igv 3.0.3 → 3.0.5

package/dist/igv.js

@@ -25222,9 +25222,7 @@
             } else {
                 combinedFeatures = this.combineFeaturesByType(features);
             }
-            combinedFeatures.sort(function (a, b) {
-                return a.start - b.start
-            });
+
             this.numberExons(combinedFeatures, genomicInterval);
             this.nameFeatures(combinedFeatures);
             return combinedFeatures
@@ -29781,20 +29779,30 @@
                 await this.readHeader();
             }
 
+            let allFeatures;
             const index = await this.getIndex();
             if (index) {
                 this.indexed = true;
-                return this.loadFeaturesWithIndex(chr, start, end)
+                allFeatures = await this.loadFeaturesWithIndex(chr, start, end);
             } else if (this.dataURI) {
                 this.indexed = false;
-                return this.loadFeaturesFromDataURI()
+                allFeatures = await this.loadFeaturesFromDataURI();
             } else if ("service" === this.config.sourceType) {
-                return this.loadFeaturesFromService(chr, start, end)
+                allFeatures = await this.loadFeaturesFromService(chr, start, end);
             } else {
                 this.indexed = false;
-                return this.loadFeaturesNoIndex()
+                allFeatures = await this.loadFeaturesNoIndex();
             }
 
+            allFeatures.sort(function (a, b) {
+                if (a.chr === b.chr) {
+                    return a.start - b.start
+                } else {
+                    return a.chr.localeCompare(b.chr)
+                }
+            });
+
+            return allFeatures
         }
 
         async readHeader() {
@@ -29966,9 +29974,6 @@
                     await this._parse(allFeatures, dataWrapper, chr, end, start);
 
                 }
-                allFeatures.sort(function (a, b) {
-                    return a.start - b.start
-                });
 
                 return allFeatures
             }
@@ -29998,8 +30003,13 @@
 
             let features = await this.parser.parseFeatures(dataWrapper);
 
-            // Filter psuedo-features (e.g. created mates for VCF SV records)  TODO why?
-            //slicedFeatures = slicedFeatures.filter(f => f._f === undefined)
+            features.sort(function (a, b) {
+                if (a.chr === b.chr) {
+                    return a.start - b.start
+                } else {
+                    return a.chr.localeCompare(b.chr)
+                }
+            });
 
             // Filter features not in requested range.
             if (undefined === chr) {
@@ -30008,26 +30018,21 @@
                 let inInterval = false;
                 for (let i = 0; i < features.length; i++) {
                     const f = features[i];
-                    if (f.chr !== chr) {
-                        if (allFeatures.length === 0) {
-                            continue  //adjacent chr to the left
-                        } else {
-                            break //adjacent chr to the right
+                    if (f.chr === chr) {
+                        if (f.start > end) {
+                            allFeatures.push(f);  // First feature beyond interval
+                            break
                         }
-                    }
-                    if (f.start > end) {
-                        allFeatures.push(f);  // First feature beyond interval
-                        break
-                    }
-                    if (f.end >= start && f.start <= end) {
-                        // All this to grab first feature before start of interval.  Needed for some track renderers, like line plot
-                        if (!inInterval) {
-                            inInterval = true;
-                            if (i > 0) {
-                                allFeatures.push(features[i - 1]);
+                        if (f.end >= start && f.start <= end) {
+                            // All this to grab first feature before start of interval.  Needed for some track renderers, like line plot
+                            if (!inInterval) {
+                                inInterval = true;
+                                if (i > 0) {
+                                    allFeatures.push(features[i - 1]);
+                                }
                             }
+                            allFeatures.push(f);
                         }
-                        allFeatures.push(f);
                     }
                 }
             }
@@ -34501,7 +34506,11 @@
             if (name === undefined) name = feature.id || feature.ID;
             if (!name || name === '.') return
 
-            let centerX = (featureX + featureX1) / 2;
+            let pixelXOffset = options.pixelXOffset || 0;
+            const t1 = Math.max(featureX, -pixelXOffset);
+            const t2 = Math.min(featureX1, -pixelXOffset + options.viewportWidth);
+            let centerX = (t1 + t2) / 2;
+            //let centerX = (featureX + featureX1) / 2
 
             let transform;
             if (this.displayMode === "COLLAPSED" && this.labelDisplayMode === "SLANT") {
@@ -34780,7 +34789,6 @@
             displayMode: "EXPANDED", // COLLAPSED | EXPANDED | SQUISHED
             margin: 10,
             featureHeight: 14,
-            autoHeight: false,
             useScore: false
         }
 
@@ -35312,7 +35320,8 @@
 
         function onDragEnd() {
             if (track.trackView && track.displayMode !== "SQUISHED") {
-                track.trackView.updateViews();      // TODO -- refine this to the viewport that was dragged after DOM refactor
+                // Repaint views to adjust feature name if center is moved out of view
+                track.trackView.repaintViews();
             }
         }
 
@@ -39602,6 +39611,10 @@
             if (this.featureMap[chr]) {
                 const match = `${chr}-${start}-${end}`;
                 this.featureMap[chr] = this.featureMap[chr].filter(feature => match !== `${feature.chr}-${feature.start}-${feature.end}`);
+                // Check if featureMap for a specific chromosome is empty now and delete it if yes
+                if (this.featureMap[chr].length === 0) {
+                    delete this.featureMap[chr];
+                }
             }
         }
     }
@@ -43049,7 +43062,7 @@
             const viewportsToRepaint = visibleViewports.filter(vp => vp.needsRepaint()).filter(viewport => viewport.checkZoomIn());
 
             // Get viewports that require a data load
-            const viewportsToReload = viewportsToRepaint.filter(viewport => viewport.needsReload());
+            const viewportsToReload = visibleViewports.filter(viewport => viewport.checkZoomIn()).filter(viewport => viewport.needsReload());
 
             // Trigger viewport to load features needed to cover current genomic range
             // NOTE: these must be loaded synchronously, do not user Promise.all,  not all file readers are thread safe
@@ -67614,8 +67627,6 @@
                     this.trackView.setTrackHeight(this.config.height || CNVPytorTrack.DEFAULT_TRACK_HEIGHT);
                     this.trackView.checkContentHeight();
                     this.trackView.updateViews();
-                    this.trackView.track.autoHeight = false;
-
 
                 } finally {
                     this.trackView.stopSpinner();
@@ -68036,13 +68047,8 @@
             this.divider = config.divider || "rgb(225,225,225)";
             this.dotSize = config.dotSize || 2;
             this.height = config.height || 100;
-            this.autoHeight = false;
             this.disableButtons = config.disableButtons;
 
-            // Limit visibility window to 2 mb,  gtex server gets flaky beyond that
-            //this.visibilityWindow = config.visibilityWindow === undefined ?
-            //    2000000 : config.visibilityWindow >= 0 ? Math.min(2000000, config.visibilityWindow) : 2000000
-
             this.featureSource = FeatureSource(config, this.browser.genome);
         }
 
@@ -70521,7 +70527,7 @@
         })
     }
 
-    const _version = "3.0.3";
+    const _version = "3.0.5";
     function version() {
         return _version
     }
@@ -72071,9 +72077,16 @@
                     '<hr/>',
                     {
                         label: 'Delete',
-                        click: () => {
-                            this.browser.roiManager.deleteRegionWithKey(regionElement.dataset.region, this.browser.columnContainer);
-                            this.browser.roiManager.repaintTable();
+                        click: async () => {
+                            roiSet.removeFeature(feature);
+                            const userDefinedFeatures = await roiSet.getAllFeatures();
+                            
+                            // Delete user defined ROI Set if it is empty
+                            if (Object.keys(userDefinedFeatures).length === 0) {
+                                roiManager.deleteUserDefinedROISet();
+                            }
+                            roiManager.deleteRegionWithKey(regionElement.dataset.region, columnContainer);
+                            roiManager.repaintTable();
                         }
                     }
                 );
@@ -72601,6 +72614,10 @@
             return this.roiSets.find(roiSet => true === roiSet.isUserDefined)
         }
 
+        deleteUserDefinedROISet(){
+            this.roiSets = this.roiSets.filter(roiSet => roiSet.isUserDefined !== true);
+        }
+        
         initializeUserDefinedROISet() {
 
             const config =
@@ -72616,15 +72633,8 @@
         }
 
         async deleteRegionWithKey(regionKey, columnContainer) {
-
             columnContainer.querySelectorAll(createSelector(regionKey)).forEach(node => node.remove());
 
-            const {feature, set} = await this.findRegionWithKey(regionKey);
-
-            if (set) {
-                set.removeFeature(feature);
-            }
-
             const records = await this.getTableRecords();
 
             if (0 === records.length) {
@@ -72634,23 +72644,6 @@
 
         }
 
-        async findRegionWithKey(regionKey) {
-
-            const {chr, start, end} = parseRegionKey(regionKey);
-
-            for (let set of this.roiSets) {
-                const features = await set.getFeatures(chr, start, end);
-
-                for (let feature of features) {
-                    if (feature.chr === chr && feature.start >= start && feature.end <= end) {
-                        return {feature, set}
-                    }
-                }
-            }
-
-            return {feature: undefined, set: undefined}
-        }
-
         toJSON() {
             return this.roiSets.map(roiSet => roiSet.toJSON())
         }
@@ -74625,7 +74618,7 @@
          */
         async loadGenome(idOrConfig) {
 
-            if(idOrConfig.genarkAccession) {
+            if (idOrConfig.genarkAccession) {
                 idOrConfig.url = convertToHubURL(idOrConfig.genarkAccession);
             }
 
@@ -75921,7 +75914,7 @@
 
             if (dragObject && dragObject.viewport.referenceFrame.start !== dragObject.start) {
                 this.updateViews();
-                this.fireEvent('trackdragend');
+                this.fireEvent('trackdragend', [dragObject.viewport]);
             }
         }