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Preliminary restoration of transcript deletion, exon addition, exon d…
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…eletion, exon extension operations to WebApollo/JBrowse1.7 merge.
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gregg committed Nov 16, 2012
1 parent 768afc1 commit c486515
Showing 1 changed file with 19 additions and 45 deletions.
64 changes: 19 additions & 45 deletions plugins/WebApollo/js/View/Track/AnnotTrack.js
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ define( [
'jquery',
'jqueryui/draggable',
'jqueryui/droppable',
'jqueryui/resizable',
'dijit/Menu',
'dijit/MenuItem',
'dijit/Dialog',
Expand All @@ -14,7 +15,7 @@ define( [
'JBrowse/Model/SimpleFeature',
'JBrowse/Util'
],
function( declare, $, draggable, droppable, dijitMenu, dijitMenuItem, dijitDialog, DraggableFeatureTrack, FeatureSelectionManager, JSONUtils, BioFeatureUtils, Permission, SimpleFeature, Util ) {
function( declare, $, draggable, droppable, resizable, dijitMenu, dijitMenuItem, dijitDialog, DraggableFeatureTrack, FeatureSelectionManager, JSONUtils, BioFeatureUtils, Permission, SimpleFeature, Util ) {

var listeners = [];

Expand Down Expand Up @@ -100,8 +101,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,
this.verbose_mouseleave = false;
this.verbose_render = false;

// this.inherited( arguments );

var track = this;
// for AnnotTrack, features currently MUST be an NCList
// var features = this.features;
Expand Down Expand Up @@ -193,8 +192,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,

createAnnotationChangeListener: function() {
var track = this;
var features = this.features;

if (listeners[track.getUniqueTrackName()]) {
if (listeners[track.getUniqueTrackName()].fired == -1) {
listeners[track.getUniqueTrackName()].cancel();
Expand Down Expand Up @@ -293,10 +290,8 @@ var AnnotTrack = declare( DraggableFeatureTrack,

addFeatures: function(responseFeatures) {
for (var i = 0; i < responseFeatures.length; ++i) {
// var featureArray = JSONUtils.createJBrowseFeature(responseFeatures[i], this.fields, this.subFields);
var feat = JSONUtils.createJBrowseFeature( responseFeatures[i] );
var id = responseFeatures[i].uniquename;
// if (this.features.featIdMap[id] == null) {
if (! this.store.getFeatureById(id)) {
// note that proper handling of subfeatures requires annotation trackData.json resource to
// set sublistIndex one past last feature array index used by other fields
Expand Down Expand Up @@ -436,7 +431,10 @@ var AnnotTrack = declare( DraggableFeatureTrack,
if (verbose_resize || track.verbose_mousedown) { console.log("AnnotTrack.onAnnotMouseDown called"); }
event = event || window.event;
var elem = (event.currentTarget || event.srcElement);
var featdiv = DraggableFeatureTrack.prototype.getLowestFeatureDiv(elem);
// need to redo getLowestFeatureDiv
// var featdiv = DraggableFeatureTrack.prototype.getLowestFeatureDiv(elem);
var featdiv = track.getLowestFeatureDiv(elem);

if (featdiv && (featdiv != null)) {
if (dojo.hasClass(featdiv, "ui-resizable")) {
if (verbose_resize) {
Expand All @@ -450,9 +448,14 @@ var AnnotTrack = declare( DraggableFeatureTrack,
console.log(featdiv);
}
var scale = track.gview.bpToPx(1);

var gridvals = false;
// if zoomed int to showing sequence residues, then make edge-dragging snap to interbase pixels
if (scale === track.browserParams.charWidth) { var gridvals = [track.browserParams.charWidth, 1]; }
else { var gridvals = false; }

// GAH TODO JBrowse1.7 merge -- restore grid snap when resolve charWidth
// if (scale === track.browserParams.charWidth) { var gridvals = [track.browserParams.charWidth, 1]; }
// else { var gridvals = false; }

$(featdiv).resizable( {
handles: "e, w",
helper: "ui-resizable-helper",
Expand Down Expand Up @@ -534,13 +537,15 @@ var AnnotTrack = declare( DraggableFeatureTrack,
// event.stopPropagation();
},

addToAnnotation: function(annot, feats_to_add) {
/* feature_records ==> { feature: the_feature, track: track_feature_is_from } */
addToAnnotation: function(annot, feature_records) {
var target_track = this;

var subfeats = new Array();
var allSameStrand = 1;
for (var i = 0; i < feats_to_add.length; ++i) {
var feat = feats_to_add[i];
for (var i = 0; i < feature_records.length; ++i) {
var feature_record = feature_records[i];
var feat = feature_record.feature;
var isSubfeature = !! feat.parent(); // !! is shorthand for returning true if value is defined and non-null
var annotStrand = annot.get('strand');
if (isSubfeature) {
Expand All @@ -555,7 +560,7 @@ var AnnotTrack = declare( DraggableFeatureTrack,
subfeats.push(featToAdd);
}
else {
var source_track = feat.track;
var source_track = feature_record.track;
// if (source_track.fields["subfeatures"]) {
if ( feat.get('subfeatures') ) {
// var subs = feat[source_track.fields["subfeatures"]];
Expand Down Expand Up @@ -677,7 +682,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,

createAnnotations: function(selection_records) {
var target_track = this;
var features_nclist = target_track.features;
var featuresToAdd = new Array();
var parentFeatures = new Object();
for (var i in selection_records) {
Expand Down Expand Up @@ -730,33 +734,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,
}
}

/*
{
var source_track = dragfeat.track;
if (this.verbose_create) {
console.log("creating annotation based on feature: ");
console.log(dragfeat);
}
var dragdiv = source_track.getFeatDiv(dragfeat);
var newfeat = JSONUtils.convertToTrack(dragfeat, source_track, target_track);
var source_fields = source_track.fields;
var source_subFields = source_track.subFields;
var target_fields = target_track.fields;
var target_subFields = target_track.subFields;
if (this.verbose_create) {
console.log("local feat conversion: " );
console.log(newfeat);
}
var afeat = JSONUtils.createApolloFeature(source_track.attrs, dragfeat, "transcript");
featuresToAdd.push(afeat);
}
*/

dojo.xhrPost( {
postData: '{ "track": "' + target_track.getUniqueTrackName() + '", "features": ' + JSON.stringify(featuresToAdd) + ', "operation": "add_transcript" }',
url: context_path + "/AnnotationEditorService",
Expand Down Expand Up @@ -861,7 +838,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,

deleteAnnotations: function(selection_records) {
var track = this;
// var features_nclist = track.features;
var features = '"features": [';
var uniqueNames = [];
for (var i in selection_records) {
Expand Down Expand Up @@ -1683,7 +1659,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,

undoSelectedFeatures: function(annots) {
var track = this;
var features_nclist = track.features;
var features = '"features": [';
for (var i in annots) {
var annot = AnnotTrack.getTopLevelAnnotation(annots[i]);
Expand Down Expand Up @@ -1744,7 +1719,6 @@ var AnnotTrack = declare( DraggableFeatureTrack,

redoSelectedFeatures: function(annots) {
var track = this;
var features_nclist = track.features;
var features = '"features": [';
for (var i in annots) {
var annot = AnnotTrack.getTopLevelAnnotation(annots[i]);
Expand Down

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