loom-browser 0.0.4 → 0.0.6

package/dist/loom.js

@@ -9102,6 +9102,72 @@
         }
     }
 
+    /**
+     * DataSource backed by an in-memory feature array.
+     *
+     * Wraps a pre-loaded feature array in a FeatureCache for spatial queries,
+     * enabling inline features to flow through the same data lifecycle as
+     * URL-based data sources.
+     *
+     * Layer 1 (Data + Layout): no DOM, no canvas.
+     */
+    /**
+     * DataSource that serves features from an in-memory array.
+     *
+     * Features are indexed in a FeatureCache on construction for efficient
+     * spatial queries. Calling `setFeatures()` replaces the cache entirely.
+     */
+    class MemoryDataSource {
+        constructor(features) {
+            this.cache = new FeatureCache(features);
+        }
+        /** Replace the in-memory features and rebuild the spatial index. */
+        setFeatures(features) {
+            this.cache = new FeatureCache(features);
+        }
+        /** Set a chromosome name resolver for alias resolution. */
+        setChromNameResolver(resolver) {
+            this._resolveChromName = resolver;
+        }
+        /** Set cumulative offsets for whole genome view coordinate transformation. */
+        setCumulativeOffsets(offsets) {
+            this._cumulativeOffsets = offsets;
+        }
+        async fetch(locus, _bpPerPixel, _signal) {
+            if (isWholeGenomeView(locus) && this._cumulativeOffsets) {
+                return this.fetchWG();
+            }
+            const chr = this._resolveChromName
+                ? this._resolveChromName(locus.chr)
+                : locus.chr;
+            return this.cache.queryFeatures(chr, locus.start, locus.end);
+        }
+        fetchWG() {
+            const offsets = this._cumulativeOffsets;
+            const chrNames = mainChromosomeNames(Object.fromEntries(offsets.chromosomeNames.map(name => { var _a; return [name, (_a = offsets.offsets[name]) !== null && _a !== void 0 ? _a : 0]; })));
+            const wgFeatures = [];
+            const allByChrom = this.cache.getAllFeatures();
+            for (const chr of chrNames) {
+                const features = allByChrom[chr];
+                if (!features)
+                    continue;
+                const offset = offsets.offsets[chr];
+                if (offset === undefined)
+                    continue;
+                for (const f of features) {
+                    wgFeatures.push({
+                        ...f,
+                        chr: 'all',
+                        start: offset + f.start,
+                        end: offset + f.end,
+                    });
+                }
+            }
+            wgFeatures.sort((a, b) => a.start - b.start);
+            return wgFeatures;
+        }
+    }
+
     /**
      * Stateless renderer for interaction (arc/BEDPE) tracks.
      *
@@ -9672,6 +9738,11 @@
                     indexed: config.indexed,
                     workerProvider,
                 });
+            case 'memory':
+                // Memory data sources are created directly with features by the caller.
+                // This path is only hit during session restore, where in-memory features
+                // are not available — return an empty MemoryDataSource as a placeholder.
+                return new MemoryDataSource([]);
         }
     }
     // ─── Built-in track creators ─────────────────────────────────────────────────
@@ -10123,6 +10194,9 @@
                 return `ucsc:${(_b = config.genome) !== null && _b !== void 0 ? _b : ''}:${(_c = config.track) !== null && _c !== void 0 ? _c : ''}`;
             case 'text':
                 return `text:${config.url}:${(_d = config.format) !== null && _d !== void 0 ? _d : ''}:${(_e = config.indexURL) !== null && _e !== void 0 ? _e : ''}`;
+            case 'memory':
+                // Each memory data source is unique — no deduplication.
+                return `memory:${Math.random()}`;
         }
     }
 
@@ -11233,6 +11307,60 @@
                 this.managedTracks[this.managedTracks.length - 1].metadata = options.metadata;
             return track;
         }
+        /** Add a BigWig-style signal track backed by in-memory features (no URL required). */
+        addWigTrackWithFeatures(features, options) {
+            const { canvas } = this.canvasProvider.createCanvas(0, 0);
+            const track = new WigTrackCanvas(canvas, {
+                locus: this._locus,
+                features: [],
+                config: options === null || options === void 0 ? void 0 : options.config,
+                height: options === null || options === void 0 ? void 0 : options.height,
+                background: options === null || options === void 0 ? void 0 : options.background,
+                theme: this.theme,
+                canvasProvider: this.canvasProvider,
+                name: options === null || options === void 0 ? void 0 : options.name,
+                sequenceProvider: this.sequenceProvider,
+            });
+            const dataSource = new MemoryDataSource(features);
+            if (this.cumulativeOffsets) {
+                dataSource.setCumulativeOffsets(this.cumulativeOffsets);
+            }
+            if (this.genome) {
+                dataSource.setChromNameResolver(alias => this.genome.getChromosomeName(alias));
+            }
+            const dataSourceConfig = { type: 'memory' };
+            this.addTrack(track, dataSource, dataSourceConfig, options === null || options === void 0 ? void 0 : options.maxTrackHeight);
+            if (options === null || options === void 0 ? void 0 : options.metadata)
+                this.managedTracks[this.managedTracks.length - 1].metadata = options.metadata;
+            return track;
+        }
+        /** Add a BED/annotation track backed by in-memory features (no URL required). Features must include `chr`. */
+        addBedTrackWithFeatures(features, options) {
+            const { canvas } = this.canvasProvider.createCanvas(0, 0);
+            const track = new AnnotationTrackCanvas(canvas, {
+                locus: this._locus,
+                features: [],
+                config: options === null || options === void 0 ? void 0 : options.config,
+                height: options === null || options === void 0 ? void 0 : options.height,
+                background: options === null || options === void 0 ? void 0 : options.background,
+                theme: this.theme,
+                canvasProvider: this.canvasProvider,
+                workerProvider: this.workerProvider,
+                name: options === null || options === void 0 ? void 0 : options.name,
+            });
+            const dataSource = new MemoryDataSource(features);
+            if (this.cumulativeOffsets) {
+                dataSource.setCumulativeOffsets(this.cumulativeOffsets);
+            }
+            if (this.genome) {
+                dataSource.setChromNameResolver(alias => this.genome.getChromosomeName(alias));
+            }
+            const dataSourceConfig = { type: 'memory' };
+            this.addTrack(track, dataSource, dataSourceConfig, options === null || options === void 0 ? void 0 : options.maxTrackHeight);
+            if (options === null || options === void 0 ? void 0 : options.metadata)
+                this.managedTracks[this.managedTracks.length - 1].metadata = options.metadata;
+            return track;
+        }
         /** Add a DNA/RNA sequence track. Data fetching is handled automatically via the genome's sequence provider. */
         addSequenceTrack(options) {
             const trackConfig = { type: 'sequence', config: options === null || options === void 0 ? void 0 : options.config };
@@ -12102,6 +12230,13 @@
             this.events.on(BrowserEvent.DataLoaded, ({ track }) => {
                 this.updateAxisContent(track);
             });
+            // Repaint axis canvases when theme changes (track canvases update via
+            // track.setTheme(), but axis sidebar is managed here in GenomeBrowser).
+            this.events.on(BrowserEvent.ThemeChanged, () => {
+                for (const mt of this.managedTracks) {
+                    this.updateAxisContent(mt.track);
+                }
+            });
             // Re-render ROI overlays when ROIs change or viewport moves
             this.events.on(BrowserEvent.ROIAdded, () => this.renderROIOverlays());
             this.events.on(BrowserEvent.ROIRemoved, () => this.renderROIOverlays());
@@ -12304,9 +12439,10 @@
             const { axisDiv } = entry;
             const rawInfo = (_a = track.getAxisInfo) === null || _a === void 0 ? void 0 : _a.call(track);
             if (!rawInfo) {
-                // No axis info — clear content and hide border (e.g., ruler tracks)
+                // No axis info — keep the column for alignment but clear content
                 axisDiv.innerHTML = "";
                 axisDiv.style.borderRight = "none";
+                axisDiv.style.backgroundColor = this.theme.palette.background;
                 entry.axisCanvas = null;
                 return;
             }
@@ -14985,6 +15121,7 @@ tr.border-top td {
     exports.LoomWindowSize = LoomWindowSize;
     exports.LoomZoomControls = LoomZoomControls;
     exports.MainThreadProvider = MainThreadProvider;
+    exports.MemoryDataSource = MemoryDataSource;
     exports.NodeWorkerProvider = NodeWorkerProvider;
     exports.READY_STATE_OPEN = READY_STATE_OPEN;
     exports.ROISet = ROISet;