mutli store

js/Store/SeqFeature/NucleotideDensityStore.js

@@ -0,0 +1,115 @@
+define( 'NucleotideDensityPlugin/Store/SeqFeature/NucleotideDensityStore', [
+ 'dojo/_base/declare',
+ 'dojo/_base/array',
+ 'dojo/_base/lang',
+ 'dojo/promise/all',
+ 'JBrowse/Store/SeqFeature',
+ 'JBrowse/Util',
+ 'NucletotideDensityPlugin/Store/Util',
+ 'NucleotideDensityPlugin/Store/SeqFeature/NucDensStore'
+],
+function(
+ declare,
+ array,
+ lang,
+ all,
+ SeqFeatureStore,
+ Util,
+ storeUtil,
+ NucDens
+){
+ /**
+ This class is similar to the bigwig storage class used in MethylationPlugin
+ Used to store multiple storage tracks, one for each sequence context
+ */
+ return declare(SeqFeatureStore,{
+ constuctor: function(args){
+ var thisB = this;
+ this.windowSize = args.windowSize;
+ this.windowDelta = args.windowDelta;
+ if(args.config.context == undefined )
+ this.config.context = ['CG', 'CHG', 'CHH'];
+ else
+ this.config.context = array.map(args.config.context, function(x){ x.toUpperCase()});
+ // get prep info
+ var contextInfo = array.map(this.config.context, function(ctx){
+ return {name: ctx, nuc: storeUtil.getPossibilities(ctx), nLength:ctx.length};
+ })
+
+ // get storage classes
+ this.stores = array.map(contextInfo, function(ctx){
+ return new NucDens( lang.mixin(args, ctx));
+ });
+
+ // get the features
+ all( array.map( this.stores, function(store) {
+ return store._deferred.features
+ })).then( function() {
+ thisB._deferred.features.resolve({success: true});
+ },
+ lang.hitch( this, '_failAllDeferred' )
+ );
+ },
+
+ getGlobalStats: function(callback, errorCallback){
+ callback({});
+ },
+ getRegionStats: function(query, callback, errorCallback){
+ callback({});
+ },
+
+ _getFeatures( query, featureCallback, endCallback, errorCallback){
+ var thisB = this;
+ var finished = 0;
+ var finishCallback = function() {
+ if(thisB.stores.length == ++finished) {
+ endCallback();
+ }
+ }
+ array.forEach( this.stores, function(store) {
+ store._getFeatures( query,
+ featureCallback, finishCallback, errorCallback
+ );
+ });
+ }
+
+ /*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);
+ }*/
+
+ });
+});