jbrowse-plugin-msaview 2.6.7 → 2.6.8

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/PreLoadedMSA/PreLoadedMSADataPanel.js

@@ -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/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,