jbrowse-plugin-msaview 2.0.3 → 2.0.4

package/dist/utils/msa.js

@@ -61,6 +61,7 @@ async function runMafft({ sequence, onProgress, }) {
     };
 }
 async function wait({ onProgress, jobId, algorithm, }) {
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     while (true) {
         for (let i = 0; i < 10; i++) {
             await timeout(1000);
@@ -70,6 +71,9 @@ async function wait({ onProgress, jobId, algorithm, }) {
         if (result === 'FINISHED') {
             break;
         }
+        else if (result.includes('FAILURE')) {
+            throw new Error(`Failed to run: jobId ${jobId}`);
+        }
     }
 }
 export async function launchMSA({ algorithm, sequence, onProgress, }) {

package/dist/utils/msa.js.map

@@ -1 +1 @@
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+{"version":3,"file":"msa.js","sourceRoot":"","sources":["../../src/utils/msa.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AAE5C,MAAM,IAAI,GAAG,2CAA2C,CAAA;AAExD,KAAK,UAAU,eAAe,CAAC,EAC7B,QAAQ,EACR,UAAU,GAIX;IACC,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,eAAe,EAAE;QACpD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,KAAK,EAAE,uBAAuB;YAC9B,QAAQ;SACT,CAAC;KACH,CAAC,CAAA;IACF,MAAM,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,UAAU,EAAE,CAAC,CAAA;IACxD,OAAO;QACL,GAAG,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,oBAAoB,KAAK,kBAAkB,CAAC;QACxE,IAAI,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,oBAAoB,KAAK,YAAY,CAAC;KACpE,CAAA;AACH,CAAC;AAED,KAAK,UAAU,SAAS,CAAC,EACvB,QAAQ,EACR,UAAU,GAIX;IACC,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,aAAa,EAAE;QAClD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,KAAK,EAAE,uBAAuB;YAC9B,MAAM,EAAE,KAAK;YACb,IAAI,EAAE,OAAO;YACb,QAAQ;SACT,CAAC;KACH,CAAC,CAAA;IACF,MAAM,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAA;IACtD,OAAO;QACL,GAAG,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,kBAAkB,KAAK,KAAK,CAAC;QACzD,IAAI,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,kBAAkB,KAAK,YAAY,CAAC;KAClE,CAAA;AACH,CAAC;AAED,KAAK,UAAU,SAAS,CAAC,EACvB,QAAQ,EACR,UAAU,GAIX;IACC,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,aAAa,EAAE;QAClD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,KAAK,EAAE,uBAAuB;YAC9B,KAAK,EAAE,SAAS;YAChB,QAAQ;SACT,CAAC;KACH,CAAC,CAAA;IACF,MAAM,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAA;IACtD,OAAO;QACL,GAAG,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,kBAAkB,KAAK,KAAK,CAAC;QACzD,IAAI,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,kBAAkB,KAAK,YAAY,CAAC;KAClE,CAAA;AACH,CAAC;AAED,KAAK,UAAU,QAAQ,CAAC,EACtB,QAAQ,EACR,UAAU,GAIX;IACC,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,YAAY,EAAE;QACjD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,KAAK,EAAE,uBAAuB;YAC9B,KAAK,EAAE,SAAS;YAChB,QAAQ;SACT,CAAC;KACH,CAAC,CAAA;IACF,MAAM,IAAI,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,OAAO,EAAE,UAAU,EAAE,CAAC,CAAA;IACrD,OAAO;QACL,GAAG,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,iBAAiB,KAAK,KAAK,CAAC;QACxD,IAAI,EAAE,MAAM,SAAS,CAAC,GAAG,IAAI,iBAAiB,KAAK,YAAY,CAAC;KACjE,CAAA;AACH,CAAC;AACD,KAAK,UAAU,IAAI,CAAC,EAClB,UAAU,EACV,KAAK,EACL,SAAS,GAKV;IACC,uEAAuE;IACvE,OAAO,IAAI,EAAE,CAAC;QACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YAC5B,MAAM,OAAO,CAAC,IAAI,CAAC,CAAA;YACnB,UAAU,CAAC,gCAAgC,EAAE,GAAG,CAAC,EAAE,CAAC,CAAA;QACtD,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,IAAI,SAAS,WAAW,KAAK,EAAE,CAAC,CAAA;QAEtE,IAAI,MAAM,KAAK,UAAU,EAAE,CAAC;YAC1B,MAAK;QACP,CAAC;aAAM,IAAI,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;YACtC,MAAM,IAAI,KAAK,CAAC,wBAAwB,KAAK,EAAE,CAAC,CAAA;QAClD,CAAC;IACH,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,EAC9B,SAAS,EACT,QAAQ,EACR,UAAU,GAKX;IACC,UAAU,CAAC,aAAa,SAAS,SAAS,CAAC,CAAA;IAC3C,QAAQ,SAAS,EAAE,CAAC;QAClB,KAAK,UAAU,CAAC,CAAC,CAAC;YAChB,OAAO,eAAe,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAA;QAClD,CAAC;QACD,KAAK,QAAQ,CAAC,CAAC,CAAC;YACd,OAAO,SAAS,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAA;QAC5C,CAAC;QACD,KAAK,QAAQ,CAAC,CAAC,CAAC;YACd,OAAO,SAAS,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAA;QAC5C,CAAC;QACD,KAAK,OAAO,CAAC,CAAC,CAAC;YACb,OAAO,QAAQ,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,CAAA;QAC3C,CAAC;QACD,OAAO,CAAC,CAAC,CAAC;YACR,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;QACtC,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/utils/ncbiBlast.js

@@ -9,9 +9,11 @@ export async function queryBlast({ query, blastDatabase, blastProgram, onProgres
     });
     onRid(rid);
     await waitForRid({ rid, onProgress });
-    const ret = await jsonfetch(`${BLAST_URL}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`);
-    const hits = ret.BlastOutput2[0].report.results.search.hits;
-    return { rid, hits };
+    const ret = (await jsonfetch(`${BLAST_URL}?CMD=Get&RID=${rid}&FORMAT_TYPE=JSON2_S&FORMAT_OBJECT=Alignment`));
+    return {
+        rid,
+        hits: ret.BlastOutput2[0]?.report.results.search.hits ?? [],
+    };
 }
 async function initialQuery({ query, blastProgram, blastDatabase, }) {
     const res = await textfetch(BLAST_URL, {
@@ -32,14 +34,15 @@ async function initialQuery({ query, blastProgram, blastDatabase, }) {
     // the initial submission/query to the BLAST "REST API" does not return JSON
     // as a response (e.g. FORMAT_TYPE=JSON does not work), so the RID is
     // literally parsed from the text of the HTML that is returned
-    const rid = /^    RID = (.*$)/m.exec(res)?.[1];
-    const rtoe = /^    RTOE = (.*$)/m.exec(res)?.[1];
+    const rid = /^ {4}RID = (.*$)/m.exec(res)?.[1];
+    const rtoe = /^ {4}RTOE = (.*$)/m.exec(res)?.[1];
     if (!rid) {
         throw new Error('Failed to get RID from BLAST request');
     }
     return { rid, rtoe };
 }
 async function waitForRid({ rid, onProgress, }) {
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     while (true) {
         const iter = 20;
         for (let i = 0; i < iter; i++) {

package/dist/utils/ncbiBlast.js.map

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+{"version":3,"file":"ncbiBlast.js","sourceRoot":"","sources":["../../src/utils/ncbiBlast.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,SAAS,CAAA;AAEvD,MAAM,CAAC,MAAM,SAAS,GAAG,gDAAgD,CAAA;AAEzE,MAAM,CAAC,KAAK,UAAU,UAAU,CAAC,EAC/B,KAAK,EACL,aAAa,EACb,YAAY,EACZ,UAAU,EACV,KAAK,GAON;IACC,UAAU,CAAC,6BAA6B,CAAC,CAAA;IACzC,MAAM,EAAE,GAAG,EAAE,GAAG,MAAM,YAAY,CAAC;QACjC,KAAK;QACL,aAAa;QACb,YAAY;KACb,CAAC,CAAA;IACF,KAAK,CAAC,GAAG,CAAC,CAAA;IACV,MAAM,UAAU,CAAC,EAAE,GAAG,EAAE,UAAU,EAAE,CAAC,CAAA;IACrC,MAAM,GAAG,GAAG,CAAC,MAAM,SAAS,CAC1B,GAAG,SAAS,gBAAgB,GAAG,8CAA8C,CAC9E,CAaA,CAAA;IACD,OAAO;QACL,GAAG;QACH,IAAI,EAAE,GAAG,CAAC,YAAY,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,IAAI,EAAE;KAC5D,CAAA;AACH,CAAC;AAED,KAAK,UAAU,YAAY,CAAC,EAC1B,KAAK,EACL,YAAY,EACZ,aAAa,GAKd;IACC,MAAM,GAAG,GAAG,MAAM,SAAS,CAAC,SAAS,EAAE;QACrC,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,GAAG,EAAE,KAAK;YACV,OAAO,EAAE,YAAY;YACrB,QAAQ,EAAE,aAAa;YACvB,KAAK,EAAE,KAAK;YACZ,GAAG,CAAC,aAAa,KAAK,kBAAkB;gBACtC,CAAC,CAAC;oBACE,YAAY,EAAE,IAAI;oBAClB,OAAO,EAAE,wBAAwB;iBAClC;gBACH,CAAC,CAAC,EAAE,CAAC;SACR,CAAC;KACH,CAAC,CAAA;IAEF,4EAA4E;IAC5E,qEAAqE;IACrE,8DAA8D;IAC9D,MAAM,GAAG,GAAG,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IAC9C,MAAM,IAAI,GAAG,oBAAoB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IAEhD,IAAI,CAAC,GAAG,EAAE,CAAC;QACT,MAAM,IAAI,KAAK,CAAC,sCAAsC,CAAC,CAAA;IACzD,CAAC;IACD,OAAO,EAAE,GAAG,EAAE,IAAI,EAAE,CAAA;AACtB,CAAC;AAED,KAAK,UAAU,UAAU,CAAC,EACxB,GAAG,EACH,UAAU,GAIX;IACC,uEAAuE;IACvE,OAAO,IAAI,EAAE,CAAC;QACZ,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,CAAC;YAC9B,MAAM,OAAO,CAAC,IAAI,CAAC,CAAA;YACnB,UAAU,CAAC,kCAAkC,IAAI,GAAG,CAAC,EAAE,CAAC,CAAA;QAC1D,CAAC;QAED,MAAM,GAAG,GAAG,MAAM,SAAS,CACzB,GAAG,SAAS,yCAAyC,GAAG,EAAE,CAC3D,CAAA;QACD,IAAI,oBAAoB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YACnC,SAAQ;QACV,CAAC;aAAM,IAAI,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YACzC,MAAM,IAAI,KAAK,CACb,SAAS,GAAG,uDAAuD,CACpE,CAAA;QACH,CAAC;aAAM,IAAI,kBAAkB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;YACxC,IAAI,sBAAsB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBACrC,OAAO,IAAI,CAAA;YACb,CAAC;iBAAM,CAAC;gBACN,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;YAClC,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.0.3",
+  "version": "2.0.4",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "keywords": [
@@ -25,9 +25,10 @@
   "scripts": {
     "clean": "rimraf dist",
     "start": "node esbuild.mjs",
+    "format": "prettier --write .",
     "build": "tsc && NODE_ENV=production node esbuild.mjs",
     "prebuild": "npm run clean",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src/",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "prepack": "npm run build",
     "postversion": "git push --follow-tags"
   },
@@ -41,14 +42,13 @@
   },
   "devDependencies": {
     "@emotion/react": "^11.10.4",
-    "@eslint/compat": "^1.1.0",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
     "@jbrowse/core": "^2.10.1",
     "@jbrowse/plugin-linear-genome-view": "^2.7.0",
     "@mui/icons-material": "^5.15.6",
     "@mui/material": "^5.14.12",
     "@mui/system": "^5.14.12",
-    "@mui/x-data-grid": "^7.3.0",
+    "@mui/x-data-grid": "^7.13.0",
     "@types/node": "^20.8.6",
     "@types/pako": "^2.0.1",
     "@types/react": "^18.2.28",
@@ -56,10 +56,9 @@
     "@typescript-eslint/parser": "^8.0.1",
     "esbuild": "^0.23.0",
     "eslint": "^9.0.0",
-    "eslint-config-prettier": "^9.1.0",
-    "eslint-plugin-prettier": "^5.1.0",
     "eslint-plugin-react": "^7.20.3",
-    "eslint-plugin-react-hooks": "^4.6.0",
+    "eslint-plugin-react-hooks": "next",
+    "eslint-plugin-react-refresh": "^0.4.9",
     "eslint-plugin-unicorn": "^55.0.0",
     "mobx": "^6.10.2",
     "mobx-react": "^9.0.1",
@@ -71,6 +70,7 @@
     "rimraf": "^6.0.0",
     "rxjs": "^7.8.1",
     "tss-react": "^4.9.2",
-    "typescript": "^5.2.2"
+    "typescript": "^5.2.2",
+    "typescript-eslint": "^8.1.0"
   }
 }

package/src/AddHighlightModel/MsaToGenomeHighlight.tsx

@@ -22,8 +22,10 @@ const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({
 }) {
   const { classes } = useStyles()
   const { assemblyManager, views } = getSession(model)
-  const p = views.find(f => f.type === 'MsaView') as JBrowsePluginMsaViewModel
-  const assembly = assemblyManager.get(model.assemblyNames[0])
+  const p = views.find(f => f.type === 'MsaView') as
+    | JBrowsePluginMsaViewModel
+    | undefined
+  const assembly = assemblyManager.get(model.assemblyNames[0]!)
   return assembly ? (
     <>
       {p?.connectedHighlights.map((r, idx) => {

package/src/AddHighlightModel/util.ts

@@ -6,7 +6,7 @@ export const useStyles = makeStyles()({
     background: 'rgba(255,255,0,0.2)',
     border: '1px solid rgba(50,50,0,0.2)',
     position: 'absolute',
-    zIndex: 1000,
+    zIndex: 99,
     textAlign: 'center',
     pointerEvents: 'none',
     overflow: 'hidden',

package/src/LaunchMsaView/components/LaunchMsaViewDialog.tsx

@@ -5,9 +5,10 @@ import { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 
 // locals
 
-import { CustomTabPanel, a11yProps } from './TabUtils'
+import CustomTabPanel from './TabUtils'
 import NewNcbiBlastQueryPanel from './NewNCBIBlastQuery'
 import PreLoadedMSA from './PreLoadedMSA/PreLoadedMSADataPanel'
+import { a11yProps } from './tabUtil'
 
 export default function LaunchProteinViewDialog({
   handleClose,
@@ -24,11 +25,18 @@ export default function LaunchProteinViewDialog({
     <Dialog
       maxWidth="xl"
       title="Launch MSA view"
-      onClose={() => handleClose()}
+      onClose={() => {
+        handleClose()
+      }}
       open
     >
       <Box sx={{ borderBottom: 1, borderColor: 'divider' }}>
-        <Tabs value={value} onChange={(_, val) => setValue(val)}>
+        <Tabs
+          value={value}
+          onChange={(_, val) => {
+            setValue(val)
+          }}
+        >
           <Tab label="NCBI BLAST query" {...a11yProps(0)} />
           <Tab label="UCSC 100-way dataset" {...a11yProps(1)} />
         </Tabs>

package/src/LaunchMsaView/components/NewNCBIBlastQuery/NcbiBlastPanel.tsx

@@ -67,7 +67,9 @@ const NcbiBlastPanel = observer(function NcbiBlastPanel2({
       {error ? <ErrorMessage error={error} /> : null}
       <TextField2
         value={blastDatabase}
-        onChange={event => setBlastDatabase(event.target.value)}
+        onChange={event => {
+          setBlastDatabase(event.target.value)
+        }}
         label="BLAST blastDatabase"
         select
       >
@@ -80,7 +82,9 @@ const NcbiBlastPanel = observer(function NcbiBlastPanel2({
 
       <TextField2
         value={msaAlgorithm}
-        onChange={event => setMsaAlgorithm(event.target.value)}
+        onChange={event => {
+          setMsaAlgorithm(event.target.value)
+        }}
         label="MSA Algorithm"
         select
       >
@@ -93,7 +97,9 @@ const NcbiBlastPanel = observer(function NcbiBlastPanel2({
 
       <TextField2
         value={userSelection}
-        onChange={event => setUserSelection(event.target.value)}
+        onChange={event => {
+          setUserSelection(event.target.value)
+        }}
         label="Choose isoform to BLAST"
         select
       >
@@ -148,7 +154,9 @@ const NcbiBlastPanel = observer(function NcbiBlastPanel2({
         <Button
           color="secondary"
           variant="contained"
-          onClick={() => handleClose()}
+          onClick={() => {
+            handleClose()
+          }}
         >
           Cancel
         </Button>

package/src/LaunchMsaView/components/NewNCBIBlastQuery/calculateProteinSequence.ts

@@ -28,7 +28,7 @@ export function calculateProteinSequence({
   let protein = ''
   for (let i = 0; i < str.length; i += 3) {
     // use & symbol for undefined codon, or partial slice
-    protein += codonTable[str.slice(i, i + 3)] || '&'
+    protein += codonTable[str.slice(i, i + 3)] ?? '&'
   }
   return protein
 }
@@ -54,7 +54,7 @@ function getItemId(feat: Feat) {
 // filters if successive elements share same start/end
 export function dedupe(list: Feat[]) {
   return list.filter(
-    (item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]),
+    (item, pos, ary) => !pos || getItemId(item) !== getItemId(ary[pos - 1]!),
   )
 }
 

package/src/LaunchMsaView/components/NewNCBIBlastQuery/useFeatureSequence.ts

@@ -1,6 +1,6 @@
 import { useEffect, useState } from 'react'
 
-import { Feature, getSession } from '@jbrowse/core/util'
+import { AbstractSessionModel, Feature, getSession } from '@jbrowse/core/util'
 import { getConf } from '@jbrowse/core/configuration'
 
 export interface SeqState {
@@ -14,6 +14,40 @@ export interface ErrorState {
 }
 const BPLIMIT = 500_000
 
+async function fetchSeq({
+  start,
+  end,
+  refName,
+  session,
+  assemblyName,
+}: {
+  start: number
+  end: number
+  refName: string
+  assemblyName: string
+  session: AbstractSessionModel
+}) {
+  const { assemblyManager, rpcManager } = session
+  const assembly = await assemblyManager.waitForAssembly(assemblyName)
+  if (!assembly) {
+    throw new Error('assembly not found')
+  }
+  const sessionId = 'getSequence'
+  const feats = (await rpcManager.call(sessionId, 'CoreGetFeatures', {
+    adapterConfig: getConf(assembly, ['sequence', 'adapter']),
+    sessionId,
+    regions: [
+      {
+        start,
+        end,
+        refName: assembly.getCanonicalRefName(refName),
+        assemblyName,
+      },
+    ],
+  })) as Feature[]
+  return (feats[0]?.get('seq') as string | undefined) ?? ''
+}
+
 export function useFeatureSequence({
   view,
   feature,
@@ -27,41 +61,23 @@ export function useFeatureSequence({
 }) {
   const [sequence, setSequence] = useState<SeqState | ErrorState>()
   const [error, setError] = useState<unknown>()
+  const assemblyName = view?.assemblyNames?.[0]
   useEffect(() => {
     if (view) {
-      const { assemblyManager, rpcManager } = getSession(view)
-      const [assemblyName] = view?.assemblyNames || []
-      async function fetchSeq(start: number, end: number, refName: string) {
-        const assembly = await assemblyManager.waitForAssembly(assemblyName)
-        if (!assembly) {
-          throw new Error('assembly not found')
-        }
-        const sessionId = 'getSequence'
-        const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', {
-          adapterConfig: getConf(assembly, ['sequence', 'adapter']),
-          sessionId,
-          regions: [
-            {
-              start,
-              end,
-              refName: assembly.getCanonicalRefName(refName),
-              assemblyName,
-            },
-          ],
-        })
-
-        const [feat] = feats as Feature[]
-        return (feat?.get('seq') as string | undefined) || ''
-      }
-
       // eslint-disable-next-line @typescript-eslint/no-floating-promises
       ;(async () => {
         try {
           setError(undefined)
           setSequence(undefined)
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any
-          const { start, end, refName } = feature.toJSON() as any
-
+          const session = getSession(view)
+          const { start, end, refName } = feature.toJSON() as {
+            start: number
+            end: number
+            refName: string
+          }
+          if (!assemblyName) {
+            throw new Error('No assembly found')
+          }
           if (!forceLoad && end - start > BPLIMIT) {
             setSequence({
               error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
@@ -69,10 +85,29 @@ export function useFeatureSequence({
           } else {
             const b = start - upDownBp
             const e = end + upDownBp
-            const seq = await fetchSeq(start, end, refName)
-            const up = await fetchSeq(Math.max(0, b), start, refName)
-            const down = await fetchSeq(end, e, refName)
-            setSequence({ seq, upstream: up, downstream: down })
+            setSequence({
+              seq: await fetchSeq({
+                start,
+                end,
+                refName,
+                assemblyName,
+                session,
+              }),
+              upstream: await fetchSeq({
+                start: Math.max(0, b),
+                end: start,
+                refName,
+                assemblyName,
+                session,
+              }),
+              downstream: await fetchSeq({
+                start: end,
+                end: e,
+                refName,
+                assemblyName,
+                session,
+              }),
+            })
           }
         } catch (e) {
           console.error(e)
@@ -80,6 +115,6 @@ export function useFeatureSequence({
         }
       })()
     }
-  }, [feature, view, upDownBp, forceLoad])
+  }, [feature, view, upDownBp, assemblyName, forceLoad])
   return { sequence, error }
 }

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

@@ -86,7 +86,9 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({
         ) : null}
         <TextField
           value={userSelection}
-          onChange={event => setUserSelection(event.target.value)}
+          onChange={event => {
+            setUserSelection(event.target.value)
+          }}
           label="Choose isoform to view MSA for"
           select
         >
@@ -138,7 +140,9 @@ const PreLoadedMSA = observer(function PreLoadedMSA2({
         <Button
           color="secondary"
           variant="contained"
-          onClick={() => handleClose()}
+          onClick={() => {
+            handleClose()
+          }}
         >
           Cancel
         </Button>

package/src/LaunchMsaView/components/TabUtils.tsx

@@ -7,7 +7,7 @@ interface TabPanelProps {
   value: number
 }
 
-export function CustomTabPanel(props: TabPanelProps) {
+export default function CustomTabPanel(props: TabPanelProps) {
   const { children, value, index, ...other } = props
 
   return (
@@ -22,9 +22,3 @@ export function CustomTabPanel(props: TabPanelProps) {
     </div>
   )
 }
-export function a11yProps(index: number) {
-  return {
-    id: `gtab-${index}`,
-    'aria-controls': `gtabpanel-${index}`,
-  }
-}

package/src/LaunchMsaView/components/tabUtil.ts

@@ -0,0 +1,6 @@
+export function a11yProps(index: number) {
+  return {
+    id: `gtab-${index}`,
+    'aria-controls': `gtabpanel-${index}`,
+  }
+}

package/src/LaunchMsaView/index.ts

@@ -2,50 +2,55 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
 import { PluggableElementType } from '@jbrowse/core/pluggableElementTypes'
 import { IAnyModelType } from 'mobx-state-tree'
-import { getSession, getContainingTrack } from '@jbrowse/core/util'
+import { getSession, getContainingTrack, Feature } from '@jbrowse/core/util'
 
 // icons
 import AddIcon from '@mui/icons-material/Add'
 
 // locals
 import LaunchMsaViewDialog from './components/LaunchMsaViewDialog'
+import { MenuItem } from '@jbrowse/core/ui'
 
 function isDisplay(elt: { name: string }): elt is DisplayType {
   return elt.name === 'LinearBasicDisplay'
 }
 
 function extendStateModel(stateModel: IAnyModelType) {
-  return stateModel.views(self => {
-    const superContextMenuItems = self.contextMenuItems
-    return {
-      contextMenuItems() {
-        const feature = self.contextMenuFeature
-        const track = getContainingTrack(self)
-        return [
-          ...superContextMenuItems(),
-          ...(feature
-            ? [
-                {
-                  label: 'Launch MSA view',
-                  icon: AddIcon,
-                  onClick: () => {
-                    const session = getSession(track)
-                    session.queueDialog(handleClose => [
-                      LaunchMsaViewDialog,
-                      {
-                        model: track,
-                        handleClose,
-                        feature,
-                      },
-                    ])
+  return stateModel.views(
+    (self: {
+      contextMenuItems: () => MenuItem[]
+      contextMenuFeature?: Feature
+    }) => {
+      const superContextMenuItems = self.contextMenuItems
+      return {
+        contextMenuItems() {
+          const feature = self.contextMenuFeature
+          const track = getContainingTrack(self)
+          return [
+            ...superContextMenuItems(),
+            ...(feature
+              ? [
+                  {
+                    label: 'Launch MSA view',
+                    icon: AddIcon,
+                    onClick: () => {
+                      getSession(track).queueDialog(handleClose => [
+                        LaunchMsaViewDialog,
+                        {
+                          model: track,
+                          handleClose,
+                          feature,
+                        },
+                      ])
+                    },
                   },
-                },
-              ]
-            : []),
-        ]
-      },
-    }
-  })
+                ]
+              : []),
+          ]
+        },
+      }
+    },
+  )
 }
 
 export default function LaunchMsaViewF(pluginManager: PluginManager) {

package/src/LaunchMsaView/util.ts

@@ -11,8 +11,8 @@ export function getTranscriptFeatures(feature: Feature) {
         f.get('subfeatures')?.some(f => f.get('type') === 'CDS'),
       )
 }
-export function getId(val?: Feature) {
-  return val === undefined ? '' : val.get('name') || val.get('id')
+export function getId(val?: Feature): string {
+  return val?.get('name') || val?.get('id') || ''
 }
 
 export function getTranscriptDisplayName(val?: Feature) {

package/src/MsaViewPanel/components/LoadingBLAST.tsx

@@ -48,9 +48,9 @@ const LoadingBLAST = observer(function LoadingBLAST2({
       <LoadingEllipses message="Running NCBI BLAST" variant="h5" />
       {error ? (
         <RIDError rid={rid} error={error} />
-      ) : rid ? (
+      ) : (rid ? (
         <RIDProgress rid={rid} progress={progress} />
-      ) : null}
+      ) : null)}
       <Typography>{processing || 'Initializing BLAST query'}</Typography>
     </div>
   )

package/src/MsaViewPanel/doLaunchBlast.ts

@@ -18,21 +18,39 @@ export async function doLaunchBlast({
     query,
     blastDatabase,
     blastProgram,
-    onProgress: arg => self.setProgress(arg),
-    onRid: rid => self.setRid(rid),
+    onProgress: arg => {
+      self.setProgress(arg)
+    },
+    onRid: rid => {
+      self.setRid(rid)
+    },
   })
 
   const sequence = [
     `>QUERY\n${query}`,
     ...hits
-      .map(h => [makeId(h.description[0]), strip(h.hsps[0].hseq)] as const)
+      .map(
+        h =>
+          [
+            makeId(
+              h.description[0] ?? {
+                accession: 'unknown',
+                id: 'unknown',
+                sciname: 'unknown',
+              },
+            ),
+            strip(h.hsps[0]?.hseq ?? ''),
+          ] as const,
+      )
       .map(([id, seq]) => `>${id}\n${seq}`),
   ].join('\n')
 
   const data = await launchMSA({
     algorithm: msaAlgorithm,
     sequence,
-    onProgress: arg => self.setProgress(arg),
+    onProgress: arg => {
+      self.setProgress(arg)
+    },
   })
   return data
 }

package/src/MsaViewPanel/model.ts

@@ -199,7 +199,9 @@ export default function stateModelFactory() {
             label: 'Zoom to base level on click?',
             checked: self.zoomToBaseLevel,
             type: 'checkbox',
-            onClick: () => self.setZoomToBaseLevel(!self.zoomToBaseLevel),
+            onClick: () => {
+              self.setZoomToBaseLevel(!self.zoomToBaseLevel)
+            },
           },
         ]
       },
@@ -280,7 +282,7 @@ export default function stateModelFactory() {
             } else {
               const r =
                 assemblyManager
-                  .get(connectedView.assemblyNames[0])
+                  .get(connectedView.assemblyNames[0]!)
                   ?.getCanonicalRefName(r2.refName) ?? r2.refName
               connectedView.centerAt(r2.start, r)
             }

package/src/MsaViewPanel/msaCoordToGenomeCoord.ts

@@ -9,13 +9,13 @@ export function msaCoordToGenomeCoord({
   coord: number
 }) {
   const { transcriptToMsaMap } = model
-  if (mouseCol === undefined || transcriptToMsaMap === undefined) {
+  if (transcriptToMsaMap === undefined) {
     return
   }
 
-  const c = mouseCol - 1
-  const k1 = model.globalCoordToRowSpecificSeqCoord('QUERY', c) || 0
-  const k2 = model.globalCoordToRowSpecificSeqCoord('QUERY', c + 1) || 0
+  const c = mouseCol
+  const k1 = model.seqCoordToRowSpecificGlobalCoord('QUERY', c) || 0
+  const k2 = model.seqCoordToRowSpecificGlobalCoord('QUERY', c + 1) || 0
   const { refName, p2g } = transcriptToMsaMap
   const s = p2g[k1]
   const e = p2g[k2]

package/src/utils/msa.ts

@@ -98,6 +98,7 @@ async function wait({
   algorithm: string
   onProgress: (arg: string) => void
 }) {
+  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
   while (true) {
     for (let i = 0; i < 10; i++) {
       await timeout(1000)
@@ -107,6 +108,8 @@ async function wait({
 
     if (result === 'FINISHED') {
       break
+    } else if (result.includes('FAILURE')) {
+      throw new Error(`Failed to run: jobId ${jobId}`)
     }
   }
 }