igv 3.0.3 → 3.0.5

package/dist/igv.esm.js

@@ -25216,9 +25216,7 @@ class GFFHelper {
         } else {
             combinedFeatures = this.combineFeaturesByType(features);
         }
-        combinedFeatures.sort(function (a, b) {
-            return a.start - b.start
-        });
+
         this.numberExons(combinedFeatures, genomicInterval);
         this.nameFeatures(combinedFeatures);
         return combinedFeatures
@@ -29775,20 +29773,30 @@ class FeatureFileReader {
             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() {
@@ -29960,9 +29968,6 @@ class FeatureFileReader {
                 await this._parse(allFeatures, dataWrapper, chr, end, start);
 
             }
-            allFeatures.sort(function (a, b) {
-                return a.start - b.start
-            });
 
             return allFeatures
         }
@@ -29992,8 +29997,13 @@ class FeatureFileReader {
 
         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) {
@@ -30002,26 +30012,21 @@ class FeatureFileReader {
             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);
                 }
             }
         }
@@ -34495,7 +34500,11 @@ function renderFeatureLabel(ctx, feature, featureX, featureX1, featureY, referen
         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") {
@@ -34774,7 +34783,6 @@ class FeatureTrack extends TrackBase {
         displayMode: "EXPANDED", // COLLAPSED | EXPANDED | SQUISHED
         margin: 10,
         featureHeight: 14,
-        autoHeight: false,
         useScore: false
     }
 
@@ -35306,7 +35314,8 @@ function monitorTrackDrag(track) {
 
     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();
         }
     }
 
@@ -39596,6 +39605,10 @@ class DynamicFeatureSource {
         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];
+            }
         }
     }
 }
@@ -43043,7 +43056,7 @@ class TrackView {
         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
@@ -67608,8 +67621,6 @@ class VariantTrack extends TrackBase {
                 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();
@@ -68030,13 +68041,8 @@ class QTLTrack extends TrackBase {
         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);
     }
 
@@ -70515,7 +70521,7 @@ function createReferenceFrameList(loci, genome, browserFlanking, minimumBases, v
     })
 }
 
-const _version = "3.0.3";
+const _version = "3.0.5";
 function version() {
     return _version
 }
@@ -72065,9 +72071,16 @@ class ROIMenu {
                 '<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();
                     }
                 }
             );
@@ -72595,6 +72608,10 @@ class ROIManager {
         return this.roiSets.find(roiSet => true === roiSet.isUserDefined)
     }
 
+    deleteUserDefinedROISet(){
+        this.roiSets = this.roiSets.filter(roiSet => roiSet.isUserDefined !== true);
+    }
+    
     initializeUserDefinedROISet() {
 
         const config =
@@ -72610,15 +72627,8 @@ class ROIManager {
     }
 
     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) {
@@ -72628,23 +72638,6 @@ class ROIManager {
 
     }
 
-    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())
     }
@@ -74619,7 +74612,7 @@ class Browser {
      */
     async loadGenome(idOrConfig) {
 
-        if(idOrConfig.genarkAccession) {
+        if (idOrConfig.genarkAccession) {
             idOrConfig.url = convertToHubURL(idOrConfig.genarkAccession);
         }
 
@@ -75915,7 +75908,7 @@ class Browser {
 
         if (dragObject && dragObject.viewport.referenceFrame.start !== dragObject.start) {
             this.updateViews();
-            this.fireEvent('trackdragend');
+            this.fireEvent('trackdragend', [dragObject.viewport]);
         }
     }