loom-browser 0.0.15 → 0.0.17

package/dist/loom.esm.js

@@ -22998,60 +22998,62 @@ function createFallbackProvider(primary, fallback) {
 /**
  * Resolve a sequence provider from config.
  *
- * Exactly one sequence source must be set. Throws if multiple are provided.
- * Sources: sequenceProvider, twoBitURL, fastaURL, ucscGenome.
- * When none is set, falls back to UCSC API via `id` if available.
+ * If a custom `sequenceProvider` is set, it is used directly. Otherwise,
+ * all available sources (twoBitURL, fastaURL, ucscGenome/id) are chained
+ * as a prioritized fallback list:
  *
- * When twoBitURL is used and a genome ID is available, the UCSC REST API is
- * automatically added as a fallback — if the 2-bit server is unreachable,
- * the API is tried instead.
+ *   1. twoBitURL  — most efficient (binary range requests)
+ *   2. fastaURL   — reliable CDN fallback (igv.org hosts FASTA for common genomes)
+ *   3. UCSC API   — last resort (api.genome.ucsc.edu REST endpoint)
+ *
+ * This mirrors igv.js genomes3.json which provides both twoBitURL and fastaURL
+ * for common genomes. On networks where one server is unreachable (e.g.,
+ * hgdownload.soe.ucsc.edu blocked but igv.org reachable), the chain
+ * automatically falls through to the next available source.
  */
 function resolveSequenceProvider(config) {
-    var _a, _b;
-    const sources = [
-        config.sequenceProvider && 'sequenceProvider',
-        config.twoBitURL && 'twoBitURL',
-        config.fastaURL && 'fastaURL',
-        config.ucscGenome && 'ucscGenome',
-    ].filter(Boolean);
-    if (sources.length > 1) {
-        throw new Error(`GenomeConfig has multiple sequence sources: ${sources.join(', ')}. ` +
-            'Set exactly one of: sequenceProvider, twoBitURL, fastaURL, or ucscGenome.');
-    }
+    var _a;
+    // Custom provider — use directly, no chaining
     if (config.sequenceProvider) {
         return config.sequenceProvider;
     }
+    // Build prioritized provider list from available config fields
+    const providers = [];
     if (config.twoBitURL) {
-        const primary = createTwoBitSequenceProvider(config.twoBitURL, config.fetchImpl);
-        // Add UCSC REST API fallback when a genome ID is known
-        const genomeId = (_a = config.ucscGenome) !== null && _a !== void 0 ? _a : config.id;
-        if (genomeId) {
-            const fallback = (locus, signal) => fetchSequence(locus, { genome: genomeId }, signal);
-            return createCachedSequence(createFallbackProvider(primary, fallback));
-        }
-        return createCachedSequence(primary);
+        providers.push(createTwoBitSequenceProvider(config.twoBitURL, config.fetchImpl));
     }
     if (config.fastaURL) {
-        return createCachedSequence(createFastaSequenceProvider(config.fastaURL, config.indexURL, config.compressedIndexURL, config.fetchImpl));
+        providers.push(createFastaSequenceProvider(config.fastaURL, config.indexURL, config.compressedIndexURL, config.fetchImpl));
     }
-    // UCSC API — explicit ucscGenome, or implicit via id
-    const ucscGenome = (_b = config.ucscGenome) !== null && _b !== void 0 ? _b : config.id;
+    const ucscGenome = (_a = config.ucscGenome) !== null && _a !== void 0 ? _a : config.id;
     if (ucscGenome) {
-        return createCachedSequence((locus, signal) => fetchSequence(locus, { genome: ucscGenome }, signal));
+        providers.push((locus, signal) => fetchSequence(locus, { genome: ucscGenome }, signal));
     }
-    return undefined;
+    if (providers.length === 0)
+        return undefined;
+    if (providers.length === 1)
+        return createCachedSequence(providers[0]);
+    // Chain all providers: try each in order, fall back on failure
+    const chained = providers.reduceRight((fallback, primary) => createFallbackProvider(primary, fallback));
+    return createCachedSequence(chained);
 }
 // ─── Pre-built singletons ��─────────��─────────────────────────────────────────
 /**
- * Pre-built hg38 genome with 2-bit sequence (UCSC API fallback).
+ * Pre-built hg38 genome with triple-fallback sequence chain.
  *
  * This is the default genome used by HeadlessGenomeBrowser when no genome
- * is specified. Matches igv.js's default behavior: 2-bit file as primary
- * sequence source, with UCSC REST API as automatic fallback for resilience.
+ * is specified. Sequence sources are tried in order:
+ *   1. 2-bit from hgdownload.soe.ucsc.edu (most efficient, binary range requests)
+ *   2. Indexed FASTA from igv.org (reliable CDN, reachable on restricted networks)
+ *   3. UCSC REST API from api.genome.ucsc.edu (last resort)
+ *
+ * URLs match igv.js genomes3.json configuration for hg38.
  */
 const hg38Genome = createGenomeSync({
     id: 'hg38',
     twoBitURL: 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit',
+    fastaURL: 'https://igv.org/genomes/data/hg38/hg38.fa',
+    indexURL: 'https://igv.org/genomes/data/hg38/hg38.fa.fai',
     chromSizes: hg38ChromSizes,
 });
 
@@ -29889,6 +29891,14 @@ class HeadlessGenomeBrowser {
         }
         return matches.length;
     }
+    /** Merge partial render config into all tracks matching a selector. Returns the number of tracks updated. */
+    updateTrackConfig(selector, config) {
+        const matches = selectTracks(this.managedTracks, selector);
+        for (const mt of matches) {
+            mt.track.setConfig(config);
+        }
+        return matches.length;
+    }
     // ─── Navigation ──────────────────────────────────────────────────────────
     /** Update the locus and re-render all tracks. Clamped to chromosome bounds. Operates on primary frame. */
     setLocus(locus) {
@@ -31005,6 +31015,11 @@ class CommandDispatcher {
                     results.push({ action: 'update_metadata', success: count > 0, count });
                     break;
                 }
+                case 'update_config': {
+                    const count = this.browser.updateTrackConfig(toTrackSelector(action.selector), action.config);
+                    results.push({ action: 'update_config', success: count > 0, count });
+                    break;
+                }
                 default:
                     results.push({
                         action: action.action,