jbrowse-plugin-msaview 2.3.2 → 2.3.5

package/dist/utils/blastCache.js

@@ -15,11 +15,10 @@ async function getDB() {
     });
 }
 function createCacheKey(proteinSequence, blastDatabase, blastProgram, transcriptId) {
-    const seqKey = proteinSequence.slice(0, 100);
     if (transcriptId) {
-        return `${blastDatabase}:${blastProgram}:${transcriptId}:${seqKey}`;
+        return `${blastDatabase}:${blastProgram}:${transcriptId}:${proteinSequence}`;
     }
-    return `${blastDatabase}:${blastProgram}:${seqKey}`;
+    return `${blastDatabase}:${blastProgram}:${proteinSequence}`;
 }
 export async function getCachedBlastResult({ proteinSequence, blastDatabase, blastProgram, transcriptId, }) {
     const db = await getDB();

package/dist/utils/blastCache.js.map

@@ -1 +1 @@
-{"version":3,"file":"blastCache.js","sourceRoot":"","sources":["../../src/utils/blastCache.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,KAAK,CAAA;AAE5B,MAAM,OAAO,GAAG,6BAA6B,CAAA;AAC7C,MAAM,UAAU,GAAG,eAAe,CAAA;AAClC,MAAM,UAAU,GAAG,CAAC,CAAA;AAmBpB,KAAK,UAAU,KAAK;IAClB,OAAO,MAAM,CAAC,OAAO,EAAE,UAAU,EAAE;QACjC,OAAO,CAAC,EAAE,EAAE,UAAU;YACpB,IAAI,UAAU,GAAG,CAAC,IAAI,EAAE,CAAC,gBAAgB,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;gBAC/D,EAAE,CAAC,iBAAiB,CAAC,UAAU,CAAC,CAAA;YAClC,CAAC;YACD,IAAI,CAAC,EAAE,CAAC,gBAAgB,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;gBAC9C,EAAE,CAAC,iBAAiB,CAAC,UAAU,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;YACrD,CAAC;QACH,CAAC;KACF,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,cAAc,CACrB,eAAuB,EACvB,aAAqB,EACrB,YAAoB,EACpB,YAAqB;IAErB,MAAM,MAAM,GAAG,eAAe,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;IAC5C,IAAI,YAAY,EAAE,CAAC;QACjB,OAAO,GAAG,aAAa,IAAI,YAAY,IAAI,YAAY,IAAI,MAAM,EAAE,CAAA;IACrE,CAAC;IACD,OAAO,GAAG,aAAa,IAAI,YAAY,IAAI,MAAM,EAAE,CAAA;AACrD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,oBAAoB,CAAC,EACzC,eAAe,EACf,aAAa,EACb,YAAY,EACZ,YAAY,GAMb;IACC,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,GAAG,cAAc,CACvB,eAAe,EACf,aAAa,EACb,YAAY,EACZ,YAAY,CACb,CAAA;IACD,OAAO,EAAE,CAAC,GAAG,CAAC,UAAU,EAAE,EAAE,CAAC,CAAA;AAC/B,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,eAAe,CAAC,EACpC,eAAe,EACf,aAAa,EACb,YAAY,EACZ,YAAY,EACZ,GAAG,EACH,IAAI,EACJ,YAAY,EACZ,GAAG,EACH,MAAM,EACN,YAAY,EACZ,cAAc,EACd,QAAQ,GAcT;IACC,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,GAAG,cAAc,CACvB,eAAe,EACf,aAAa,EACb,YAAY,EACZ,YAAY,CACb,CAAA;IACD,MAAM,KAAK,GAAsB;QAC/B,EAAE;QACF,eAAe;QACf,aAAa;QACb,YAAY;QACZ,YAAY;QACZ,GAAG;QACH,IAAI;QACJ,YAAY;QACZ,GAAG;QACH,SAAS,EAAE,IAAI,CAAC,GAAG,EAAE;QACrB,MAAM;QACN,YAAY;QACZ,cAAc;QACd,QAAQ;KACT,CAAA;IACD,MAAM,EAAE,CAAC,GAAG,CAAC,UAAU,EAAE,KAAK,CAAC,CAAA;IAC/B,OAAO,KAAK,CAAA;AACd,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,mBAAmB;IACvC,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,OAAO,GAAG,MAAM,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IAC3C,OAAO,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,CAAC,CAAA;AAC9D,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,wBAAwB,CAAC,MAAc;IAC3D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,OAAO,GAAG,MAAM,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IAC3C,OAAO,OAAO;SACX,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC;SAChC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,CAAC,CAAA;AAClD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,EAAU;IACjD,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,CAAC,MAAM,CAAC,UAAU,EAAE,EAAE,CAAC,CAAA;AACjC,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,qBAAqB;IACzC,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,CAAC,KAAK,CAAC,UAAU,CAAC,CAAA;AAC5B,CAAC"}
+{"version":3,"file":"blastCache.js","sourceRoot":"","sources":["../../src/utils/blastCache.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,KAAK,CAAA;AAE5B,MAAM,OAAO,GAAG,6BAA6B,CAAA;AAC7C,MAAM,UAAU,GAAG,eAAe,CAAA;AAClC,MAAM,UAAU,GAAG,CAAC,CAAA;AAmBpB,KAAK,UAAU,KAAK;IAClB,OAAO,MAAM,CAAC,OAAO,EAAE,UAAU,EAAE;QACjC,OAAO,CAAC,EAAE,EAAE,UAAU;YACpB,IAAI,UAAU,GAAG,CAAC,IAAI,EAAE,CAAC,gBAAgB,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;gBAC/D,EAAE,CAAC,iBAAiB,CAAC,UAAU,CAAC,CAAA;YAClC,CAAC;YACD,IAAI,CAAC,EAAE,CAAC,gBAAgB,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;gBAC9C,EAAE,CAAC,iBAAiB,CAAC,UAAU,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;YACrD,CAAC;QACH,CAAC;KACF,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,cAAc,CACrB,eAAuB,EACvB,aAAqB,EACrB,YAAoB,EACpB,YAAqB;IAErB,IAAI,YAAY,EAAE,CAAC;QACjB,OAAO,GAAG,aAAa,IAAI,YAAY,IAAI,YAAY,IAAI,eAAe,EAAE,CAAA;IAC9E,CAAC;IACD,OAAO,GAAG,aAAa,IAAI,YAAY,IAAI,eAAe,EAAE,CAAA;AAC9D,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,oBAAoB,CAAC,EACzC,eAAe,EACf,aAAa,EACb,YAAY,EACZ,YAAY,GAMb;IACC,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,GAAG,cAAc,CACvB,eAAe,EACf,aAAa,EACb,YAAY,EACZ,YAAY,CACb,CAAA;IACD,OAAO,EAAE,CAAC,GAAG,CAAC,UAAU,EAAE,EAAE,CAAC,CAAA;AAC/B,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,eAAe,CAAC,EACpC,eAAe,EACf,aAAa,EACb,YAAY,EACZ,YAAY,EACZ,GAAG,EACH,IAAI,EACJ,YAAY,EACZ,GAAG,EACH,MAAM,EACN,YAAY,EACZ,cAAc,EACd,QAAQ,GAcT;IACC,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,GAAG,cAAc,CACvB,eAAe,EACf,aAAa,EACb,YAAY,EACZ,YAAY,CACb,CAAA;IACD,MAAM,KAAK,GAAsB;QAC/B,EAAE;QACF,eAAe;QACf,aAAa;QACb,YAAY;QACZ,YAAY;QACZ,GAAG;QACH,IAAI;QACJ,YAAY;QACZ,GAAG;QACH,SAAS,EAAE,IAAI,CAAC,GAAG,EAAE;QACrB,MAAM;QACN,YAAY;QACZ,cAAc;QACd,QAAQ;KACT,CAAA;IACD,MAAM,EAAE,CAAC,GAAG,CAAC,UAAU,EAAE,KAAK,CAAC,CAAA;IAC/B,OAAO,KAAK,CAAA;AACd,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,mBAAmB;IACvC,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,OAAO,GAAG,MAAM,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IAC3C,OAAO,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,CAAC,CAAA;AAC9D,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,wBAAwB,CAAC,MAAc;IAC3D,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,OAAO,GAAG,MAAM,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;IAC3C,OAAO,OAAO;SACX,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,MAAM,CAAC;SAChC,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,CAAC,CAAA;AAClD,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,EAAU;IACjD,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,CAAC,MAAM,CAAC,UAAU,EAAE,EAAE,CAAC,CAAA;AACjC,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,qBAAqB;IACzC,MAAM,EAAE,GAAG,MAAM,KAAK,EAAE,CAAA;IACxB,MAAM,EAAE,CAAC,KAAK,CAAC,UAAU,CAAC,CAAA;AAC5B,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.2.11";
+export declare const version = "2.3.5";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '2.2.11';
+export const version = '2.3.5';
 //# sourceMappingURL=version.js.map

package/dist/version.js.map

@@ -1 +1 @@
-{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,QAAQ,CAAA"}
+{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,OAAO,CAAA"}

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.3.2",
+  "version": "2.3.5",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -15,65 +15,66 @@
     "dist",
     "src"
   ],
-  "scripts": {
-    "clean": "rimraf dist",
-    "start": "node esbuild.mjs --watch",
-    "format": "prettier --write .",
-    "build": "tsc && NODE_ENV=production node esbuild.mjs && cp distconfig.json dist/config.json",
-    "prebuild": "yarn clean",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
-    "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": "node -e \"console.log('export const version = \\'' + require('./package.json').version + '\\'')\" > src/version.ts && git add -A src && git diff --cached --quiet || git commit -m '[skip ci] Bump version.ts' && git push --follow-tags",
-    "preversion": "yarn lint"
-  },
   "dependencies": {
     "@emotion/styled": "^11.14.1",
-    "g2p_mapper": "^2.0.0",
+    "g2p_mapper": "^2.0.1",
     "idb": "^8.0.3",
     "pako-esm2": "^2.0.2",
-    "react-msaview": "^5.0.13",
+    "react-msaview": "^5.0.16",
     "swr": "^2.4.1"
   },
   "devDependencies": {
     "@emotion/react": "^11.14.0",
-    "@eslint/js": "^9.39.4",
+    "@eslint/js": "^10.0.1",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
-    "@jbrowse/core": "^4.1.15",
+    "@jbrowse/core": "^4.2.0",
     "@jbrowse/mobx-state-tree": "^5.6.0",
-    "@jbrowse/plugin-linear-genome-view": "^4.1.15",
+    "@jbrowse/plugin-linear-genome-view": "^4.2.0",
     "@mui/icons-material": "^7.3.10",
     "@mui/material": "^7.3.10",
     "@mui/system": "^7.3.10",
     "@mui/x-data-grid": "^8.28.2",
     "@types/node": "^25.6.0",
     "@types/react": "^19.2.14",
+    "@typescript-eslint/eslint-plugin": "^8.59.1",
+    "@typescript-eslint/parser": "^8.59.1",
     "esbuild": "^0.28.0",
-    "eslint": "^9.39.4",
-    "eslint-plugin-import": "^2.32.0",
+    "eslint": "^10.2.1",
+    "eslint-plugin-import-x": "^4.16.2",
     "eslint-plugin-react": "^7.37.5",
-    "eslint-plugin-react-hooks": "^7.0.1",
-    "eslint-plugin-react-refresh": "^0.5.2",
+    "eslint-plugin-react-hooks": "^7.1.1",
     "eslint-plugin-unicorn": "^64.0.0",
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
-    "prettier": "^3.8.2",
+    "prettier": "^3.8.3",
     "pretty-bytes": "^7.1.0",
-    "puppeteer": "^24.40.0",
+    "puppeteer": "^24.42.0",
     "react": "^19.2.5",
     "react-dom": "^19.2.5",
     "rimraf": "^6.1.3",
     "rxjs": "^7.8.2",
     "serve": "^14.2.6",
     "tss-react": "^4.9.20",
-    "typescript": "^6.0.2",
-    "typescript-eslint": "^8.58.2",
-    "vitest": "^4.1.4"
+    "typescript": "^6.0.3",
+    "typescript-eslint": "^8.59.1",
+    "vitest": "^4.1.5"
+  },
+  "scripts": {
+    "clean": "rimraf dist",
+    "start": "node esbuild.mjs --watch",
+    "format": "pnpm prettier --write .",
+    "build": "tsc && NODE_ENV=production node esbuild.mjs && cp distconfig.json dist/config.json",
+    "prebuild": "pnpm clean",
+    "lint": "eslint src --report-unused-disable-directives --max-warnings 0",
+    "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",
+    "preversion": "pnpm lint",
+    "version": "node -e \"console.log('export const version = \\'' + require('./package.json').version + '\\'')\" > src/version.ts && git add src/version.ts",
+    "postversion": "git push --follow-tags"
   }
-}
+}

package/src/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.ts

@@ -42,25 +42,16 @@ export default class BgzipFastaMsaAdapter extends BaseAdapter {
 
   async getMSAList() {
     const refNames = await this.getMSARefs()
-    const list = new Set<string>()
     const val = this.getConf('msaRegex')
     const re = new RegExp(val)
-    for (let i = 0, l = refNames.length; i < l; i++) {
-      list.add(refNames[i]!.split(re)[0]!)
-    }
+    const list = new Set(refNames.map(name => name.split(re)[0]!))
     return [...list]
   }
 
   async getMSA(id: string) {
     const adapter = await this.configure()
     const refNames = await adapter.getRefNames()
-    const rows = []
-    for (let i = 0, l = refNames.length; i < l; i++) {
-      const refName = refNames[i]!
-      if (refName.startsWith(id)) {
-        rows.push(refName)
-      }
-    }
+    const rows = refNames.filter(refName => refName.startsWith(id))
     return firstValueFrom(
       adapter
         .getFeaturesInMultipleRegions(

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

@@ -1,4 +1,4 @@
-import React, { useEffect, useMemo, useState } from 'react'
+import React, { useMemo, useState } from 'react'
 
 import { ErrorMessage } from '@jbrowse/core/ui'
 import { getContainingView } from '@jbrowse/core/util'
@@ -15,11 +15,7 @@ import {
 import { observer } from 'mobx-react'
 
 import { blastLaunchViewFromCache } from './blastLaunchView'
-import {
-  clearAllCachedResults,
-  deleteCachedResult,
-  getAllCachedResults,
-} from '../../../utils/blastCache'
+import { useCachedBlastResults } from './useCachedBlastResults'
 import { getGeneIdentifiers } from '../../util'
 
 import type { CachedBlastResult } from '../../../utils/blastCache'
@@ -49,44 +45,13 @@ const CachedBlastResults = observer(function ({
   handleClose: () => void
   feature: Feature
 }) {
-  const [results, setResults] = useState<CachedBlastResult[]>([])
-  const [loading, setLoading] = useState(true)
-  const [error, setError] = useState<unknown>()
   const view = getContainingView(model) as LinearGenomeViewModel
+  const [operationError, setOperationError] = useState<unknown>()
 
   const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature])
 
-  useEffect(() => {
-    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-    ;(async () => {
-      try {
-        const cached = await getAllCachedResults()
-        setResults(cached.filter(r => r.geneId && geneIds.includes(r.geneId)))
-        setLoading(false)
-      } catch (e) {
-        console.error(e)
-        setError(e)
-      }
-    })()
-  }, [geneIds])
-
-  const handleDelete = async (id: string) => {
-    try {
-      await deleteCachedResult(id)
-      setResults(r => r.filter(result => result.id !== id))
-    } catch (e) {
-      setError(e)
-    }
-  }
-
-  const handleClearAll = async () => {
-    try {
-      await clearAllCachedResults()
-      setResults([])
-    } catch (e) {
-      setError(e)
-    }
-  }
+  const { results, error, isLoading, handleDelete, handleClearAll } =
+    useCachedBlastResults(geneIds)
 
   const handleUseCached = (cached: CachedBlastResult) => {
     blastLaunchViewFromCache({
@@ -97,11 +62,12 @@ const CachedBlastResults = observer(function ({
     handleClose()
   }
 
-  if (error) {
-    return <ErrorMessage error={error} />
+  const displayError = error ?? operationError
+  if (displayError) {
+    return <ErrorMessage error={displayError} />
   }
 
-  if (loading) {
+  if (isLoading) {
     return <Typography>Loading cached results...</Typography>
   }
 
@@ -130,9 +96,13 @@ const CachedBlastResults = observer(function ({
         <Button
           size="small"
           color="error"
-          onClick={() => {
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
-            handleClearAll()
+          onClick={async () => {
+            try {
+              setOperationError(undefined)
+              await handleClearAll()
+            } catch (e) {
+              setOperationError(e)
+            }
           }}
         >
           Clear All
@@ -147,10 +117,14 @@ const CachedBlastResults = observer(function ({
               <IconButton
                 edge="end"
                 size="small"
-                onClick={e => {
+                onClick={async e => {
                   e.stopPropagation()
-                  // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                  handleDelete(result.id)
+                  try {
+                    setOperationError(undefined)
+                    await handleDelete(result.id)
+                  } catch (err) {
+                    setOperationError(err)
+                  }
                 }}
               >
                 <DeleteIcon fontSize="small" />

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

@@ -1,4 +1,4 @@
-import React, { useEffect, useMemo, useState } from 'react'
+import React, { useMemo, useState } from 'react'
 
 import { ErrorMessage } from '@jbrowse/core/ui'
 import { getContainingView } from '@jbrowse/core/util'
@@ -19,8 +19,8 @@ import { makeStyles } from 'tss-react/mui'
 import CachedBlastResults from './CachedBlastResults'
 import { blastLaunchView } from './blastLaunchView'
 import { msaAlgorithms } from './consts'
+import { useCachedBlastResults } from './useCachedBlastResults'
 import TextField2 from '../../../components/TextField2'
-import { getAllCachedResults } from '../../../utils/blastCache'
 import {
   getGeneDisplayName,
   getGeneIdentifiers,
@@ -83,24 +83,10 @@ const NCBIBlastAutomaticPanel = observer(function ({
     useState<MsaAlgorithm>('clustalo')
   const [selectedBlastProgram, setSelectedBlastProgram] =
     useState<blastProgramsT>('quick-blastp')
-  const [hasCachedResults, setHasCachedResults] = useState(false)
-  const [error, setError] = useState<unknown>()
 
   const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature])
-  useEffect(() => {
-    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-    ;(async () => {
-      try {
-        const results = await getAllCachedResults()
-        setHasCachedResults(
-          results.some(r => r.geneId && geneIds.includes(r.geneId)),
-        )
-      } catch (e) {
-        console.error(e)
-        setError(e)
-      }
-    })()
-  }, [geneIds])
+  const { results: cachedResults, error: cachedResultsError } =
+    useCachedBlastResults(geneIds)
 
   const {
     options,
@@ -110,7 +96,7 @@ const NCBIBlastAutomaticPanel = observer(function ({
     proteinSequence,
     error: proteinSequenceError,
   } = useTranscriptSelection({ feature, view })
-  const e = proteinSequenceError ?? launchViewError ?? error
+  const e = proteinSequenceError ?? launchViewError ?? cachedResultsError
   return (
     <>
       <DialogContent className={classes.dialogContent}>
@@ -205,7 +191,7 @@ const NCBIBlastAutomaticPanel = observer(function ({
           submitting BLAST yourself and downloading the resulting files
         </Typography>
 
-        {hasCachedResults ? (
+        {cachedResults.length > 0 ? (
           <Accordion className={classes.cachedResultsAccordion}>
             <AccordionSummary expandIcon={<ExpandMoreIcon />}>
               <Typography>Previous BLAST Results</Typography>

package/src/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.ts

@@ -0,0 +1,49 @@
+import useSWR from 'swr'
+
+import {
+  clearAllCachedResults,
+  deleteCachedResult,
+  getAllCachedResults,
+} from '../../../utils/blastCache'
+
+const swrConfig = {
+  revalidateOnFocus: false,
+  revalidateOnReconnect: false,
+  revalidateIfStale: false,
+}
+
+export function useCachedBlastResults(geneIds: string[]) {
+  const {
+    data: results,
+    error,
+    mutate,
+  } = useSWR(
+    `cached-blast-${geneIds.join(',')}`,
+    async () => {
+      const cached = await getAllCachedResults()
+      return cached.filter(r => r.geneId && geneIds.includes(r.geneId))
+    },
+    swrConfig,
+  )
+
+  const handleDelete = async (id: string) => {
+    await deleteCachedResult(id)
+    await mutate(
+      results => results?.filter(result => result.id !== id) ?? [],
+      false,
+    )
+  }
+
+  const handleClearAll = async () => {
+    await clearAllCachedResults()
+    await mutate([], false)
+  }
+
+  return {
+    results: results ?? [],
+    error,
+    isLoading: !results && !error,
+    handleDelete,
+    handleClearAll,
+  }
+}

package/src/LaunchMsaView/components/useTranscriptSelection.ts

@@ -1,4 +1,4 @@
-import { useEffect, useMemo, useState } from 'react'
+import { useMemo, useState } from 'react'
 
 import { featureMatchesId, getId, getSortedTranscriptFeatures } from '../util'
 import { useFeatureSequence } from './useFeatureSequence'
@@ -9,6 +9,24 @@ function featureInValidIds(feature: Feature, validIds: string[]): boolean {
   return validIds.some(id => featureMatchesId(feature, id))
 }
 
+function findValidSelection(
+  currentId: string,
+  options: Feature[],
+  validIds: string[] | undefined,
+): string | undefined {
+  if (!validIds || validIds.length === 0) {
+    return undefined
+  }
+
+  const currentFeature = options.find(opt => getId(opt) === currentId)
+  if (!currentFeature || featureInValidIds(currentFeature, validIds)) {
+    return undefined
+  }
+
+  const validOption = options.find(opt => featureInValidIds(opt, validIds))
+  return validOption ? getId(validOption) : undefined
+}
+
 export function useTranscriptSelection({
   feature,
   view,
@@ -20,29 +38,19 @@ export function useTranscriptSelection({
 }) {
   const options = useMemo(() => getSortedTranscriptFeatures(feature), [feature])
   const [selectedId, setSelectedId] = useState(() => getId(options[0]))
-  const selectedTranscript = options.find(val => getId(val) === selectedId)
+  const validatedSelectedId =
+    findValidSelection(selectedId, options, validIds) || selectedId
+  const selectedTranscript = options.find(
+    val => getId(val) === validatedSelectedId,
+  )
   const { proteinSequence, error } = useFeatureSequence({
     view,
     feature: selectedTranscript,
   })
 
-  useEffect(() => {
-    if (validIds && validIds.length > 0) {
-      const currentFeature = options.find(opt => getId(opt) === selectedId)
-      if (currentFeature && !featureInValidIds(currentFeature, validIds)) {
-        const validOption = options.find(opt =>
-          featureInValidIds(opt, validIds),
-        )
-        if (validOption) {
-          setSelectedId(getId(validOption))
-        }
-      }
-    }
-  }, [validIds, options, selectedId])
-
   return {
     options,
-    selectedId,
+    selectedId: validatedSelectedId,
     setSelectedId,
     selectedTranscript,
     proteinSequence,

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -13,6 +13,22 @@ import { getUniprotIdFromAlphaFoldUrl } from './util'
 
 import type { JBrowsePluginMsaViewModel } from './model'
 
+interface ProteinView {
+  type: 'ProteinView'
+  id: string
+  structures: {
+    connectedViewId?: string
+    uniprotId?: string
+    structureSequences?: unknown[]
+    hoverGenomeHighlights?: { start: number; end: number }[]
+  }[]
+}
+
+function isProteinView(view: unknown): view is ProteinView {
+  const v = view as Record<string, unknown>
+  return v.type === 'ProteinView' && Array.isArray(v.structures)
+}
+
 export function loadStoredData(self: JBrowsePluginMsaViewModel) {
   const { dataStoreId, rows } = self
   if (dataStoreId && rows.length === 0) {
@@ -202,10 +218,10 @@ export function autoConnectStructures(self: JBrowsePluginMsaViewModel) {
   }
 
   for (const view of views) {
-    const v = view as any
-    if (v.type !== 'ProteinView' || !v.structures) {
+    if (!isProteinView(view)) {
       continue
     }
+    const v = view
 
     for (
       let structureIdx = 0;
@@ -213,6 +229,9 @@ export function autoConnectStructures(self: JBrowsePluginMsaViewModel) {
       structureIdx++
     ) {
       const structure = v.structures[structureIdx]
+      if (!structure) {
+        continue
+      }
 
       if (structure.connectedViewId !== connectedViewId) {
         continue
@@ -250,13 +269,13 @@ export function observeProteinHighlights(self: JBrowsePluginMsaViewModel) {
     return
   }
 
-  const columns: number[] = []
+  const columns = new Set<number>()
 
   for (const view of views) {
-    const v = view as any
-    if (v.type !== 'ProteinView' || !v.structures) {
+    if (!isProteinView(view)) {
       continue
     }
+    const v = view
 
     for (const structure of v.structures) {
       if (structure.connectedViewId !== connectedViewId) {
@@ -274,16 +293,14 @@ export function observeProteinHighlights(self: JBrowsePluginMsaViewModel) {
           const proteinPos = g2p[coord]
           if (proteinPos !== undefined) {
             const col = self.seqPosToGlobalCol(querySeqName, proteinPos)
-            if (!columns.includes(col)) {
-              columns.push(col)
-            }
+            columns.add(col)
           }
         }
       }
     }
   }
 
-  const visibleColumns = columns
+  const visibleColumns = Array.from(columns)
     .map(col => self.globalColToVisibleCol(col))
     .filter((col): col is number => col !== undefined)
 

package/src/MsaViewPanel/components/ErrorBoundary.tsx

@@ -0,0 +1,40 @@
+import type { ReactNode } from 'react'
+import React, { Component } from 'react'
+
+import { ErrorMessage } from '@jbrowse/core/ui'
+
+interface Props {
+  children: ReactNode
+}
+
+interface State {
+  hasError: boolean
+  error: unknown
+}
+
+export class ErrorBoundary extends Component<Props, State> {
+  constructor(props: Props) {
+    super(props)
+    this.state = { hasError: false, error: null }
+  }
+
+  static getDerivedStateFromError(error: unknown) {
+    return { hasError: true, error }
+  }
+
+  componentDidCatch(error: unknown, info: React.ErrorInfo) {
+    console.error('MsaViewPanel error:', error, info.componentStack)
+  }
+
+  render() {
+    if (this.state.hasError) {
+      return (
+        <div style={{ padding: 20 }}>
+          <ErrorMessage error={this.state.error} />
+        </div>
+      )
+    }
+
+    return this.props.children
+  }
+}

package/src/MsaViewPanel/components/MsaViewPanel.tsx

@@ -4,6 +4,7 @@ import { LoadingEllipses } from '@jbrowse/core/ui'
 import { observer } from 'mobx-react'
 import { MSAView } from 'react-msaview'
 
+import { ErrorBoundary } from './ErrorBoundary'
 import LoadingBLAST from './LoadingBLAST'
 
 import type { JBrowsePluginMsaViewModel } from '../model'
@@ -15,17 +16,19 @@ const MsaViewPanel = observer(function MsaViewPanel2({
 }) {
   const { blastParams, loadingStoredData } = model
   return (
-    <div>
-      {blastParams ? (
-        <LoadingBLAST model={model} baseUrl={blastParams.baseUrl} />
-      ) : loadingStoredData ? (
-        <div style={{ padding: 20 }}>
-          <LoadingEllipses message="Loading MSA data" variant="h6" />
-        </div>
-      ) : (
-        <MSAView model={model} />
-      )}
-    </div>
+    <ErrorBoundary>
+      <div>
+        {blastParams ? (
+          <LoadingBLAST model={model} baseUrl={blastParams.baseUrl} />
+        ) : loadingStoredData ? (
+          <div style={{ padding: 20 }}>
+            <LoadingEllipses message="Loading MSA data" variant="h6" />
+          </div>
+        ) : (
+          <MSAView model={model} />
+        )}
+      </div>
+    </ErrorBoundary>
   )
 })