jbrowse-plugin-msaview 2.6.7 → 2.6.8

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.6.7";
+export declare const version = "2.6.8";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.6.7';
+export const version = '2.6.8';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.6.7",
+  "version": "2.6.8",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {

package/src/LaunchMsaView/components/ManualMSALoader/ManualMSALoader.tsx

@@ -1,7 +1,6 @@
 import React, { useState } from 'react'
 
 import { FileSelector } from '@jbrowse/core/ui'
-import { getSession } from '@jbrowse/core/util'
 import {
   Alert,
   FormControl,
@@ -56,7 +55,6 @@ const ManualMSALoader = observer(function PreLoadedMSA2({
   feature: Feature
   handleClose: () => void
 }) {
-  const session = getSession(model)
   const view = getLinearGenomeView(model)
   const { classes } = useStyles()
   const [launchViewError, setLaunchViewError] = useState<unknown>()
@@ -179,7 +177,6 @@ const ManualMSALoader = observer(function PreLoadedMSA2({
             if (selectedTranscript) {
               setLaunchViewError(undefined)
               launchView({
-                session,
                 newViewTitle: getGeneDisplayName(selectedTranscript),
                 view,
                 feature: selectedTranscript,

package/src/LaunchMsaView/components/ManualMSALoader/launchView.ts

@@ -1,12 +1,9 @@
-import type {
-  AbstractSessionModel,
-  Feature,
-  FileLocation,
-} from '@jbrowse/core/util'
+import { getSession } from '@jbrowse/core/util'
+
+import type { Feature, FileLocation } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 export function launchView({
-  session,
   newViewTitle,
   view,
   feature,
@@ -15,7 +12,6 @@ export function launchView({
   querySeqName,
   data,
 }: {
-  session: AbstractSessionModel
   newViewTitle: string
   view: LinearGenomeViewModel
   feature: Feature
@@ -27,7 +23,7 @@ export function launchView({
     tree?: string
   }
 }) {
-  session.addView('MsaView', {
+  getSession(view).addView('MsaView', {
     type: 'MsaView',
     displayName: newViewTitle,
     connectedViewId: view.id,

package/src/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.tsx

@@ -16,7 +16,12 @@ 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'
 
 import type { CachedBlastResult } from '../../../utils/blastCache'
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
@@ -65,10 +70,21 @@ const CachedBlastResults = observer(function ({
     useCachedBlastResults(geneIds)
 
   const handleUseCached = (cached: CachedBlastResult) => {
+    // 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/src/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.ts

@@ -32,15 +32,18 @@ export function blastLaunchViewFromCache({
   newViewTitle,
   view,
   cached,
+  connectedFeature,
 }: {
   newViewTitle: string
   view: LinearGenomeViewModel
   cached: CachedBlastResult
+  connectedFeature?: ReturnType<Feature['toJSON']>
 }) {
   getSession(view).addView('MsaView', {
     type: 'MsaView',
     displayName: newViewTitle,
     connectedViewId: view.id,
+    connectedFeature,
     drawNodeBubbles: true,
     colWidth: 10,
     rowHeight: 12,

package/src/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.tsx

@@ -139,7 +139,6 @@ const PreLoadedMSA = observer(function ({
             if (selectedTranscript && msaData) {
               const querySeqName = `${selectedId}_${assemblyNames[0]}`
               preCalculatedLaunchView({
-                session,
                 newViewTitle: getGeneDisplayName(selectedTranscript),
                 view,
                 querySeqName,

package/src/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.ts

@@ -1,8 +1,9 @@
-import type { AbstractSessionModel, Feature } from '@jbrowse/core/util'
+import { getSession } from '@jbrowse/core/util'
+
+import type { Feature } from '@jbrowse/core/util'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 export function preCalculatedLaunchView({
-  session,
   newViewTitle,
   view,
   feature,
@@ -10,13 +11,12 @@ export function preCalculatedLaunchView({
   querySeqName,
 }: {
   data: { msa: string }
-  session: AbstractSessionModel
   newViewTitle: string
   view: LinearGenomeViewModel
   feature: Feature
   querySeqName: string
 }) {
-  session.addView('MsaView', {
+  getSession(view).addView('MsaView', {
     type: 'MsaView',
     displayName: newViewTitle,
     treeAreaWidth: 200,

package/src/LaunchMsaView/components/useTranscriptSelection.ts

@@ -5,24 +5,25 @@ import { useFeatureSequence } from './useFeatureSequence'
 
 import type { Feature } from '@jbrowse/core/util'
 
-function findValidSelection(
+// 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: string,
   options: Feature[],
   validIds: string[] | undefined,
-): string | undefined {
-  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
-    }
+): string {
+  if (!validIds?.length) {
+    return currentId
   }
-  return undefined
+  const isValid = (opt: Feature) =>
+    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({
@@ -36,8 +37,7 @@ export function useTranscriptSelection({
 }) {
   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,
   )

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.6.7'
+export const version = '2.6.8'