: function ( invSpans, spans, containerStart, containerEnd ) {
maskBySpans: function ( invSpans, spans ) {
var blocks = this.blocks;
for ( var i in blocks ) {
if ( blocks.hasOwnProperty(i) ) {
Expand All @@ -642,16 +655,20 @@ var HTMLFeatures = declare( [ BlockBased, YScaleMixin, ExportMixin, FeatureDetai
else { return false; }
}

var makeDiv = function ( start, end, parentDiv, masked ) {
var makeDiv = function ( start, end, parentDiv, masked, voidClass ) {
// make a coverage div
var coverageNode = dojo.create('div');
var s = parentDiv.featureEdges.s;
var e = parentDiv.featureEdges.e;
var s = parentDiv.featureEdges
? parentDiv.featureEdges.s
: parentDiv.subfeatureEdges.s;
var e = parentDiv.featureEdges
? parentDiv.featureEdges.e
: parentDiv.subfeatureEdges.e;
coverageNode.span = { s:start, e:end };
coverageNode.className = masked ? (feat.className == 'basic'
coverageNode.className = masked ? (feat.className == voidClass
? feat.oldClassName + ' Boolean-transparent'
: feat.className +' Boolean-transparent')
: (feat.className == 'basic'
: (feat.className == voidClass
? feat.oldClassName
: feat.className);
coverageNode.booleanDiv = true;
Expand All @@ -661,7 +678,7 @@ var HTMLFeatures = declare( [ BlockBased, YScaleMixin, ExportMixin, FeatureDetai
return coverageNode;
}

var addDiv = function ( start, end, parentDiv, masked, isAdded ) {
var addDiv = function ( start, end, parentDiv, masked, voidClass, isAdded ) {
// Loop through coverage Nodes, combining existing nodes so they don't overlap, and add new divs.
var isAdded = isAdded || false;
for ( var key in parentDiv.childNodes ) {
Expand All @@ -671,52 +688,62 @@ var HTMLFeatures = declare( [ BlockBased, YScaleMixin, ExportMixin, FeatureDetai
if ( divStart <= start && divEnd >= end ) {isAdded = true; break;}
var u = union (start, end, divStart, divEnd );
if ( u ) {
var coverageNode = makeDiv( u.s, u.e, parentDiv, masked );
var coverageNode = makeDiv( u.s, u.e, parentDiv, masked, voidClass );
var tempIndex = parentDiv.booleanCovs.indexOf(parentDiv.childNodes[key]);
parentDiv.removeChild(parentDiv.childNodes[key]);
parentDiv.booleanCovs.splice(tempIndex, 1);
parentDiv.appendChild(coverageNode);
parentDiv.booleanCovs.push(coverageNode);
isAdded = true;
addDiv( u.s, u.e, parentDiv, masked, true );
addDiv( u.s, u.e, parentDiv, masked, voidClass, true );
break;
}
}}
if ( !isAdded ) {
var coverageNode = makeDiv( start, end, parentDiv, masked );
var coverageNode = makeDiv( start, end, parentDiv, masked, voidClass );
parentDiv.appendChild(coverageNode);
parentDiv.booleanCovs.push(coverageNode);
}
}

for ( var key in block.featureNodes ) {
if (block.featureNodes.hasOwnProperty(key)) {
var feat = block.featureNodes[key];
if ( !feat.feature ) { dojo.destroy(feat); continue;} // node also contains subfeatures. Remove for now.
var s = feat.feature.get('start');
var e = feat.feature.get('end');
var addOverlaps = function ( s, e, feat, spans, invSpans, voidClass ) {
if ( !feat.booleanCovs ) { feat.booleanCovs = []; }
// add opaque divs
for ( var index in invSpans ) {
if ( invSpans.hasOwnProperty(index) ) {
var ov = overlaps( s, e, invSpans[index].start, invSpans[index].end );
if ( ov ) {
addDiv( ov.s, ov.e, feat, false );
addDiv( ov.s, ov.e, feat, false, voidClass );
}
}}
// add masked divs
for ( var index in spans ) {
if ( spans.hasOwnProperty(index) ) {
var ov = overlaps( s, e, spans[index].start, spans[index].end );
if ( ov ) {
addDiv( ov.s, ov.e, feat, true );
addDiv( ov.s, ov.e, feat, true, voidClass );
}
}}

feat.oldClassName = feat.className == 'basic'
feat.oldClassName = feat.className == voidClass
? feat.oldClassName
: feat.className;
feat.className = 'basic';
feat.className = voidClass;
}

for ( var key in block.featureNodes ) {
if (block.featureNodes.hasOwnProperty(key)) {
var feat = block.featureNodes[key];
if ( !feat.feature ) {
// If there is no feature property, than it is a subfeature
var s = feat.subfeatureEdges.s;
var e = feat.subfeatureEdges.e;
addOverlaps( s, e, feat, spans, invSpans, 'basicSubfeature' );
continue;
}
var s = feat.feature.get('start');
var e = feat.feature.get('end');
addOverlaps( s, e, feat, spans, invSpans, 'basic' );
}}
}}
},
Expand Down Expand Up @@ -1157,6 +1184,9 @@ var HTMLFeatures = declare( [ BlockBased, YScaleMixin, ExportMixin, FeatureDetai
return null;

var subDiv = document.createElement("div");
// used by boolean tracks to do positionning
subDiv.subfeatureEdges = { s: subStart, e: subEnd };

dojo.addClass(subDiv, "subfeature");
// check for className to avoid adding "null", "plus-null", "minus-null"
if (className) {
Expand Down

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