jbrowse-plugin-msaview 2.4.4 → 2.4.5

package/dist/utils/blastCache.js

@@ -15,10 +15,8 @@ async function getDB() {
     });
 }
 function createCacheKey(proteinSequence, blastDatabase, blastProgram, transcriptId) {
-    if (transcriptId) {
-        return `${blastDatabase}:${blastProgram}:${transcriptId}:${proteinSequence}`;
-    }
-    return `${blastDatabase}:${blastProgram}:${proteinSequence}`;
+    const idPart = transcriptId ? `:${transcriptId}` : '';
+    return `${blastDatabase}:${blastProgram}${idPart}:${proteinSequence}`;
 }
 export async function saveBlastResult({ proteinSequence, blastDatabase, blastProgram, msaAlgorithm, msa, tree, treeMetadata, rid, geneId, transcriptId, transcriptName, geneName, }) {
     const db = await getDB();
@@ -55,4 +53,3 @@ export async function clearAllCachedResults() {
     const db = await getDB();
     await db.clear(STORE_NAME);
 }
-//# sourceMappingURL=blastCache.js.map

package/dist/utils/fetch.js

@@ -37,4 +37,3 @@ export async function unzipfetch(url, arg) {
     const res = await handleFetch(url, arg);
     return ungzip(await res.arrayBuffer(), { to: 'string' });
 }
-//# sourceMappingURL=fetch.js.map

package/dist/utils/msa.js

@@ -51,4 +51,3 @@ export async function launchMSA({ algorithm, sequence, onProgress, }) {
         tree: await textfetch(`${base}/${algorithm}/result/${jobId}/${config.treeResult}`),
     };
 }
-//# sourceMappingURL=msa.js.map

package/dist/utils/ncbiBlast.js

@@ -84,4 +84,3 @@ async function waitForRid({ rid, onProgress, baseUrl, }) {
         throw new Error(`BLAST ${rid} returned unexpected status: ${status ?? 'unknown'}`);
     }
 }
-//# sourceMappingURL=ncbiBlast.js.map

package/dist/utils/swrConfig.js

@@ -6,4 +6,3 @@ export const staticSwrConfig = {
     refreshWhenOffline: false,
     shouldRetryOnError: false,
 };
-//# sourceMappingURL=swrConfig.js.map

package/dist/utils/taxonomyNames.js

@@ -112,4 +112,3 @@ export async function fetchTaxonomyInfo(taxids) {
     }
     return result;
 }
-//# sourceMappingURL=taxonomyNames.js.map

package/dist/utils/types.js

@@ -1,2 +1 @@
 export {};
-//# sourceMappingURL=types.js.map

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.4.4";
+export declare const version = "2.4.5";

package/dist/version.js

@@ -1,2 +1 @@
-export const version = '2.4.4';
-//# sourceMappingURL=version.js.map
+export const version = '2.4.5';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.4.4",
+  "version": "2.4.5",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -27,9 +27,9 @@
     "@emotion/react": "^11.14.0",
     "@eslint/js": "^10.0.1",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
-    "@jbrowse/core": "^4.2.1",
-    "@jbrowse/mobx-state-tree": "^5.6.0",
-    "@jbrowse/plugin-linear-genome-view": "^4.2.1",
+    "@jbrowse/core": "^4.3.0",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
+    "@jbrowse/plugin-linear-genome-view": "^4.3.0",
     "@mui/icons-material": "^7.3.11",
     "@mui/material": "^7.3.11",
     "@mui/system": "^7.3.11",

package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx

@@ -4,6 +4,7 @@ import { getSession } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 
 import { hasHoverPosition, useStyles } from './util'
+import { isMsaView } from '../MsaViewPanel/model'
 
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
@@ -13,7 +14,9 @@ const GenomeMouseoverHighlight = observer(function ({
   model: LinearGenomeViewModel
 }) {
   const { hovered, views } = getSession(model)
-  const hasMsaView = views.some(s => s.type === 'MsaView')
+  const hasMsaView = views.some(
+    s => isMsaView(s) && s.connectedViewId === model.id,
+  )
   return hasMsaView && hasHoverPosition(hovered) ? (
     <GenomeMouseoverHighlightRenderer model={model} hovered={hovered} />
   ) : null

package/src/AddHighlightModel/MsaToGenomeHighlight.tsx

@@ -4,9 +4,9 @@ import { getSession } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 
 import { hasHoverPosition, useStyles } from './util'
+import { isMsaView } from '../MsaViewPanel/model'
 import { getCanonicalRefName } from '../MsaViewPanel/util'
 
-import type { JBrowsePluginMsaViewModel } from '../MsaViewPanel/model'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 type LGV = LinearGenomeViewModel
@@ -17,18 +17,15 @@ const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({
   model: LGV
 }) {
   const { views, hovered } = getSession(model)
-  const msaView = views.find(f => f.type === 'MsaView') as
-    | JBrowsePluginMsaViewModel
-    | undefined
+  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 ? (
-    <MsaToGenomeHighlightRenderer
-      model={model}
-      highlights={Array.from(highlights)}
-    />
+    <MsaToGenomeHighlightRenderer model={model} highlights={highlights} />
   ) : null
 })
 

package/src/AddHighlightModel/index.tsx

@@ -3,6 +3,7 @@ import React from 'react'
 import { getSession } from '@jbrowse/core/util'
 
 import HighlightComponents from './HighlightComponents'
+import { isMsaView } from '../MsaViewPanel/model'
 
 import type PluginManager from '@jbrowse/core/PluginManager'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -16,7 +17,9 @@ export default function AddHighlightComponentsModelF(
     (rest: React.ReactNode[], { model }: { model: LinearGenomeViewModel }) => {
       // Quick check: don't add any components if no MSA view exists
       const { views } = getSession(model)
-      const hasMsaView = views.some(v => v.type === 'MsaView')
+      const hasMsaView = views.some(
+        v => isMsaView(v) && v.connectedViewId === model.id,
+      )
       if (!hasMsaView) {
         return rest
       }

package/src/AddHighlightModel/util.ts

@@ -1,15 +1,6 @@
 import { makeStyles } from 'tss-react/mui'
 
-export function hasHoverPosition(
-  hovered: unknown,
-): hovered is { hoverPosition: { coord: number; refName: string } } {
-  return (
-    !!hovered &&
-    typeof hovered === 'object' &&
-    'hoverPosition' in hovered &&
-    !!hovered.hoverPosition
-  )
-}
+export { hasHoverPosition } from '../MsaViewPanel/util'
 
 export const useStyles = makeStyles()({
   highlight: {

package/src/LaunchMsaView/components/TabPanel.tsx

@@ -13,7 +13,7 @@ export default function TabPanel({
 }) {
   return (
     <div role="tabpanel" hidden={value !== index} {...other}>
-      {value === index ? <div>{children}</div> : null}
+      {value === index ? children : null}
     </div>
   )
 }

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -1,7 +1,6 @@
 import { getSession } from '@jbrowse/core/util'
 
 import { doLaunchBlast } from './doLaunchBlast'
-import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord'
 import {
   cleanupOldData,
   generateDataStoreId,
@@ -19,8 +18,7 @@ import type { JBrowsePluginMsaViewModel } from './model'
 export function loadStoredData(self: JBrowsePluginMsaViewModel) {
   const { dataStoreId, rows } = self
   if (dataStoreId && rows.length === 0) {
-    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-    ;(async () => {
+    void (async () => {
       try {
         self.setLoadingStoredData(true)
         const storedData = await retrieveMsaData(dataStoreId)
@@ -56,8 +54,7 @@ export function storeDataToIndexedDB(self: JBrowsePluginMsaViewModel) {
       // data observables change while the write is pending) don't kick off a
       // duplicate write and leave an orphan IndexedDB entry
       self.setIsStoringData(true)
-      // eslint-disable-next-line @typescript-eslint/no-floating-promises
-      ;(async () => {
+      void (async () => {
         try {
           const newId = generateDataStoreId()
           const success = await storeMsaData(newId, {
@@ -80,8 +77,7 @@ export function storeDataToIndexedDB(self: JBrowsePluginMsaViewModel) {
 
 export function launchBlastIfNeeded(self: JBrowsePluginMsaViewModel) {
   if (self.blastParams) {
-    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-    ;(async () => {
+    void (async () => {
       try {
         self.setProgress('Submitting query')
         self.setError(undefined)
@@ -101,8 +97,7 @@ export function launchBlastIfNeeded(self: JBrowsePluginMsaViewModel) {
 export function processInit(self: JBrowsePluginMsaViewModel) {
   const { init } = self
   if (init) {
-    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-    ;(async () => {
+    void (async () => {
       try {
         self.setError(undefined)
         const { msaData, msaUrl, treeData, treeUrl, querySeqName } = init
@@ -150,20 +145,6 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
   }
 }
 
-export function updateGenomeHighlights(self: JBrowsePluginMsaViewModel) {
-  const { mouseCol, mouseClickCol } = self
-  const r1 =
-    mouseCol === undefined
-      ? undefined
-      : msaCoordToGenomeCoord({ model: self, coord: mouseCol })
-  const r2 =
-    mouseClickCol === undefined
-      ? undefined
-      : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
-
-  self.setConnectedHighlights([r1, r2].filter(f => !!f))
-}
-
 export function highlightConnectedStructures(self: JBrowsePluginMsaViewModel) {
   const { mouseCol, connectedProteinViews } = self
   if (connectedProteinViews.length === 0) {

package/src/MsaViewPanel/genomeToMSA.ts

@@ -1,53 +1,34 @@
 import { getSession } from '@jbrowse/core/util'
 
-import { checkHovered } from './util'
+import { hasHoverPosition } from './util'
 
 import type { JBrowsePluginMsaViewModel } from './model'
 
-/**
- * Convert a genome coordinate from session.hovered to a visible MSA column.
- *
- * @param model - The MSA view model
- * @returns The visible column index, or undefined if no mapping exists
- */
 export function genomeToMSA({ model }: { model: JBrowsePluginMsaViewModel }) {
   const { hovered } = getSession(model)
   const { querySeqName, transcriptToMsaMap, connectedView, mafRegion } = model
 
-  if (!connectedView?.initialized || !checkHovered(hovered)) {
+  if (!connectedView?.initialized || !hasHoverPosition(hovered)) {
     return undefined
   }
 
   const { coord: hoverCoord, refName } = hovered.hoverPosition
 
-  // Handle MAF region mapping
   if (mafRegion) {
-    // Check if the hover is on the same refName as the MAF region
-    if (refName !== mafRegion.refName) {
+    if (
+      refName !== mafRegion.refName ||
+      !connectedView.assemblyNames.includes(mafRegion.assemblyName) ||
+      hoverCoord < mafRegion.start ||
+      hoverCoord >= mafRegion.end
+    ) {
       return undefined
     }
-    // Check if we're on the same assembly (if assembly info is available)
-    const viewAssemblies = connectedView.assemblyNames
-    if (!viewAssemblies.includes(mafRegion.assemblyName)) {
-      return undefined
-    }
-    // Check if the hover coordinate is within the MAF region
-    if (hoverCoord < mafRegion.start || hoverCoord >= mafRegion.end) {
-      return undefined
-    }
-    // Calculate the ungapped position relative to the region start
-    const ungappedPos = hoverCoord - mafRegion.start
-    // Convert to visible column using the query sequence
-    return model.seqPosToVisibleCol(querySeqName, ungappedPos)
+    return model.seqPosToVisibleCol(querySeqName, hoverCoord - mafRegion.start)
   }
 
-  // Handle transcript mapping (original behavior)
   if (transcriptToMsaMap) {
-    const { g2p } = transcriptToMsaMap
-    // g2p maps genome coordinate to sequence position (0-based)
-    const seqPos = g2p[hoverCoord]
+    const seqPos = transcriptToMsaMap.g2p[hoverCoord]
     if (seqPos !== undefined) {
-      // Convert sequence position to visible column
       return model.seqPosToVisibleCol(querySeqName, seqPos)
     }
   }

package/src/MsaViewPanel/model.ts

@@ -2,7 +2,7 @@ import { lazy } from 'react'
 
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes'
 import { getSession } from '@jbrowse/core/util'
-import { addDisposer, cast, types } from '@jbrowse/mobx-state-tree'
+import { addDisposer, types } from '@jbrowse/mobx-state-tree'
 import { genomeToTranscriptSeqMapping } from 'g2p_mapper'
 import { autorun } from 'mobx'
 import { MSAModelF } from 'react-msaview'
@@ -16,7 +16,6 @@ import {
   processInit,
   runCleanup,
   storeDataToIndexedDB,
-  updateGenomeHighlights,
 } from './afterCreateAutoruns'
 import { genomeToMSA } from './genomeToMSA'
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord'
@@ -84,13 +83,6 @@ export default function stateModelFactory() {
         /**
          * #property
          */
-        connectedHighlights: types.array(
-          types.model({
-            refName: types.string,
-            start: types.number,
-            end: types.number,
-          }),
-        ),
         /**
          * #property
          */
@@ -246,11 +238,25 @@ export default function stateModelFactory() {
        * #getter
        */
       get mouseCol2(): number | undefined {
-        const structureCol = self.structureHoverCol
-        if (structureCol !== undefined) {
-          return structureCol
-        }
-        return genomeToMSA({ model: self as JBrowsePluginMsaViewModel })
+        return (
+          self.structureHoverCol ??
+          genomeToMSA({ model: self as JBrowsePluginMsaViewModel })
+        )
+      },
+
+      /**
+       * #getter
+       */
+      get connectedHighlights(): IRegion[] {
+        const { mouseCol, mouseClickCol } = self
+        return [
+          mouseCol === undefined
+            ? undefined
+            : msaCoordToGenomeCoord({ model: self, coord: mouseCol }),
+          mouseClickCol === undefined
+            ? undefined
+            : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol }),
+        ].filter((r): r is IRegion => r !== undefined)
       },
     }))
 
@@ -279,24 +285,6 @@ export default function stateModelFactory() {
       setRid(arg: string) {
         self.rid = arg
       },
-      /**
-       * #action
-       */
-      setConnectedHighlights(r: IRegion[]) {
-        self.connectedHighlights = cast(r)
-      },
-      /**
-       * #action
-       */
-      addToConnectedHighlights(r: IRegion) {
-        self.connectedHighlights.push(r)
-      },
-      /**
-       * #action
-       */
-      clearConnectedHighlights() {
-        self.connectedHighlights = cast([])
-      },
       /**
        * #action
        */
@@ -504,7 +492,6 @@ export default function stateModelFactory() {
           storeDataToIndexedDB,
           launchBlastIfNeeded,
           processInit,
-          updateGenomeHighlights,
           highlightConnectedStructures,
           autoConnectStructures,
           observeProteinHighlights,
@@ -526,3 +513,9 @@ export type JBrowsePluginMsaViewStateModel = ReturnType<
 export type JBrowsePluginMsaViewModel = Instance<JBrowsePluginMsaViewStateModel>
 
 export { type MafRegion, type MsaViewInitState } from './types'
+
+export function isMsaView(view: {
+  type: string
+}): view is JBrowsePluginMsaViewModel {
+  return view.type === 'MsaView'
+}

package/src/MsaViewPanel/msaCoordToGenomeCoord.ts

@@ -21,45 +21,29 @@ export function msaCoordToGenomeCoord({
 }) {
   const { querySeqName, transcriptToMsaMap, mafRegion } = model
 
-  // Get the query sequence
-  const queryRow = model.rows.find(f => f[0] === querySeqName)
-  const querySeq = queryRow?.[1]
+  const querySeq = model.rows.find(f => f[0] === querySeqName)?.[1]
   if (!querySeq) {
     return undefined
   }
 
-  // Convert gapped MSA column to ungapped sequence coordinate
-  // Returns undefined if the position is a gap
   const ungappedPos = gappedToUngappedPosition(querySeq, mouseCol)
   if (ungappedPos === undefined) {
     return undefined
   }
 
-  // Handle MAF region mapping
   if (mafRegion) {
     const genomePos = mafRegion.start + ungappedPos
-    // Check if position is within the region
-    if (genomePos >= mafRegion.end) {
-      return undefined
-    }
-    return {
-      refName: mafRegion.refName,
-      start: genomePos,
-      end: genomePos + 1,
-    }
+    return genomePos < mafRegion.end
+      ? { refName: mafRegion.refName, start: genomePos, end: genomePos + 1 }
+      : undefined
   }
 
-  // Handle transcript mapping (original behavior)
   if (transcriptToMsaMap) {
     const { refName, p2g } = transcriptToMsaMap
     const s = p2g[ungappedPos]
     const e = p2g[ungappedPos + 1]
     return s !== undefined && e !== undefined
-      ? {
-          refName,
-          start: Math.min(s, e),
-          end: Math.max(s, e),
-        }
+      ? { refName, start: Math.min(s, e), end: Math.max(s, e) }
       : undefined
   }
 

package/src/MsaViewPanel/util.ts

@@ -1,13 +1,9 @@
-import type { Feature } from '@jbrowse/core/util'
-
-export function checkHovered(hovered: unknown): hovered is {
-  hoverFeature: Feature
-  hoverPosition: { coord: number; refName: string }
-} {
+export function hasHoverPosition(
+  hovered: unknown,
+): hovered is { hoverPosition: { coord: number; refName: string } } {
   return (
     !!hovered &&
     typeof hovered === 'object' &&
-    'hoverFeature' in hovered &&
     'hoverPosition' in hovered &&
     !!hovered.hoverPosition
   )

package/src/utils/blastCache.ts

@@ -46,10 +46,8 @@ function createCacheKey(
   blastProgram: BlastProgram,
   transcriptId?: string,
 ) {
-  if (transcriptId) {
-    return `${blastDatabase}:${blastProgram}:${transcriptId}:${proteinSequence}`
-  }
-  return `${blastDatabase}:${blastProgram}:${proteinSequence}`
+  const idPart = transcriptId ? `:${transcriptId}` : ''
+  return `${blastDatabase}:${blastProgram}${idPart}:${proteinSequence}`
 }
 
 export async function saveBlastResult({

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.4.4'
+export const version = '2.4.5'

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map

@@ -1 +0,0 @@
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package/dist/AddHighlightModel/HighlightComponents.js.map

@@ -1 +0,0 @@
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package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map

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package/dist/AddHighlightModel/util.js.map

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package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map

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package/dist/BgzipFastaMsaAdapter/configSchema.js.map

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package/dist/LaunchMsaView/components/LaunchMsaViewDialog.js.map

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package/dist/LaunchMsaView/components/LaunchPanelContent.js.map

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

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package/dist/LaunchMsaView/components/ManualMSALoader/fetchGeneList.js.map

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

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

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package/dist/LaunchMsaView/components/NCBIBlastQuery/MsaAlgorithmSelect.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js.map

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