Cleanup some request logic that makes pairing better

GMOD · Nov 18, 2018 · ff65ec4 · ff65ec4
1 parent 2c8823a
commit ff65ec4
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Showing 2 changed files with 25 additions and 22 deletions.
diff --git a/src/JBrowse/Store/SeqFeature/BAM.js b/src/JBrowse/Store/SeqFeature/BAM.js
@@ -237,6 +237,7 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
         let seqName = query.ref || this.refSeq.name
         seqName = this.browser.regularizeReferenceName( seqName );
         const pairCache = {};
+        console.log(query)
 
         this.bam.getRecordsForRange(seqName, query.start, query.end, {viewAsPairs: query.viewAsPairs})
             .then(records => {
@@ -260,14 +261,13 @@ return declare( [ SeqFeatureStore, DeferredStatsMixin, DeferredFeaturesMixin, In
                                 pairCache[name] = feat
                             }
                         }
-                        else {
+                        else if(!(records[i].get('end') < query.start) && !(records[i].get('start') > query.end)){
                             let feat = this._bamRecordToFeature(records[i])
                             featCallback(feat)
                         }
                     }
-                    console.log(Object.keys(this.featureCache).length)
                     Object.entries(this.featureCache).forEach(([k, v]) => {
-                        if(v.get('end') - v.get('start') < 10000) {
+                        if(v.get('end') - v.get('start') < 10000 && (v.get('end') > query.start && v.get('start') < query.end)) {
                             featCallback(v)
                         }
                     })

diff --git a/src/JBrowse/View/Track/Alignments2.js b/src/JBrowse/View/Track/Alignments2.js
@@ -17,6 +17,10 @@ define( [
 
 return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
 
+    constructor: function() {
+        this.fetchMap = {}
+    },
+
     _defaultConfig: function() {
         var c = Util.deepUpdate(
             dojo.clone( this.inherited(arguments) ),
@@ -144,25 +148,24 @@ return declare( [ CanvasFeatureTrack, AlignmentsMixin ], {
     fillBlock: function( args ) {
         if(this.config.viewAsPairs) {
             let supermethod = this.getInherited(arguments)
-            var initial = new Promise((resolve, reject) => {
-                var reg = this.browser.view.visibleRegion()
-                var len = reg.end - reg.start
-                console.log(len)
-                const region = {
-                    ref: this.refSeq.name,
-                    start: Math.max( 0, reg.start ),
-                    end: reg.end,
-                    viewAsPairs: true
-                }
-                region.start = Math.max( 0, region.start )
-                region.end = region.end
-
-                this.store.getPairedRanges(region, range => {
-                    region.start = range.min
-                    region.end = range.max
-                    this.store.getFeatures(region, function() {}, resolve, reject)
-                }, reject)
-            }).then(() => {
+            var reg = this.browser.view.visibleRegion()
+            var len = reg.end - reg.start
+            const region = {
+                ref: this.refSeq.name,
+                start: Math.max( 0, reg.start ),
+                end: reg.end,
+                viewAsPairs: true
+            }
+
+            const min = Math.max(0, region.start - len*4)
+            const max = region.end + len*4
+            const str = min + '_' + max
+            if(!this.fetchMap[str]) {
+                this.fetchMap[str] = new Promise((resolve, reject) => {
+                    this.store.getFeatures({ ref: this.refSeq.name, start: min, end: max, viewAsPairs: true }, () => { /* do nothing */}, resolve, reject)
+                })
+            }
+            this.fetchMap[str].then(() => {
                 supermethod.apply(this, [args])
             })
         } else {