loom-browser 0.0.4 → 0.0.6

package/dist/loom.esm.js

@@ -9100,6 +9100,72 @@ class SequenceDataSource {
     }
 }
 
+/**
+ * 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.
  *
@@ -9670,6 +9736,11 @@ function createDataSource(config, workerProvider) {
                 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 ─────────────────────────────────────────────────
@@ -10121,6 +10192,9 @@ function dataSourceCacheKey(config) {
             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()}`;
     }
 }
 
@@ -11231,6 +11305,60 @@ class HeadlessGenomeBrowser {
             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 };
@@ -12100,6 +12228,13 @@ class GenomeBrowser extends HeadlessGenomeBrowser {
         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());
@@ -12302,9 +12437,10 @@ class GenomeBrowser extends HeadlessGenomeBrowser {
         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;
         }
@@ -14949,4 +15085,4 @@ function createFeatureSource(config, workerProvider) {
     return { dataSource, trackType, format };
 }
 
-export { AnnotationTrackCanvas, BaseTrackCanvas, BigWigDataSource, BigWigReader, BinaryParser, BrowserEvent, BufferedRangeReader, C2S, ChromAliasDefaults, CommandDispatcher, CommandError, DOMCanvasProvider, DefaultContextMenuProvider, DefaultPopupProvider, EventEmitter, FeatureCache, GeneDataSource, GenomeBrowser, GtxDataSource, GtxReader, HeadlessGenomeBrowser, InteractionTrackCanvas, IntervalTree, LoomBrowserShell, LoomChromosomeSelect, LoomContextMenu, LoomExportControls, LoomInputDialog, LoomLocusInput, LoomNavbar, LoomPopup, LoomWindowSize, LoomZoomControls, MainThreadProvider, NodeWorkerProvider, READY_STATE_OPEN, ROISet, ROI_DEFAULT_COLOR, ROI_USER_DEFINED_COLOR, RemoteConnection, RulerTrackCanvas, SESSION_VERSION, SequenceDataSource, SequenceTrackCanvas, StateProjection, TabixReader, TextFeatureSource, WebWorkerProvider, WigTrackCanvas, addCaseAliases, assembleGFFTranscripts, bufferLocus, cacheCoversViewport, clampLocus, classicThemeCSS, clearBigWigCache, clearGtxCache, commonContextMenuItems, complementBase, complementSequence, computeCumulativeOffsets, computeWigDataRange, createCachedSequence, createDataSource, createFeatureSource, createGenome, createGenomeSync, createShell, createTrackFromConfig, createTrackFromSession, darkRenderTheme, darkSequenceTheme, darkWigTheme, dataSourceCacheKey, decodeBed, decodeBedGraph, decodeBedpe, decodeBroadPeak, decodeGFF3, decodeGFFAttribute, decodeGTF, decodeGappedPeak, decodeGenePred, decodeGenePredExt, decodeInteract, decodeNarrowPeak, decodeRefGeneJson, decodeRefflat, defaultAnnotationRenderConfig, defaultCanvasProvider, defaultInteractionRenderConfig, defaultNucleotideColors, defaultRenderTheme, defaultRulerRenderConfig, defaultSequenceRenderConfig, defaultWigRenderConfig, drawLetterGlyph, fetchBigWigFeatures, fetchBigWigWGFeatures, fetchGeneFeatures, fetchGtxFeatures, fetchGtxMultiFeatures, fetchGtxWGFeatures, fetchRange, fetchSequence, findUTRs, fixBedPE, formatBpLength, formatLocus, fromIgvSession, generateROIId, genomeToChromCoord, getChromLength, getDecoder, getThemeCSS, getTrackCreator, hg38ChromSizes, hg38Genome, inferFormatFromPath, inferIndexURL, inferTrackType, isBinaryFormat, isCoding, isExon, isHiccups, isIntron, isLikelyIndexed, isMainChromosome, isTranscript, isTranscriptPart, isUTR, isWholeGenomeView, knownFileExtensions, knownTrackTypes, lineWigTheme, mainChromosomeNames, mainThreadProvider, matchesSelector, modernRenderTheme, modernSequenceTheme, modernThemeCSS, modernWigTheme, numericDataMenuItems, packFeatures, parseChromSizes, parseColorString, parseFeatures, parseGFFAttributes, parseHeader, parseLocus, parseStrand, positionString, prettyPrintNumber, registerTrackCreator, registerTypeAlias, renderAnnotationTrack, renderDynSeqFeature, renderInteractionTrack, renderLabelAxis, renderQuantitativeAxis, renderROIOverlays, renderRulerTrack, renderSequenceTrack, renderWholeGenomeRuler, renderWigTrack, resolveAnnotationConfig, resolveInteractionConfig, resolveRulerConfig, resolveSequenceConfig, resolveTheme, resolveWigConfig, reverseComplementSequence, roiContextMenuItems, selectTracks, summarizeWigData, toIgvSession, toTrackSelector, translateSequence, translationDict, warmWigTheme };
+export { AnnotationTrackCanvas, BaseTrackCanvas, BigWigDataSource, BigWigReader, BinaryParser, BrowserEvent, BufferedRangeReader, C2S, ChromAliasDefaults, CommandDispatcher, CommandError, DOMCanvasProvider, DefaultContextMenuProvider, DefaultPopupProvider, EventEmitter, FeatureCache, GeneDataSource, GenomeBrowser, GtxDataSource, GtxReader, HeadlessGenomeBrowser, InteractionTrackCanvas, IntervalTree, LoomBrowserShell, LoomChromosomeSelect, LoomContextMenu, LoomExportControls, LoomInputDialog, LoomLocusInput, LoomNavbar, LoomPopup, LoomWindowSize, LoomZoomControls, MainThreadProvider, MemoryDataSource, NodeWorkerProvider, READY_STATE_OPEN, ROISet, ROI_DEFAULT_COLOR, ROI_USER_DEFINED_COLOR, RemoteConnection, RulerTrackCanvas, SESSION_VERSION, SequenceDataSource, SequenceTrackCanvas, StateProjection, TabixReader, TextFeatureSource, WebWorkerProvider, WigTrackCanvas, addCaseAliases, assembleGFFTranscripts, bufferLocus, cacheCoversViewport, clampLocus, classicThemeCSS, clearBigWigCache, clearGtxCache, commonContextMenuItems, complementBase, complementSequence, computeCumulativeOffsets, computeWigDataRange, createCachedSequence, createDataSource, createFeatureSource, createGenome, createGenomeSync, createShell, createTrackFromConfig, createTrackFromSession, darkRenderTheme, darkSequenceTheme, darkWigTheme, dataSourceCacheKey, decodeBed, decodeBedGraph, decodeBedpe, decodeBroadPeak, decodeGFF3, decodeGFFAttribute, decodeGTF, decodeGappedPeak, decodeGenePred, decodeGenePredExt, decodeInteract, decodeNarrowPeak, decodeRefGeneJson, decodeRefflat, defaultAnnotationRenderConfig, defaultCanvasProvider, defaultInteractionRenderConfig, defaultNucleotideColors, defaultRenderTheme, defaultRulerRenderConfig, defaultSequenceRenderConfig, defaultWigRenderConfig, drawLetterGlyph, fetchBigWigFeatures, fetchBigWigWGFeatures, fetchGeneFeatures, fetchGtxFeatures, fetchGtxMultiFeatures, fetchGtxWGFeatures, fetchRange, fetchSequence, findUTRs, fixBedPE, formatBpLength, formatLocus, fromIgvSession, generateROIId, genomeToChromCoord, getChromLength, getDecoder, getThemeCSS, getTrackCreator, hg38ChromSizes, hg38Genome, inferFormatFromPath, inferIndexURL, inferTrackType, isBinaryFormat, isCoding, isExon, isHiccups, isIntron, isLikelyIndexed, isMainChromosome, isTranscript, isTranscriptPart, isUTR, isWholeGenomeView, knownFileExtensions, knownTrackTypes, lineWigTheme, mainChromosomeNames, mainThreadProvider, matchesSelector, modernRenderTheme, modernSequenceTheme, modernThemeCSS, modernWigTheme, numericDataMenuItems, packFeatures, parseChromSizes, parseColorString, parseFeatures, parseGFFAttributes, parseHeader, parseLocus, parseStrand, positionString, prettyPrintNumber, registerTrackCreator, registerTypeAlias, renderAnnotationTrack, renderDynSeqFeature, renderInteractionTrack, renderLabelAxis, renderQuantitativeAxis, renderROIOverlays, renderRulerTrack, renderSequenceTrack, renderWholeGenomeRuler, renderWigTrack, resolveAnnotationConfig, resolveInteractionConfig, resolveRulerConfig, resolveSequenceConfig, resolveTheme, resolveWigConfig, reverseComplementSequence, roiContextMenuItems, selectTracks, summarizeWigData, toIgvSession, toTrackSelector, translateSequence, translationDict, warmWigTheme };