storage class for single nucleotide sequence density

js/Store/SeqFeature/NucDensStore.js

@@ -0,0 +1,73 @@
+define( 'NucleotideDensityPlugin/Store/SeqFeature/NucDensStore', [
+ 'dojo/_base/declare',
+ 'dojo/_base/array',
+ 'JBrowse/Store/SeqFeature',
+ 'JBrowse/Util',
+ 'JBrowse/Model/CoverageFeature'
+],
+function(
+ declare,
+ array,
+ SeqFeatureStore,
+ Util,
+ CoverageFeature
+){
+ /**
+ This class is almost identitical to GCContent class published by Colin
+ for the GCContent Plugin ()
+ This store class is for a single nucleotide context
+ */
+ return declare(SeqFeatureStore,{
+ constuctor: function(args){
+ this.store = args.store;
+ this.windowSize = args.windowSize;
+ this.windowDelta = args.windowDelta;
+ this.nucLength = args.nLength;
+ this.nuc = args.nuc; // array of nucleotide sequence contexts to look for
+ // note: all possibilities in nuc must be the same length - nucLength
+ },
+
+ getGlobalStats: function(callback, errorCallback){
+ callback({});
+ },
+
+ getFeatures: function(query, featureCallback, finishCallback, errorCallback){
+ // generate features
+ var hw = this.windowSize / 2; // Half the window size
+ query.start = Math.max(0, query.start - hw);
+ query.end = Math.min(query.end + hw, this.browser.refSeq.length);
+ var thisB = this;
+
+ if (query.end < 0 || query.start > query.end) {
+ finishCallback();
+ return;
+ }
+
+ this.store.getReferenceSequence(query, function(residues) {
+ for (var i = hw; i < residues.length - hw; i += thisB.windowDelta) {
+ var r = residues.slice(i - hw, i + hw);
+ var rn = r.length - thisB.nucLength;
+ var count = 0
+ for (var j = 0; j <= rn; j++) {
+ var rs = r.slice(j, j+thisB.nucLength);
+ if( array.indexOf(thisB.nuc, rs.toUpperCase()) !== -1 )
+ count ++;
+ }
+ var pos = query.start;
+ var score = count / rn;
+
+ var feat = new CoverageFeature({
+ start: pos + i,
+ end: pos + i + thisB.windowDelta,
+ score: score
+ });
+ featureCallback(feat);
+ }
+ finishCallback();
+ },
+ finishCallback,
+ errorCallback);
+ }
+
+ });
+});