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Added dynamic handling of CDS/UTR/exon subfeatures (to support exon-b…
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…ased selection) in DraggableHTMLFeatures. Handles case with no CDS but 'wholeCDS' subfeature.

Handles case with CDS and UTR and exons.
Handles case with CDS and UTR but no exons.
 Handles sequence ontology types that are descendants of CDS, UTR, exon as well.
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gregg committed Dec 13, 2012
1 parent 94da3f1 commit 44b77d6
Showing 1 changed file with 151 additions and 39 deletions.
190 changes: 151 additions & 39 deletions plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js
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Expand Up @@ -9,9 +9,10 @@ define( [
'dijit/Dialog',
'jquery',
'jqueryui/draggable',
'JBrowse/Util'
'JBrowse/Util',
'JBrowse/Model/SimpleFeature'
],
function( declare, array, HTMLFeatureTrack, FeatureSelectionManager, dijitMenu, dijitMenuItem, dijitCheckedMenuItem, dijitDialog, $, draggable, Util ) {
function( declare, array, HTMLFeatureTrack, FeatureSelectionManager, dijitMenu, dijitMenuItem, dijitCheckedMenuItem, dijitDialog, $, draggable, Util, SimpleFeature ) {

/* Subclass of FeatureTrack that allows features to be selected,
and dragged and dropped into the annotation track to create annotations.
Expand Down Expand Up @@ -340,6 +341,148 @@ var draggableTrack = declare( HTMLFeatureTrack,
return subfeatdiv;
},

_subfeatSorter: function( a, b ) {
var as = a.get('start');
var bs = b.get('start');
if ( as == bs ) { return 0; }
else if ( as > bs ) { return 1; }
else if ( as < bs ) { return -1; }
else { return 0; /* shouldn't fall through to here */ }
},


/**
* if feature has translated region (CDS, wholeCDS, start_codon, ???),
* reworks feature's subfeatures for more annotation-editing-friendly selection
*
* Assumes:
* if translated, will either have
* CDS-ish term for each coding segment
* wholeCDS from start of translation to end of translation (so already pre-processed)
* mutually exclusive (either have CDS, or wholeCDS, but not both)
* if wholeCDS present, then pre-processed (no UTRs)
* if any exon-ish types present, then _all_ exons are present with exon-ish types
*/
_processTranslation: function( feature ) {
var track = this;

var feat_type = feature.get('type');

// most very dense genomic feature tracks do not have CDS. Trying to minimize overhead for that case --
// keep list of types that NEVER have CDS children (match, alignment, repeat, etc.)
// (WARNING in this case not sorting, but sorting (currently) only needed for features with CDS (for reading frame calcs))
if (this.webapollo.neverHasCDS[feat_type]) {
feature.normalized = true;
return;
}
var subfeats = feature.get('subfeatures');

// var cds = subfeats.filter( function(feat) { return feat.get('type') === 'CDS'; } );
var cds = subfeats.filter( function(feat) {
return track.webapollo.cdsTerms[feat.get('type')];
} );
var wholeCDS = subfeats.filter( function(feat) { return feat.get('type') === 'wholeCDS'; } );

// most very dense genomic feature tracks do not have CDS. Trying to minimize overhead for that case --
// if no CDS, no wholeCDS, consider normalized
// (WARNING in this case not sorting, but sorting (currently) only needed for features with CDS (for reading frame calcs))
//
if (cds.length === 0 && wholeCDS.length === 0) {
feature.normalized = true;
return;
}

var newsubs;
// wholeCDS is specific to WebApollo, if seen can assume no CDS, and UTR/exon already normalized
if (wholeCDS.length > 0) {
// extract wholecds from subfeats, then sort subfeats
feature.wholeCDS = wholeCDS[0];
newsubs = subfeats.filter( function(feat) { return feat.get('type') !== 'wholeCDS'; } );
}

// if has a CDS, remove CDS from subfeats and sort exons
else if (cds.length > 0) {
cds.sort(this._subfeatSorter);
var cdsmin = cds[0].get('start');
var cdsmax = cds[cds.length-1].get('end');
feature.wholeCDS = new SimpleFeature({ parent: feature,
data: { start: cdsmin, end: cdsmax, type: 'wholeCDS',
strand: feature.get('strand') }
} );
var hasExons = false;
for (var i=0; i<subfeats.length; i++) {
// if (subfeats[i].get('type') === 'exon') { hasExons = true; break; }
if (track.webapollo.exonTerms[subfeats[i].get('type')]) { hasExons = true; break; }
}
if (hasExons) {
// filter out UTR and CDS
newsubs = subfeats.filter( function(feat) {
var ftype = feat.get('type');
return (! (track.webapollo.utrTerms[ftype] || track.webapollo.cdsTerms[ftype]) );
} );
}
else { // no exons, but at least one CDS, possibly UTR
// create exons by joining abutting UTR/CDS
var sortedsubs = subfeats.slice(); // shallow copy subfeats array
sortedsubs.sort(this._subfeatSorter);
newsubs = [];
// since cds.length > 0, guaranteed to have at least one CDS
var exonCount = 0;
var prevStart, prevEnd;
// scan through sorted subfeats, joining abutting UTR/CDS regions
for (var i=0; i<sortedsubs.length; i++) {
var subfeat = sortedsubs[i];
var ftype = subfeat.get('type');
var curStart = subfeat.get('start');
var curEnd = subfeat.get('end');

if (this.webapollo.utrTerms[ftype] || this.webapollo.cdsTerms[ftype] ) {
if (! prevStart) { // first UTR/CDS, just initialize first exon
prevStart = subfeat.get('start');
prevEnd = subfeat.get('end');
}
else { // compare to previous UTR/CDS
// abutting, extend previous exon
if (curStart == prevEnd) {
prevEnd = curEnd;
}
// not abutting, create previous exon and start new one
else {
var exon = new SimpleFeature({ parent: feature,
id: feature.id() + "-exon-" + exonCount++,
data: { start: prevstart, end: prevend, type: 'exon',
strand: feature.get('strand') }
} );
console.log(exon);
newsubs.push(exon);
prevStart = curStart;
prevEnd = curEnd;
}
}
}
else { // not a CDS or UTR, just add to new subfeats array
newsubs.push(subfeat);
}
}
// add last exon after exiting loop
var exon = new SimpleFeature({ parent: feature,
id: feature.id() + "-exon-" + exonCount++,
data: { start: prevstart, end: prevend, type: 'exon',
strand: feature.get('strand') }
} );
newsubs.push(exon);

}
}
// ensure that subfeatures are sorted by ascending start (regardless of feature orientation)
// may want to revisit later and sort subfeatures of minus strand in descending order ??
// but if do this must make sure to change reading frame calcs to reflect this
newsubs.sort(this._subfeatSorter);
feature.filteredsubs = newsubs;
feature.normalized = true;
},


/**
* overriding handleSubFeatures for customized handling of UTR/CDS-segment rendering within exon divs
*/
Expand All @@ -349,48 +492,17 @@ var draggableTrack = declare( HTMLFeatureTrack,
var subfeats = feature.get('subfeatures');
if (! subfeats) { return; }

if (! feature.normalized ) {
this._processTranslation( feature );
}
var wholeCDS = feature.wholeCDS;
var parentId = this.getId(feature);

// if processing resulted in filtered subfeats, render with those instead of unfiltered subfeats
if (feature.filteredsubs) { subfeats = feature.filteredsubs; }
var slength = subfeats.length;
var subfeat;
var wholeCDS = null;
var subtype;
var i;
for (i=0; i < slength; i++) {
subfeat = subfeats[i];
subtype = subfeat.get('type');
if (subtype === "wholeCDS" || subtype === "polypeptide") {
wholeCDS = subfeat;
break;
}
}

/*
// try to make a wholeCDS if we don't have one
if( ! wholeCDS ) {
wholeCDS = (function() {
var cds = array.filter( feature.get('subfeatures'),
function(s) { return s.get('type') == 'CDS'; }
)
.sort( function( a, b ) {
var as = a.get('start'),
bs = b.get('start');
return as == bs ? 0 :
as > bs ? 1 :
as < bs ? -1 : 0;
});
if( cds.length ) {
return { start: cds[0].get('start'),
end: cds[cds.length-1].get('end'),
get: function(n) { return this[n]; }
};
}
else {
return null;
}
}).call(this);
}
*/

if (wholeCDS) {
var cdsStart = wholeCDS.get('start');
Expand Down

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