jbrowse-plugin-msaview 2.6.5 → 2.6.7

package/dist/AddHighlightModel/MsaToGenomeHighlight.js

@@ -8,10 +8,15 @@ const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, })
     const msaView = views
         .filter(isMsaView)
         .find(v => v.connectedViewId === model.id);
-    const highlights = msaView?.connectedHighlights;
-    // Suppress codon highlight while hovering the LGV — GenomeMouseoverHighlight
-    // handles the single-bp display in that case
-    return !hasHoverPosition(hovered) && highlights?.length ? (React.createElement(MsaToGenomeHighlightRenderer, { model: model, highlights: highlights })) : null;
+    // The persistent click selection always shows. The hover codon is suppressed
+    // while hovering the LGV — GenomeMouseoverHighlight handles the single-bp
+    // display in that case, so we don't stack a wider codon band on top of it.
+    const clickHighlight = msaView?.connectedClickHighlight;
+    const hoverHighlight = hasHoverPosition(hovered)
+        ? undefined
+        : msaView?.connectedHoverHighlight;
+    const highlights = [clickHighlight, hoverHighlight].filter((r) => r !== undefined);
+    return highlights.length ? (React.createElement(MsaToGenomeHighlightRenderer, { model: model, highlights: highlights })) : null;
 });
 // Inner component: handles the scroll-dependent rendering
 const MsaToGenomeHighlightRenderer = observer(function ({ model, highlights, }) {

package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js

@@ -44,7 +44,7 @@ export default class BgzipFastaMsaAdapter extends BaseAdapter {
     }
     async getMSA(id) {
         const adapter = await this.configure();
-        const refNames = await adapter.getRefNames();
+        const refNames = await this.getMSARefs();
         const rows = refNames.filter(refName => this.refNameToMsaId(refName) === id);
         return firstValueFrom(adapter
             .getFeaturesInMultipleRegions(rows.map(refName => ({

package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js

@@ -2,7 +2,7 @@ import useSWR from 'swr';
 import { clearAllCachedResults, deleteCachedResult, getAllCachedResults, } from '../../../utils/blastCache';
 import { staticSwrConfig } from '../../../utils/swrConfig';
 export function useCachedBlastResults(geneIds) {
-    const { data: results, error, mutate, } = useSWR(`cached-blast-${geneIds.join(',')}`, async () => {
+    const { data: results, error, isLoading, mutate, } = useSWR(`cached-blast-${geneIds.join(',')}`, async () => {
         const cached = await getAllCachedResults();
         return cached.filter(r => r.geneId && geneIds.includes(r.geneId));
     }, staticSwrConfig);
@@ -17,7 +17,7 @@ export function useCachedBlastResults(geneIds) {
     return {
         results: results ?? [],
         error,
-        isLoading: !results && !error,
+        isLoading,
         handleDelete,
         handleClearAll,
     };

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js

@@ -38,7 +38,7 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
     });
     const { selectedId, selectedTranscript } = transcriptSelection;
     const { data: msaData, isLoading: msaDataLoading, error: msaDataFetchError, } = useSWR(selectedId && selectedDataset && msaList
-        ? `${selectedDataset.datasetId}-${selectedId}-${msaList.length}-msa`
+        ? `${selectedDataset.datasetId}-${selectedId}-msa`
         : null, () => fetchMSA({
         msaId: selectedId,
         config: selectedDataset.adapter,

package/dist/LaunchMsaView/components/calculateProteinSequence.d.ts

@@ -1,10 +1,9 @@
 import type { Feat } from './types';
 import type { Feature } from '@jbrowse/core/util';
 export declare function stitch(subfeats: Feat[], sequence: string): string;
-export declare function calculateProteinSequence({ cds, sequence, codonTable, }: {
+export declare function calculateProteinSequence({ cds, sequence, }: {
     cds: Feat[];
     sequence: string;
-    codonTable: Record<string, string>;
 }): string;
 export declare function revlist(list: Feat[], seqlen: number): {
     start: number;

package/dist/LaunchMsaView/components/calculateProteinSequence.js

@@ -1,8 +1,11 @@
 import { dedupe, defaultCodonTable, generateCodonTable, revcom, } from '@jbrowse/core/util';
+// pure constant: the standard codon table never varies, so build it once rather
+// than on every translation (which runs on every panel re-render)
+const codonTable = generateCodonTable(defaultCodonTable);
 export function stitch(subfeats, sequence) {
     return subfeats.map(sub => sequence.slice(sub.start, sub.end)).join('');
 }
-export function calculateProteinSequence({ cds, sequence, codonTable, }) {
+export function calculateProteinSequence({ cds, sequence, }) {
     const str = stitch(cds, sequence);
     let protein = '';
     for (let i = 0; i < str.length; i += 3) {
@@ -33,6 +36,5 @@ export function getProteinSequenceFromFeature({ feature, seq, }) {
     return calculateProteinSequence({
         cds: strand === -1 ? revlist(cds, seq.length) : cds,
         sequence: strand === -1 ? revcom(seq) : seq,
-        codonTable: generateCodonTable(defaultCodonTable),
     });
 }

package/dist/MsaViewPanel/model.d.ts

@@ -526,6 +526,19 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      */
     readonly connectedView: MaybeLGV;
 } & {
+    /**
+     * #getter
+     * Genome region under the current MSA hover column. Suppressed on the LGV
+     * while it's being hovered (GenomeMouseoverHighlight shows the crisp 1bp
+     * marker there instead of this wider codon band).
+     */
+    readonly connectedHoverHighlight: IRegion | undefined;
+    /**
+     * #getter
+     * Genome region under the persistent MSA click selection. Shown
+     * regardless of LGV hover, so hovering the genome doesn't hide it.
+     */
+    readonly connectedClickHighlight: IRegion | undefined;
     /**
      * #getter
      */

package/dist/MsaViewPanel/model.js

@@ -111,19 +111,34 @@ export default function stateModelFactory() {
         },
     }))
         .views(self => ({
+        /**
+         * #getter
+         * Genome region under the current MSA hover column. Suppressed on the LGV
+         * while it's being hovered (GenomeMouseoverHighlight shows the crisp 1bp
+         * marker there instead of this wider codon band).
+         */
+        get connectedHoverHighlight() {
+            const { mouseCol } = self;
+            return mouseCol === undefined
+                ? undefined
+                : msaCoordToGenomeCoord({ model: self, coord: mouseCol });
+        },
+        /**
+         * #getter
+         * Genome region under the persistent MSA click selection. Shown
+         * regardless of LGV hover, so hovering the genome doesn't hide it.
+         */
+        get connectedClickHighlight() {
+            const { mouseClickCol } = self;
+            return mouseClickCol === undefined
+                ? undefined
+                : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol });
+        },
         /**
          * #getter
          */
         get connectedHighlights() {
-            const { mouseCol, mouseClickCol } = self;
-            return [
-                mouseCol === undefined
-                    ? undefined
-                    : msaCoordToGenomeCoord({ model: self, coord: mouseCol }),
-                mouseClickCol === undefined
-                    ? undefined
-                    : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol }),
-            ].filter((r) => r !== undefined);
+            return [this.connectedHoverHighlight, this.connectedClickHighlight].filter((r) => r !== undefined);
         },
     }))
         .actions(self => ({

package/dist/MsaViewPanel/msaDataStore.js

@@ -2,15 +2,20 @@ import { openDB } from 'idb';
 const DB_NAME = 'jbrowse-msaview-data';
 const DB_VERSION = 1;
 const STORE_NAME = 'msa-data';
-async function getDB() {
-    return openDB(DB_NAME, DB_VERSION, {
+let dbPromise;
+function getDB() {
+    dbPromise ??= openDB(DB_NAME, DB_VERSION, {
         upgrade(db) {
             if (!db.objectStoreNames.contains(STORE_NAME)) {
                 const store = db.createObjectStore(STORE_NAME, { keyPath: 'id' });
                 store.createIndex('timestamp', 'timestamp', { unique: false });
             }
         },
+    }).catch((e) => {
+        dbPromise = undefined;
+        throw e;
     });
+    return dbPromise;
 }
 export function generateDataStoreId() {
     return `msa-${Date.now()}-${Math.random().toString(36).slice(2, 11)}`;

package/dist/MsaViewPanel/util.d.ts

@@ -4,16 +4,6 @@ export declare function hasHoverPosition(hovered: unknown): hovered is {
         refName: string;
     };
 };
-interface AssemblyManagerLike {
-    get: (name: string) => {
-        getCanonicalRefName: (r: string) => string | undefined;
-    } | undefined;
-}
-export declare function getCanonicalRefName({ assemblyManager, assemblyNames, refName, }: {
-    assemblyManager: AssemblyManagerLike;
-    assemblyNames: string[] | undefined;
-    refName: string;
-}): string;
 /**
  * Extracts UniProt ID from an AlphaFold URL
  * Examples:
@@ -21,4 +11,3 @@ export declare function getCanonicalRefName({ assemblyManager, assemblyNames, re
  * - https://alphafold.ebi.ac.uk/files/msa/AF-P12345-F1-msa_v6.a3m -> P12345
  */
 export declare function getUniprotIdFromAlphaFoldUrl(url: string): string | undefined;
-export {};

package/dist/MsaViewPanel/util.js

@@ -4,13 +4,6 @@ export function hasHoverPosition(hovered) {
         'hoverPosition' in hovered &&
         !!hovered.hoverPosition);
 }
-export function getCanonicalRefName({ assemblyManager, assemblyNames, refName, }) {
-    const assemblyName = assemblyNames?.[0];
-    if (assemblyName) {
-        return (assemblyManager.get(assemblyName)?.getCanonicalRefName(refName) ?? refName);
-    }
-    return refName;
-}
 /**
  * Extracts UniProt ID from an AlphaFold URL
  * Examples: