jbrowse-plugin-msaview 2.6.6 → 2.6.8

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/ManualMSALoader/ManualMSALoader.js

@@ -1,6 +1,5 @@
 import React, { useState } from 'react';
 import { FileSelector } from '@jbrowse/core/ui';
-import { getSession } from '@jbrowse/core/util';
 import { Alert, FormControl, FormControlLabel, Radio, RadioGroup, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
@@ -32,7 +31,6 @@ const useStyles = makeStyles()({
     },
 });
 const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handleClose, }) {
-    const session = getSession(model);
     const view = getLinearGenomeView(model);
     const { classes } = useStyles();
     const [launchViewError, setLaunchViewError] = useState();
@@ -74,7 +72,6 @@ const ManualMSALoader = observer(function PreLoadedMSA2({ model, feature, handle
                     if (selectedTranscript) {
                         setLaunchViewError(undefined);
                         launchView({
-                            session,
                             newViewTitle: getGeneDisplayName(selectedTranscript),
                             view,
                             feature: selectedTranscript,

package/dist/LaunchMsaView/components/ManualMSALoader/launchView.d.ts

@@ -1,7 +1,6 @@
-import type { AbstractSessionModel, Feature, FileLocation } from '@jbrowse/core/util';
+import type { Feature, FileLocation } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function launchView({ session, newViewTitle, view, feature, msaFilehandle, treeFilehandle, querySeqName, data, }: {
-    session: AbstractSessionModel;
+export declare function launchView({ newViewTitle, view, feature, msaFilehandle, treeFilehandle, querySeqName, data, }: {
     newViewTitle: string;
     view: LinearGenomeViewModel;
     feature: Feature;

package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js

@@ -1,5 +1,6 @@
-export function launchView({ session, newViewTitle, view, feature, msaFilehandle, treeFilehandle, querySeqName, data, }) {
-    session.addView('MsaView', {
+import { getSession } from '@jbrowse/core/util';
+export function launchView({ newViewTitle, view, feature, msaFilehandle, treeFilehandle, querySeqName, data, }) {
+    getSession(view).addView('MsaView', {
         type: 'MsaView',
         displayName: newViewTitle,
         connectedViewId: view.id,

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

@@ -6,7 +6,7 @@ import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
 import { blastLaunchViewFromCache } from './blastLaunchView';
 import { useCachedBlastResults } from './useCachedBlastResults';
-import { getGeneIdentifiers, getLinearGenomeView } from '../../util';
+import { featureMatchesId, getGeneIdentifiers, getLinearGenomeView, getSortedTranscriptFeatures, } from '../../util';
 const useStyles = makeStyles()({
     header: {
         display: 'flex',
@@ -37,10 +37,19 @@ const CachedBlastResults = observer(function ({ model, handleClose, feature, })
     const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature]);
     const { results, error, isLoading, handleDelete, handleClearAll } = useCachedBlastResults(geneIds);
     const handleUseCached = (cached) => {
+        // reconnect the cached MSA to the genome: the cached query row is named
+        // 'QUERY' (react-msaview's default querySeqName) and corresponds to the
+        // transcript stored as transcriptId. Resolving it here restores the
+        // MSA<->genome navigation and hover-sync a fresh BLAST gets.
+        const { transcriptId } = cached;
+        const transcript = transcriptId
+            ? getSortedTranscriptFeatures(feature).find(t => featureMatchesId(t, transcriptId))
+            : undefined;
         blastLaunchViewFromCache({
             view,
             cached,
             newViewTitle: `BLAST - ${getResultDisplayName(cached)}`,
+            connectedFeature: transcript?.toJSON(),
         });
         handleClose();
     };

package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.d.ts

@@ -8,8 +8,9 @@ export declare function blastLaunchView({ newViewTitle, view, feature, blastPara
     feature: Feature;
     blastParams: BlastParams;
 }): void;
-export declare function blastLaunchViewFromCache({ newViewTitle, view, cached, }: {
+export declare function blastLaunchViewFromCache({ newViewTitle, view, cached, connectedFeature, }: {
     newViewTitle: string;
     view: LinearGenomeViewModel;
     cached: CachedBlastResult;
+    connectedFeature?: ReturnType<Feature['toJSON']>;
 }): void;

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

@@ -11,11 +11,12 @@ export function blastLaunchView({ newViewTitle, view, feature, blastParams, }) {
         blastParams,
     });
 }
-export function blastLaunchViewFromCache({ newViewTitle, view, cached, }) {
+export function blastLaunchViewFromCache({ newViewTitle, view, cached, connectedFeature, }) {
     getSession(view).addView('MsaView', {
         type: 'MsaView',
         displayName: newViewTitle,
         connectedViewId: view.id,
+        connectedFeature,
         drawNodeBubbles: true,
         colWidth: 10,
         rowHeight: 12,

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}-${selectedId}-msa`
         : null, () => fetchMSA({
         msaId: selectedId,
         config: selectedDataset.adapter,
@@ -64,7 +64,6 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, }) {
                     if (selectedTranscript && msaData) {
                         const querySeqName = `${selectedId}_${assemblyNames[0]}`;
                         preCalculatedLaunchView({
-                            session,
                             newViewTitle: getGeneDisplayName(selectedTranscript),
                             view,
                             querySeqName,

package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.d.ts

@@ -1,10 +1,9 @@
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-export declare function preCalculatedLaunchView({ session, newViewTitle, view, feature, data, querySeqName, }: {
+export declare function preCalculatedLaunchView({ newViewTitle, view, feature, data, querySeqName, }: {
     data: {
         msa: string;
     };
-    session: AbstractSessionModel;
     newViewTitle: string;
     view: LinearGenomeViewModel;
     feature: Feature;

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

@@ -1,5 +1,6 @@
-export function preCalculatedLaunchView({ session, newViewTitle, view, feature, data, querySeqName, }) {
-    session.addView('MsaView', {
+import { getSession } from '@jbrowse/core/util';
+export function preCalculatedLaunchView({ newViewTitle, view, feature, data, querySeqName, }) {
+    getSession(view).addView('MsaView', {
         type: 'MsaView',
         displayName: newViewTitle,
         treeAreaWidth: 200,

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/LaunchMsaView/components/useTranscriptSelection.js

@@ -1,22 +1,25 @@
 import { useMemo, useState } from 'react';
 import { featureMatchesId, getId, getSortedTranscriptFeatures } from '../util';
 import { useFeatureSequence } from './useFeatureSequence';
-function findValidSelection(currentId, options, validIds) {
-    if (validIds && validIds.length > 0) {
-        const currentFeature = options.find(opt => getId(opt) === currentId);
-        const currentIsValid = currentFeature &&
-            validIds.some(id => featureMatchesId(currentFeature, id));
-        if (currentFeature && !currentIsValid) {
-            const validOption = options.find(opt => validIds.some(id => featureMatchesId(opt, id)));
-            return validOption ? getId(validOption) : undefined;
-        }
+// Keep the current selection if it's valid for the given validIds, otherwise
+// fall back to the first valid option (or the current id if none qualify). With
+// no validIds constraint the current selection always stands.
+function pickSelectedId(currentId, options, validIds) {
+    if (!validIds?.length) {
+        return currentId;
     }
-    return undefined;
+    const isValid = (opt) => validIds.some(id => featureMatchesId(opt, id));
+    const current = options.find(opt => getId(opt) === currentId);
+    if (current && isValid(current)) {
+        return currentId;
+    }
+    const firstValid = options.find(isValid);
+    return firstValid ? getId(firstValid) : currentId;
 }
 export function useTranscriptSelection({ feature, view, validIds, }) {
     const options = useMemo(() => getSortedTranscriptFeatures(feature), [feature]);
     const [selectedId, setSelectedId] = useState(() => getId(options[0]));
-    const validatedSelectedId = findValidSelection(selectedId, options, validIds) ?? selectedId;
+    const validatedSelectedId = pickSelectedId(selectedId, options, validIds);
     const selectedTranscript = options.find(val => getId(val) === validatedSelectedId);
     const { proteinSequence, error } = useFeatureSequence({
         view,

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: