jbrowse-plugin-msaview 2.2.3 → 2.2.4

package/dist/utils/blastCache.d.ts

@@ -0,0 +1,34 @@
+export interface CachedBlastResult {
+    id: string;
+    proteinSequence: string;
+    blastDatabase: string;
+    blastProgram: string;
+    msaAlgorithm: string;
+    msa: string;
+    tree: string;
+    treeMetadata: string;
+    rid: string;
+    timestamp: number;
+    geneId?: string;
+    transcriptId?: string;
+}
+export declare function getCachedBlastResult({ proteinSequence, blastDatabase, blastProgram, }: {
+    proteinSequence: string;
+    blastDatabase: string;
+    blastProgram: string;
+}): Promise<any>;
+export declare function saveBlastResult({ proteinSequence, blastDatabase, blastProgram, msaAlgorithm, msa, tree, treeMetadata, rid, geneId, transcriptId, }: {
+    proteinSequence: string;
+    blastDatabase: string;
+    blastProgram: string;
+    msaAlgorithm: string;
+    msa: string;
+    tree: string;
+    treeMetadata: string;
+    rid: string;
+    geneId?: string;
+    transcriptId?: string;
+}): Promise<CachedBlastResult>;
+export declare function getAllCachedResults(): Promise<any[]>;
+export declare function deleteCachedResult(id: string): Promise<void>;
+export declare function clearAllCachedResults(): Promise<void>;

package/dist/utils/blastCache.js

@@ -0,0 +1,58 @@
+import { openDB } from 'idb';
+const DB_NAME = 'jbrowse-msaview-blast-cache';
+const STORE_NAME = 'blast-results';
+const DB_VERSION = 2;
+async function getDB() {
+    return openDB(DB_NAME, DB_VERSION, {
+        upgrade(db, oldVersion) {
+            if (oldVersion < 2 && db.objectStoreNames.contains(STORE_NAME)) {
+                db.deleteObjectStore(STORE_NAME);
+            }
+            if (!db.objectStoreNames.contains(STORE_NAME)) {
+                db.createObjectStore(STORE_NAME, { keyPath: 'id' });
+            }
+        },
+    });
+}
+function createCacheKey(proteinSequence, blastDatabase, blastProgram) {
+    return `${blastDatabase}:${blastProgram}:${proteinSequence.slice(0, 100)}`;
+}
+export async function getCachedBlastResult({ proteinSequence, blastDatabase, blastProgram, }) {
+    const db = await getDB();
+    const id = createCacheKey(proteinSequence, blastDatabase, blastProgram);
+    return db.get(STORE_NAME, id);
+}
+export async function saveBlastResult({ proteinSequence, blastDatabase, blastProgram, msaAlgorithm, msa, tree, treeMetadata, rid, geneId, transcriptId, }) {
+    const db = await getDB();
+    const id = createCacheKey(proteinSequence, blastDatabase, blastProgram);
+    const entry = {
+        id,
+        proteinSequence,
+        blastDatabase,
+        blastProgram,
+        msaAlgorithm,
+        msa,
+        tree,
+        treeMetadata,
+        rid,
+        timestamp: Date.now(),
+        geneId,
+        transcriptId,
+    };
+    await db.put(STORE_NAME, entry);
+    return entry;
+}
+export async function getAllCachedResults() {
+    const db = await getDB();
+    const results = await db.getAll(STORE_NAME);
+    return results.toSorted((a, b) => b.timestamp - a.timestamp);
+}
+export async function deleteCachedResult(id) {
+    const db = await getDB();
+    await db.delete(STORE_NAME, id);
+}
+export async function clearAllCachedResults() {
+    const db = await getDB();
+    await db.clear(STORE_NAME);
+}
+//# sourceMappingURL=blastCache.js.map

package/dist/utils/blastCache.js.map

@@ -0,0 +1 @@
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package/dist/utils/fetch.d.ts

@@ -3,4 +3,4 @@ export declare function textfetch(url: string, args?: RequestInit): Promise<stri
 export declare function jsonfetch<T>(url: string, args?: RequestInit): Promise<T>;
 export declare function timeout(time: number): Promise<unknown>;
 export declare function fetchWithLocalStorageCache<T>(key: string, fetchFn: () => Promise<T>): Promise<T>;
-export declare function unzipfetch(url: string, arg?: RequestInit): Promise<string>;
+export declare function unzipfetch(url: string, arg?: RequestInit): Promise<any>;

package/dist/utils/fetch.js

@@ -1,4 +1,4 @@
-import { ungzip } from 'pako';
+import { ungzip } from 'pako-esm2';
 export async function handleFetch(url, args) {
     const response = await fetch(url, args);
     if (!response.ok) {

package/dist/utils/fetch.js.map

@@ -1 +1 @@
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package/dist/utils/ncbiBlast.d.ts

@@ -8,11 +8,7 @@ export declare function queryBlast({ query, blastDatabase, blastProgram, baseUrl
 }): Promise<{
     rid: string;
     hits: {
-        description: {
-            accession: string;
-            id: string;
-            sciname: string;
-        }[];
+        description: import("./types").BlastHitDescription[];
         hsps: {
             hseq: string;
         }[];

package/dist/utils/taxonomyNames.d.ts

@@ -0,0 +1,5 @@
+export interface TaxonomyInfo {
+    sciname: string;
+    commonName?: string;
+}
+export declare function fetchTaxonomyInfo(taxids: number[]): Promise<Map<number, TaxonomyInfo>>;

package/dist/utils/taxonomyNames.js

@@ -0,0 +1,79 @@
+import { openDB } from 'idb';
+const DB_NAME = 'jbrowse-msaview-taxonomy-cache';
+const STORE_NAME = 'common-names';
+const DB_VERSION = 1;
+async function getDB() {
+    return openDB(DB_NAME, DB_VERSION, {
+        upgrade(db) {
+            if (!db.objectStoreNames.contains(STORE_NAME)) {
+                db.createObjectStore(STORE_NAME, { keyPath: 'taxid' });
+            }
+        },
+    });
+}
+async function getCachedCommonName(taxid) {
+    const db = await getDB();
+    return db.get(STORE_NAME, taxid);
+}
+async function saveTaxonomyCache(entries) {
+    const db = await getDB();
+    const tx = db.transaction(STORE_NAME, 'readwrite');
+    for (const entry of entries) {
+        await tx.store.put(entry);
+    }
+    await tx.done;
+}
+export async function fetchTaxonomyInfo(taxids) {
+    const result = new Map();
+    const uncachedTaxids = [];
+    for (const taxid of taxids) {
+        const cached = await getCachedCommonName(taxid);
+        if (cached) {
+            result.set(taxid, {
+                sciname: cached.sciname,
+                commonName: cached.commonName,
+            });
+        }
+        else {
+            uncachedTaxids.push(taxid);
+        }
+    }
+    if (uncachedTaxids.length === 0) {
+        return result;
+    }
+    const batchSize = 100;
+    const toCache = [];
+    for (let i = 0; i < uncachedTaxids.length; i += batchSize) {
+        const batch = uncachedTaxids.slice(i, i + batchSize);
+        const idsParam = batch.join(',');
+        try {
+            const response = await fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=${idsParam}&retmode=xml`);
+            const text = await response.text();
+            for (const taxid of batch) {
+                const taxonRegex = new RegExp(`<Taxon>.*?<TaxId>${taxid}</TaxId>.*?</Taxon>`, 's');
+                const taxonMatch = taxonRegex.exec(text);
+                if (taxonMatch) {
+                    const taxonXml = taxonMatch[0];
+                    const genbankCommon = /<GenbankCommonName>(.*?)<\/GenbankCommonName>/.exec(taxonXml);
+                    const commonName = /<CommonName>(.*?)<\/CommonName>/.exec(taxonXml);
+                    const sciName = /<ScientificName>(.*?)<\/ScientificName>/.exec(taxonXml);
+                    const name = genbankCommon?.[1] ?? commonName?.[1];
+                    const sci = sciName?.[1] ?? '';
+                    result.set(taxid, { sciname: sci, commonName: name });
+                    toCache.push({ taxid, sciname: sci, commonName: name });
+                }
+                else {
+                    toCache.push({ taxid, sciname: '', commonName: undefined });
+                }
+            }
+        }
+        catch (error) {
+            console.error('Failed to fetch taxonomy data:', error);
+        }
+    }
+    if (toCache.length > 0) {
+        await saveTaxonomyCache(toCache);
+    }
+    return result;
+}
+//# sourceMappingURL=taxonomyNames.js.map

package/dist/utils/taxonomyNames.js.map

@@ -0,0 +1 @@
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package/dist/utils/types.d.ts

@@ -1,14 +1,17 @@
+export interface BlastHitDescription {
+    accession: string;
+    id: string;
+    sciname: string;
+    taxid?: number;
+    title?: string;
+}
 export interface BlastResults {
     BlastOutput2: {
         report: {
             results: {
                 search: {
                     hits: {
-                        description: {
-                            accession: string;
-                            id: string;
-                            sciname: string;
-                        }[];
+                        description: BlastHitDescription[];
                         hsps: {
                             hseq: string;
                         }[];

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.2.3",
+  "version": "2.2.4",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "keywords": [
@@ -11,69 +11,65 @@
     "dist",
     "src"
   ],
-  "config": {
-    "port": 9000,
-    "browse": {
-      "port": 8999
-    },
-    "jbrowse": {
-      "plugin": {
-        "name": "MsaView"
-      }
-    }
-  },
   "scripts": {
     "clean": "rimraf dist",
-    "start": "node esbuild-watch.mjs",
+    "start": "node esbuild.mjs --watch",
     "format": "prettier --write .",
     "build": "tsc && NODE_ENV=production node esbuild.mjs && cp distconfig.json dist/config.json",
-    "prebuild": "npm run clean",
+    "prebuild": "yarn clean",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0",
-    "prepack": "npm run build",
+    "pretest": "rm -rf .test-jbrowse && npx @jbrowse/cli create .test-jbrowse --nightly",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "test:setup": "node scripts/test-versions.mjs setup",
+    "test:setup:version": "node scripts/test-versions.mjs setup",
+    "test:versions": "node scripts/test-versions.mjs run",
+    "test:version": "node scripts/test-versions.mjs run",
+    "prepack": "yarn build",
     "postversion": "git push --follow-tags"
   },
-  "jbrowse-plugin": {
-    "name": "MsaView"
-  },
   "dependencies": {
-    "@emotion/styled": "^11.14.0",
-    "g2p_mapper": "^1.0.4",
-    "pako": "^2.1.0",
-    "react-msaview": "^4.4.1",
-    "swr": "^2.3.3"
+    "@emotion/styled": "^11.14.1",
+    "g2p_mapper": "^2.0.0",
+    "idb": "^8.0.3",
+    "pako-esm2": "^2.0.0",
+    "react-msaview": "^5.0.5",
+    "swr": "^2.3.8"
   },
   "devDependencies": {
-    "@emotion/react": "^11.10.4",
+    "@emotion/react": "^11.14.0",
+    "@eslint/js": "^9.39.2",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
-    "@jbrowse/core": "^3.0.1",
-    "@jbrowse/plugin-linear-genome-view": "^3.0.1",
-    "@mui/icons-material": "^7.1.0",
-    "@mui/material": "^7.1.0",
-    "@mui/system": "^7.1.0",
-    "@mui/x-data-grid": "^8.2.0",
-    "@types/node": "^24.1.0",
-    "@types/pako": "^2.0.1",
-    "@types/react": "^19.1.6",
-    "@typescript-eslint/eslint-plugin": "^8.0.1",
-    "@typescript-eslint/parser": "^8.0.1",
-    "esbuild": "^0.25.5",
-    "eslint": "^9.28.0",
-    "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-react": "^7.20.3",
-    "eslint-plugin-react-hooks": "^7.0.0",
-    "eslint-plugin-react-refresh": "^0.4.9",
-    "eslint-plugin-unicorn": "^61.0.2",
-    "mobx": "^6.10.2",
-    "mobx-react": "^9.0.1",
-    "mobx-state-tree": "^5.3.0",
-    "prettier": "^3.0.3",
-    "pretty-bytes": "^7.0.0",
-    "react": "^19.0.0",
-    "react-dom": "^19.0.0",
-    "rimraf": "^6.0.0",
-    "rxjs": "^7.8.1",
-    "tss-react": "^4.9.2",
-    "typescript": "^5.2.2",
-    "typescript-eslint": "^8.1.0"
+    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/mobx-state-tree": "^5.4.2",
+    "@jbrowse/plugin-linear-genome-view": "^4.1.1",
+    "@mui/icons-material": "^7.3.7",
+    "@mui/material": "^7.3.7",
+    "@mui/system": "^7.3.7",
+    "@mui/x-data-grid": "^8.24.0",
+    "@types/node": "^24.10.4",
+    "@types/pako": "^2.0.4",
+    "@types/react": "^19.2.7",
+    "esbuild": "^0.27.2",
+    "eslint": "^9.39.2",
+    "eslint-plugin-import": "^2.32.0",
+    "eslint-plugin-react": "^7.37.5",
+    "eslint-plugin-react-hooks": "^7.0.1",
+    "eslint-plugin-react-refresh": "^0.4.26",
+    "eslint-plugin-unicorn": "^62.0.0",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "prettier": "^3.7.4",
+    "pretty-bytes": "^7.1.0",
+    "puppeteer": "^24.34.0",
+    "react": "^19.2.3",
+    "react-dom": "^19.2.3",
+    "rimraf": "^6.1.2",
+    "rxjs": "^7.8.2",
+    "serve": "^14.2.5",
+    "tss-react": "^4.9.20",
+    "typescript": "^5.9.3",
+    "typescript-eslint": "^8.52.0",
+    "vitest": "^4.0.16"
   }
 }

package/src/AddHighlightModel/GenomeMouseoverHighlight.tsx

@@ -12,35 +12,51 @@ const GenomeMouseoverHighlight = observer(function ({
 }: {
   model: LinearGenomeViewModel
 }) {
-  const { hovered } = getSession(model)
-  return hovered &&
-    typeof hovered === 'object' &&
-    'hoverPosition' in hovered ? (
-    <GenomeMouseoverHighlightPostNullCheck model={model} />
-  ) : null
+  const session = getSession(model)
+  const { hovered, views } = session
+
+  // Early return if no MSA view exists
+  const hasMsaView = views.some(s => s.type === 'MsaView')
+  if (!hasMsaView) {
+    return null
+  }
+
+  // Early return if no hover position
+  if (
+    !hovered ||
+    typeof hovered !== 'object' ||
+    !('hoverPosition' in hovered)
+  ) {
+    return null
+  }
+
+  return <GenomeMouseoverHighlightRenderer model={model} hovered={hovered} />
 })
 
-const GenomeMouseoverHighlightPostNullCheck = observer(function ({
+const GenomeMouseoverHighlightRenderer = observer(function ({
   model,
+  hovered,
 }: {
   model: LinearGenomeViewModel
+
+  hovered: any
 }) {
   const { classes } = useStyles()
-  const session = getSession(model)
-  if (session.views.some(s => s.type === 'MsaView')) {
-    const { hovered } = session
-    const { offsetPx } = model
-    // @ts-expect-error
-    const { coord, refName } = hovered.hoverPosition
-
-    const s = model.bpToPx({ refName, coord: coord - 1 })
-    const e = model.bpToPx({ refName, coord: coord })
-    if (s && e) {
-      const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4)
-      const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx
-      return <div className={classes.highlight} style={{ left, width }} />
-    }
+  const { offsetPx } = model
+  const { coord, refName } = hovered.hoverPosition as {
+    coord: number
+    refName: string
+  }
+
+  const s = model.bpToPx({ refName, coord: coord - 1 })
+  const e = model.bpToPx({ refName, coord: coord })
+
+  if (s && e) {
+    const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4)
+    const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx
+    return <div className={classes.highlight} style={{ left, width }} />
   }
+
   return null
 })
 

package/src/AddHighlightModel/MsaToGenomeHighlight.tsx

@@ -1,53 +1,74 @@
 import React from 'react'
 
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { getSession } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 
 import { useStyles } from './util'
-import { JBrowsePluginMsaViewModel } from '../MsaViewPanel/model'
 
+import type { JBrowsePluginMsaViewModel } from '../MsaViewPanel/model'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 type LGV = LinearGenomeViewModel
 
-function getCanonicalName(assembly: Assembly, s: string) {
-  return assembly.getCanonicalRefName(s) ?? s
-}
-
+// Outer component: only re-renders when MSA view or highlights change
 const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({
   model,
 }: {
   model: LGV
 }) {
-  const { classes } = useStyles()
-  const { assemblyManager, views } = getSession(model)
-  const p = views.find(f => f.type === 'MsaView') as
+  const { views } = getSession(model)
+  const msaView = views.find(f => f.type === 'MsaView') as
     | JBrowsePluginMsaViewModel
     | undefined
+
+  const highlights = msaView?.connectedHighlights
+
+  // Early return if no highlights - avoid all other work
+  if (!highlights || highlights.length === 0) {
+    return null
+  }
+
+  return <MsaToGenomeHighlightRenderer model={model} highlights={highlights} />
+})
+
+// Inner component: handles the scroll-dependent rendering
+const MsaToGenomeHighlightRenderer = observer(function ({
+  model,
+  highlights,
+}: {
+  model: LGV
+  highlights: { refName: string; start: number; end: number }[]
+}) {
+  const { classes } = useStyles()
+  const { assemblyManager } = getSession(model)
   const assembly = assemblyManager.get(model.assemblyNames[0]!)
-  return assembly ? (
+  const { offsetPx } = model
+
+  if (!assembly) {
+    return null
+  }
+
+  return (
     <>
-      {p?.connectedHighlights.map((r, idx) => {
-        const refName = getCanonicalName(assembly, r.refName)
+      {highlights.map((r, idx) => {
+        const refName = assembly.getCanonicalRefName(r.refName) ?? r.refName
         const s = model.bpToPx({ refName, coord: r.start })
         const e = model.bpToPx({ refName, coord: r.end })
         if (s && e) {
           const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4)
-          const left = Math.min(s.offsetPx, e.offsetPx) - model.offsetPx
+          const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx
           return (
             <div
-              key={`${JSON.stringify(r)}-${idx}`}
+              key={`${r.refName}-${r.start}-${r.end}-${idx}`}
               className={classes.highlight}
               style={{ left, width }}
             />
           )
-        } else {
-          return null
         }
+        return null
       })}
     </>
-  ) : null
+  )
 })
 
 export default MsaToGenomeHighlight

package/src/AddHighlightModel/index.tsx

@@ -1,6 +1,7 @@
 import React from 'react'
 
 import PluginManager from '@jbrowse/core/PluginManager'
+import { getSession } from '@jbrowse/core/util'
 
 import HighlightComponents from './HighlightComponents'
 
@@ -12,10 +13,14 @@ export default function AddHighlightComponentsModelF(
   pluginManager.addToExtensionPoint(
     'LinearGenomeView-TracksContainerComponent',
     // @ts-expect-error
-    (
-      rest: React.ReactNode[] = [],
-      { model }: { model: LinearGenomeViewModel },
-    ) => {
+    (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')
+      if (!hasMsaView) {
+        return rest
+      }
+
       return [
         ...rest,
         <HighlightComponents

package/src/LaunchMsaView/components/EnsemblGeneTree/EnsemblGeneTree.tsx

@@ -13,9 +13,9 @@ import { makeStyles } from 'tss-react/mui'
 
 import { ensemblGeneTreeLaunchView } from './ensemblGeneTreeLaunchView'
 import { useGeneTree } from './useGeneTree'
-import { getGeneDisplayName, getId, getTranscriptFeatures } from '../../util'
+import { getGeneDisplayName } from '../../util'
 import TranscriptSelector from '../TranscriptSelector'
-import { useFeatureSequence } from '../useFeatureSequence'
+import { useTranscriptSelection } from '../useTranscriptSelection'
 
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
@@ -41,15 +41,15 @@ const EnsemblGeneTree = observer(function ({
   const view = getContainingView(model) as LinearGenomeViewModel
   const { classes } = useStyles()
   const [launchViewError, setLaunchViewError] = useState<unknown>()
-  const options = getTranscriptFeatures(feature)
-  const [userSelection, setUserSelection] = useState(getId(options[0]))
-  const { treeData, isTreeLoading, treeError } = useGeneTree(userSelection)
-  const selectedTranscript = options.find(val => getId(val) === userSelection)!
-
-  const { proteinSequence, error: featureSequenceError } = useFeatureSequence({
-    view,
-    feature: selectedTranscript,
-  })
+  const {
+    options,
+    selectedId,
+    setSelectedId,
+    selectedTranscript,
+    proteinSequence,
+    error: featureSequenceError,
+  } = useTranscriptSelection({ feature, view })
+  const { treeData, isTreeLoading, treeError } = useGeneTree(selectedId)
 
   const loadingMessage = isTreeLoading
     ? 'Loading tree data from Ensembl GeneTree'
@@ -76,8 +76,8 @@ const EnsemblGeneTree = observer(function ({
         <TranscriptSelector
           feature={feature}
           options={options}
-          selectedTranscriptId={userSelection}
-          onTranscriptChange={setUserSelection}
+          selectedTranscript={selectedTranscript}
+          onTranscriptChange={setSelectedId}
           proteinSequence={proteinSequence}
         />
       </DialogContent>

package/src/LaunchMsaView/components/EnsemblGeneTree/useGeneTree.ts

@@ -1,10 +1,16 @@
 import useSWR from 'swr'
+
 import { geneTreeFetcher } from './ensemblGeneTreeUtils'
 
 export function useGeneTree(geneId: string) {
   const { data, error, isLoading } = useSWR(
     () => (geneId ? ['geneTree', geneId] : null),
     ([, geneId]) => geneTreeFetcher(geneId),
+    {
+      revalidateOnFocus: false,
+      revalidateOnReconnect: false,
+      revalidateIfStale: false,
+    },
   )
 
   return { treeData: data, isTreeLoading: isLoading, treeError: error }