jbrowse-plugin-msaview 3.3.0 → 3.4.0

package/src/LaunchMsaView/components/BlastQuery/BlastAutomaticPanel.tsx

@@ -11,11 +11,6 @@ import {
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-import CachedBlastResults from './CachedBlastResults'
-import MsaAlgorithmSelect from './MsaAlgorithmSelect'
-import { blastLaunchView } from './blastLaunchView'
-import { blastDatabaseOptions, defaultBlastDatabase } from './consts'
-import { useCachedBlastResults } from './useCachedBlastResults'
 import TextField2 from '../../../components/TextField2'
 import {
   getBlastViewTitle,
@@ -26,14 +21,30 @@ import LaunchPanelContent from '../LaunchPanelContent'
 import SubmitCancelActions from '../SubmitCancelActions'
 import TranscriptSelector from '../TranscriptSelector'
 import { useTranscriptSelection } from '../useTranscriptSelection'
+import CachedBlastResults from './CachedBlastResults'
+import MsaAlgorithmSelect from './MsaAlgorithmSelect'
+import { blastLaunchView } from './blastLaunchView'
+import {
+  databaseOptionsFor,
+  defaultBlastDatabase,
+  defaultSearchFor,
+  searchPrograms,
+} from './consts'
+import { useCachedBlastResults } from './useCachedBlastResults'
 
-import type { BlastDatabase, MsaAlgorithm } from './consts'
+import type { MsaAlgorithm, SearchChoice, SearchProgram } from './consts'
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 
 const useStyles = makeStyles()({
   selectField: {
     width: 150,
   },
+  // wider than the rest because the values are what the user came to read, and
+  // `uniprotkb_swissprot` is 19 characters — at 150 the field showed
+  // `uniprotkb_swis…`, which does not distinguish it from `uniprotkb_trembl`
+  databaseField: {
+    width: 230,
+  },
   cachedResultsAccordion: {
     marginTop: 20,
   },
@@ -56,10 +67,16 @@ const BlastAutomaticPanel = observer(function ({
   const { classes } = useStyles()
   const view = getLinearGenomeView(model)
   const [launchViewError, setLaunchViewError] = useState<unknown>()
-  const [selectedBlastDatabase, setSelectedBlastDatabase] =
-    useState<BlastDatabase>(defaultBlastDatabase)
+  // one piece of state, not two: a program and a database that program does not
+  // have is a 400 from EBI minutes after Submit, and holding them apart is what
+  // would let them drift into that
+  const [search, setSearch] = useState<SearchChoice>({
+    program: 'blastp',
+    database: defaultBlastDatabase,
+  })
   const [selectedMsaAlgorithm, setSelectedMsaAlgorithm] =
     useState<MsaAlgorithm>('clustalo')
+  const isPhmmer = search.program === 'phmmer'
 
   const geneIds = useMemo(() => getGeneIdentifiers(feature), [feature])
   const { results: cachedResults, error: cachedResultsError } =
@@ -74,37 +91,69 @@ const BlastAutomaticPanel = observer(function ({
         {children}
         <TextField2
           variant="outlined"
-          label="BLAST database"
+          label="Search program"
           className={classes.selectField}
           select
-          value={selectedBlastDatabase}
+          value={search.program}
           onChange={event => {
-            setSelectedBlastDatabase(event.target.value as BlastDatabase)
+            // the two services name their databases differently, so switching
+            // program replaces the database rather than keeping a name the new
+            // one has never heard of
+            setSearch(defaultSearchFor(event.target.value as SearchProgram))
           }}
         >
-          {blastDatabaseOptions.map(val => (
+          {searchPrograms.map(val => (
             <MenuItem value={val} key={val}>
               {val}
             </MenuItem>
           ))}
         </TextField2>
 
-        <MsaAlgorithmSelect
-          className={classes.selectField}
-          value={selectedMsaAlgorithm}
-          onChange={setSelectedMsaAlgorithm}
-        />
+        <TextField2
+          variant="outlined"
+          label="Database"
+          className={classes.databaseField}
+          select
+          value={search.database}
+          onChange={event => {
+            setSearch({
+              program: search.program,
+              database: event.target.value,
+            } as SearchChoice)
+          }}
+        >
+          {databaseOptionsFor(search.program).map(val => (
+            <MenuItem value={val} key={val}>
+              {val}
+            </MenuItem>
+          ))}
+        </TextField2>
+
+        {isPhmmer ? null : (
+          <MsaAlgorithmSelect
+            className={classes.selectField}
+            value={selectedMsaAlgorithm}
+            onChange={setSelectedMsaAlgorithm}
+          />
+        )}
 
         <TranscriptSelector feature={feature} {...transcriptSelection} />
 
         <Typography className={classes.infoText}>
-          This panel will automatically submit a blastp query to EBI, which
-          searches UniProtKB. Searches usually finish in under a minute, and
-          swissprot returns curated sequences that align more cleanly than the
-          many near-identical entries a TrEMBL search brings back. After
-          completion, all the hits will be run through a multiple sequence
-          alignment. Searching NCBI's nr needs the manual approach: NCBI no
-          longer lets a browser read responses from Blast.cgi.
+          {isPhmmer
+            ? `phmmer searches UniProtKB with a profile HMM built from the query,
+               so it aligns the hits as it finds them and that alignment is used
+               directly — nothing is realigned afterwards. The tree is then built
+               from it by neighbour-joining. A hit matching the query in more
+               than one place appears once per matched region.`
+            : `This panel will automatically submit a blastp query to EBI, which
+               searches UniProtKB. Searches usually finish in under a minute, and
+               swissprot returns curated sequences that align more cleanly than
+               the many near-identical entries a TrEMBL search brings back. After
+               completion, all the hits will be run through a multiple sequence
+               alignment.`}{' '}
+          Searching NCBI's nr needs the manual approach: NCBI no longer lets a
+          browser read responses from Blast.cgi.
         </Typography>
 
         {cachedResults.length > 0 ? (
@@ -133,12 +182,21 @@ const BlastAutomaticPanel = observer(function ({
                 feature: selectedTranscript,
                 view,
                 newViewTitle: getBlastViewTitle(feature, selectedTranscript),
-                blastParams: {
-                  blastDatabase: selectedBlastDatabase,
-                  msaAlgorithm: selectedMsaAlgorithm,
-                  selectedTranscript,
-                  proteinSequence,
-                },
+                blastParams:
+                  search.program === 'phmmer'
+                    ? {
+                        searchProgram: 'phmmer',
+                        blastDatabase: search.database,
+                        selectedTranscript,
+                        proteinSequence,
+                      }
+                    : {
+                        searchProgram: 'blastp',
+                        blastDatabase: search.database,
+                        msaAlgorithm: selectedMsaAlgorithm,
+                        selectedTranscript,
+                        proteinSequence,
+                      },
               })
               handleClose()
             }

package/src/LaunchMsaView/components/BlastQuery/BlastManualPanel.tsx

@@ -5,7 +5,6 @@ import { Alert, Typography } from '@mui/material'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-import { BASE_BLAST_URL } from './consts'
 import ExternalLink from '../../../components/ExternalLink'
 import TextField2 from '../../../components/TextField2'
 import { useQueryRowName } from '../../useQueryRowName'
@@ -20,6 +19,7 @@ import QueryRowSelector from '../QueryRowSelector'
 import SubmitCancelActions from '../SubmitCancelActions'
 import TranscriptSelector from '../TranscriptSelector'
 import { useTranscriptSelection } from '../useTranscriptSelection'
+import { BASE_BLAST_URL } from './consts'
 
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 

package/src/LaunchMsaView/components/BlastQuery/BlastPanel.tsx

@@ -4,15 +4,15 @@ import SettingsIcon from '@mui/icons-material/Settings'
 import { IconButton } from '@mui/material'
 import { makeStyles } from 'tss-react/mui'
 
-import BlastAutomaticPanel from './BlastAutomaticPanel'
-import BlastManualPanel from './BlastManualPanel'
-import BlastMethodSelector from './BlastMethodSelector'
-import BlastSettingsDialog from './BlastSettingsDialog'
 import {
   DEFAULT_EBI_EMAIL,
   EBI_EMAIL_STORAGE_KEY,
 } from '../../../utils/ebiJobDispatcher'
 import { useLocalStorage } from '../../../utils/useLocalStorage'
+import BlastAutomaticPanel from './BlastAutomaticPanel'
+import BlastManualPanel from './BlastManualPanel'
+import BlastMethodSelector from './BlastMethodSelector'
+import BlastSettingsDialog from './BlastSettingsDialog'
 
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
 

package/src/LaunchMsaView/components/BlastQuery/CachedBlastResults.test.ts

@@ -0,0 +1,50 @@
+import { expect, test } from 'vitest'
+
+import { describeSearch } from './CachedBlastResults'
+
+import type { CachedBlastResult } from '../../../utils/blastCache'
+
+const base: CachedBlastResult = {
+  id: 'k',
+  proteinSequence: 'MKV',
+  blastDatabase: 'uniprotkb_swissprot',
+  msa: '',
+  tree: '',
+  treeMetadata: '{}',
+  rid: 'r',
+  timestamp: 0,
+}
+
+function row(fields: Partial<CachedBlastResult>): CachedBlastResult {
+  return { ...base, ...fields }
+}
+
+test('a blastp row names its database, program and aligner', () => {
+  expect(
+    describeSearch(row({ searchProgram: 'blastp', msaAlgorithm: 'muscle' })),
+  ).toBe('uniprotkb_swissprot / blastp / muscle')
+})
+
+// phmmer aligns as it searches, so its rows carry no msaAlgorithm at all --
+// which read as "(undefined)" while this assumed one
+test('a phmmer row names no aligner, because none ran', () => {
+  expect(
+    describeSearch(
+      row({ blastDatabase: 'swissprot', searchProgram: 'phmmer' }),
+    ),
+  ).toBe('swissprot / phmmer')
+})
+
+test('a row cached before searchProgram existed reads as blastp', () => {
+  expect(describeSearch(row({ msaAlgorithm: 'clustalo' }))).toBe(
+    'uniprotkb_swissprot / blastp / clustalo',
+  )
+})
+
+test('a row from the NCBI era keeps the program it recorded', () => {
+  expect(
+    describeSearch(
+      row({ blastProgram: 'quick-blastp', msaAlgorithm: 'clustalo' }),
+    ),
+  ).toBe('uniprotkb_swissprot / quick-blastp / clustalo')
+})

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

@@ -14,14 +14,14 @@ import {
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-import { blastLaunchViewFromCache } from './blastLaunchView'
-import { useCachedBlastResults } from './useCachedBlastResults'
 import {
   featureMatchesId,
   getGeneIdentifiers,
   getLinearGenomeView,
   getSortedTranscriptFeatures,
 } from '../../util'
+import { blastLaunchViewFromCache } from './blastLaunchView'
+import { useCachedBlastResults } from './useCachedBlastResults'
 
 import type { CachedBlastResult } from '../../../utils/blastCache'
 import type { AbstractTrackModel, Feature } from '@jbrowse/core/util'
@@ -51,6 +51,26 @@ function getResultDisplayName(result: CachedBlastResult): string {
     : (result.geneId ?? result.transcriptId ?? 'Unknown')
 }
 
+/**
+ * How the row was produced: `uniprotkb_swissprot / blastp / clustalo`, or
+ * `swissprot / phmmer` for a row phmmer aligned as it searched and that
+ * therefore ran no aligner. Each part is dropped when absent rather than
+ * printed empty — `msaAlgorithm` became optional when phmmer arrived, and a
+ * phmmer row read `(undefined)` until this stopped assuming one.
+ *
+ * `blastProgram` is the older field, written only while the plugin still
+ * queried NCBI directly and blastp/quick-blastp was a real choice.
+ */
+export function describeSearch(result: CachedBlastResult) {
+  return [
+    result.blastDatabase,
+    result.searchProgram ?? result.blastProgram ?? 'blastp',
+    result.msaAlgorithm,
+  ]
+    .filter(Boolean)
+    .join(' / ')
+}
+
 const CachedBlastResults = observer(function ({
   model,
   handleClose,
@@ -149,7 +169,7 @@ const CachedBlastResults = observer(function ({
               }}
             >
               <ListItemText
-                primary={`${getResultDisplayName(result)} - ${result.blastDatabase}${result.blastProgram ? `/${result.blastProgram}` : ''} (${result.msaAlgorithm})`}
+                primary={`${getResultDisplayName(result)} - ${describeSearch(result)}`}
                 secondary={`${new Date(result.timestamp).toLocaleString()} - Seq: ${result.proteinSequence.slice(0, 30)}...`}
               />
             </ListItemButton>

package/src/LaunchMsaView/components/BlastQuery/MsaAlgorithmSelect.tsx

@@ -2,8 +2,8 @@ import React from 'react'
 
 import { MenuItem } from '@mui/material'
 
-import { msaAlgorithms } from './consts'
 import TextField2 from '../../../components/TextField2'
+import { msaAlgorithms } from './consts'
 
 import type { MsaAlgorithm } from './consts'
 

package/src/LaunchMsaView/components/BlastQuery/consts.ts

@@ -27,3 +27,43 @@ export type BlastDatabase = (typeof blastDatabaseOptions)[number]
 // curated, so it returns roughly one good sequence per species rather than the
 // many near-identical TrEMBL entries an alignment reads poorly
 export const defaultBlastDatabase: BlastDatabase = 'uniprotkb_swissprot'
+
+export const searchPrograms = ['blastp', 'phmmer'] as const
+export type SearchProgram = (typeof searchPrograms)[number]
+
+/**
+ * phmmer offers PDB, AlphaFold, Ensembl Genomes, MEROPS and ChEMBL too, but
+ * targets outside UniProt carry no OS=/OX= in their description, so those rows
+ * would lose their species and common name. Only the databases that label their
+ * hits are offered.
+ */
+export const phmmerDatabaseOptions = [
+  'swissprot',
+  'uniprotkb',
+  'uniprotrefprot',
+] as const
+export type PhmmerDatabase = (typeof phmmerDatabaseOptions)[number]
+
+export const defaultPhmmerDatabase: PhmmerDatabase = 'swissprot'
+
+/**
+ * A program together with a database that program actually has.
+ *
+ * The pair travels as one value because neither service knows the other's
+ * database names — `swissprot` is a phmmer database and `uniprotkb_swissprot` a
+ * blastp one — so a program held apart from its database can drift into a
+ * combination EBI answers with a 400, minutes after the user pressed Submit.
+ */
+export type SearchChoice =
+  | { program: 'blastp'; database: BlastDatabase }
+  | { program: 'phmmer'; database: PhmmerDatabase }
+
+export function defaultSearchFor(program: SearchProgram): SearchChoice {
+  return program === 'phmmer'
+    ? { program, database: defaultPhmmerDatabase }
+    : { program, database: defaultBlastDatabase }
+}
+
+export function databaseOptionsFor(program: SearchProgram) {
+  return program === 'phmmer' ? phmmerDatabaseOptions : blastDatabaseOptions
+}

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

@@ -5,7 +5,6 @@ import { FormControl, FormControlLabel, Radio, RadioGroup } from '@mui/material'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-import { launchView } from './launchView'
 import TextField2 from '../../../components/TextField2'
 import { useQueryRowName } from '../../useQueryRowName'
 import { getGeneDisplayName, getLinearGenomeView } from '../../util'
@@ -14,6 +13,7 @@ import QueryRowSelector from '../QueryRowSelector'
 import SubmitCancelActions from '../SubmitCancelActions'
 import TranscriptSelector from '../TranscriptSelector'
 import { useTranscriptSelection } from '../useTranscriptSelection'
+import { launchView } from './launchView'
 
 import type {
   AbstractTrackModel,

package/src/LaunchMsaView/components/OrthologQuery/OrthologPanel.tsx

@@ -4,11 +4,6 @@ import { Typography } from '@mui/material'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-import OrthologSourceSelect, {
-  ORTHOLOG_SOURCE_STORAGE_KEY,
-} from './OrthologSourceSelect'
-import QuerySpeciesSelect from './QuerySpeciesSelect'
-import { orthologLaunchView } from './orthologLaunchView'
 import TextField2 from '../../../components/TextField2'
 import { defaultMaxSpecies } from '../../../utils/ncbiOrthologs'
 import { useLocalStorage } from '../../../utils/useLocalStorage'
@@ -23,6 +18,11 @@ import LaunchPanelContent from '../LaunchPanelContent'
 import SubmitCancelActions from '../SubmitCancelActions'
 import TranscriptSelector from '../TranscriptSelector'
 import { useTranscriptSelection } from '../useTranscriptSelection'
+import OrthologSourceSelect, {
+  ORTHOLOG_SOURCE_STORAGE_KEY,
+} from './OrthologSourceSelect'
+import QuerySpeciesSelect from './QuerySpeciesSelect'
+import { orthologLaunchView } from './orthologLaunchView'
 
 import type { OrthologSource } from '../../../MsaViewPanel/model'
 import type { MsaAlgorithm } from '../BlastQuery/consts'

package/src/LaunchMsaView/components/SubmitCancelActions.test.tsx

@@ -4,8 +4,8 @@ import React from 'react'
 import { cleanup, render, screen } from '@testing-library/react'
 import { afterEach, beforeEach, expect, test, vi } from 'vitest'
 
-import SubmitCancelActions from './SubmitCancelActions'
 import { LAUNCH_PLACEMENT_KEY } from '../../utils/workspaces'
+import SubmitCancelActions from './SubmitCancelActions'
 
 import type { AbstractTrackModel } from '@jbrowse/core/util'
 

package/src/LaunchMsaView/components/useFeatureSequence.ts

@@ -1,8 +1,8 @@
 import { getSession } from '@jbrowse/core/util'
 
+import { useFetch } from '../../utils/useFetch'
 import { getProteinSequenceFromFeature } from './calculateProteinSequence'
 import { fetchSeq } from './fetchSeq'
-import { useFetch } from '../../utils/useFetch'
 
 import type { Feature } from '@jbrowse/core/util'
 

package/src/LaunchMsaView/detectQueryRow.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, test } from 'vitest'
 
-import { detectQueryRow, getMsaRowNames } from './detectQueryRow'
+import { findQueryRow } from './detectQueryRow'
 
 const protein = 'MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFD'
 
@@ -18,25 +18,25 @@ MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFD
 MKWVTFISLLLLFSSAYSRG--RRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPYD
 `
 
-describe('detectQueryRow', () => {
+describe('findQueryRow', () => {
   test('finds the query by sequence when the aligner renamed it', () => {
-    expect(detectQueryRow(clustal, protein)).toMatchObject({
+    expect(findQueryRow(clustal, protein).match).toMatchObject({
       name: 'Query_1',
       quality: 'exact',
     })
   })
 
   test('ignores gaps in the aligned row', () => {
-    expect(detectQueryRow(fasta, protein)?.name).toBe('Query_1')
+    expect(findQueryRow(fasta, protein).match?.name).toBe('Query_1')
   })
 
   test('tolerates the trailing stop codon the translation carries', () => {
-    expect(detectQueryRow(clustal, `${protein}*`)?.name).toBe('Query_1')
+    expect(findQueryRow(clustal, `${protein}*`).match?.name).toBe('Query_1')
   })
 
   test('matches a row that is the query trimmed to the aligned region', () => {
     const trimmed = `>hit_one\nWRONGWRONGWRONGWRONG\n>aligned_query\n${protein.slice(5, 40)}\n`
-    expect(detectQueryRow(trimmed, protein)).toMatchObject({
+    expect(findQueryRow(trimmed, protein).match).toMatchObject({
       name: 'aligned_query',
       quality: 'partial',
     })
@@ -51,21 +51,23 @@ MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFD
 MKWVTFISLLLLFSSAYSRGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFD
 `
     expect(
-      detectQueryRow(homologsOnly, 'WWWWWWWWWWWWWWWWWWWWWWWWWWWWWW'),
+      findQueryRow(homologsOnly, 'WWWWWWWWWWWWWWWWWWWWWWWWWWWWWW').match,
     ).toBeUndefined()
   })
 
   test('returns nothing rather than throwing on a half-pasted alignment', () => {
-    expect(detectQueryRow('>partial\nMKWV', protein)).toBeUndefined()
-    expect(detectQueryRow('not an alignment at all', protein)).toBeUndefined()
-    expect(detectQueryRow('', protein)).toBeUndefined()
-    expect(detectQueryRow(clustal, '')).toBeUndefined()
+    expect(findQueryRow('>partial\nMKWV', protein).match).toBeUndefined()
+    expect(
+      findQueryRow('not an alignment at all', protein).match,
+    ).toBeUndefined()
+    expect(findQueryRow('', protein).match).toBeUndefined()
+    expect(findQueryRow(clustal, '').match).toBeUndefined()
   })
 })
 
-describe('getMsaRowNames', () => {
+describe('findQueryRow row names', () => {
   test('lists the rows for the override dropdown', () => {
-    expect(getMsaRowNames(clustal)).toEqual([
+    expect(findQueryRow(clustal, protein).names).toEqual([
       'Query_1',
       'sp|P02769|ALBU',
       'sp|Q5XLE4|OTHE',
@@ -73,7 +75,7 @@ describe('getMsaRowNames', () => {
   })
 
   test('is empty rather than throwing while the user is still pasting', () => {
-    expect(getMsaRowNames('CLUSTAL W')).toEqual([])
-    expect(getMsaRowNames('')).toEqual([])
+    expect(findQueryRow('CLUSTAL W', protein).names).toEqual([])
+    expect(findQueryRow('', protein).names).toEqual([])
   })
 })

package/src/LaunchMsaView/detectQueryRow.ts

@@ -65,27 +65,48 @@ const SIMILARITY_FLOOR = 0.9
  */
 const PARTIAL_COVERAGE_FLOOR = 0.5
 
-export function detectQueryRow(
+export interface MsaQueryRow {
+  /** every row name, in file order, for the picker to offer */
+  names: string[]
+  /** the row whose residues are the query's, if one of them is */
+  match?: QueryRowMatch
+}
+
+/**
+ * The picker's whole answer for a pasted alignment: its row names, and which of
+ * them is the query.
+ *
+ * One function rather than two because there is one parse. Both answers were
+ * wanted on every keystroke in the paste box, and asking separately parsed a
+ * few-hundred-row alignment twice per character.
+ */
+export function findQueryRow(
   msaText: string,
   proteinSequence: string,
-): QueryRowMatch | undefined {
-  const query = normalize(proteinSequence)
-  if (!query || !msaText.trim()) {
-    return undefined
+): MsaQueryRow {
+  if (!msaText.trim()) {
+    return { names: [] }
   }
 
-  let names: string[]
-  let parsed: { getRow: (name: string) => string }
+  let parsed
   try {
-    const msa = parseMSA(msaText)
-    names = msa.getNames()
-    parsed = msa
+    parsed = parseMSA(msaText)
   } catch {
     // a half-pasted alignment throws here on every keystroke; the caller shows
     // the field rather than an error
-    return undefined
+    return { names: [] }
   }
 
+  const names = parsed.getNames()
+  const query = normalize(proteinSequence)
+  return { names, match: query ? bestMatch(parsed, names, query) : undefined }
+}
+
+function bestMatch(
+  parsed: { getRow: (name: string) => string },
+  names: string[],
+  query: string,
+): QueryRowMatch | undefined {
   const candidates: QueryRowMatch[] = []
   for (const name of names) {
     const row = normalize(getUngappedSequence(parsed.getRow(name)))
@@ -112,21 +133,11 @@ export function detectQueryRow(
     }
   }
 
-  const order: MatchQuality[] = ['exact', 'partial', 'similar']
+  // an exact match returns above, so only these two can be here
+  const order: MatchQuality[] = ['partial', 'similar']
   return candidates.sort(
     (a, b) =>
       order.indexOf(a.quality) - order.indexOf(b.quality) ||
       b.identity - a.identity,
   )[0]
 }
-
-export function getMsaRowNames(msaText: string): string[] {
-  if (!msaText.trim()) {
-    return []
-  }
-  try {
-    return parseMSA(msaText).getNames()
-  } catch {
-    return []
-  }
-}

package/src/LaunchMsaView/useQueryRowName.ts

@@ -1,6 +1,6 @@
 import { useMemo, useState } from 'react'
 
-import { detectQueryRow, getMsaRowNames } from './detectQueryRow'
+import { findQueryRow } from './detectQueryRow'
 
 /**
  * The MSA row name to launch with, found by sequence rather than typed.
@@ -15,19 +15,16 @@ export function useQueryRowName(msaText: string, proteinSequence: string) {
 
   // parsing runs on every keystroke in the paste box otherwise, and an
   // alignment of a few hundred rows is not free
-  const { detected, names } = useMemo(
-    () => ({
-      detected: detectQueryRow(msaText, proteinSequence),
-      names: getMsaRowNames(msaText),
-    }),
+  const { names, match } = useMemo(
+    () => findQueryRow(msaText, proteinSequence),
     [msaText, proteinSequence],
   )
 
   return {
-    detected,
+    detected: match,
     names,
-    querySeqName: override ?? detected?.name ?? '',
+    querySeqName: override ?? match?.name ?? '',
     setQuerySeqName: setOverride,
-    isAutoDetected: override === undefined && !!detected,
+    isAutoDetected: override === undefined && !!match,
   }
 }

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -12,7 +12,7 @@ import {
   storeMsaData,
 } from './msaDataStore'
 import { getProteinViews } from './structureConnection'
-import { getUniprotIdFromAlphaFoldUrl } from './util'
+import { getUniprotIdFromAlphaFoldUrl, hasQueryRow } from './util'
 
 import type { JBrowsePluginMsaViewModel } from './model'
 
@@ -233,7 +233,7 @@ function genomeHighlightsToVisibleColumns(
   field: 'hoverGenomeHighlights' | 'clickGenomeHighlights',
 ) {
   const { connectedViewId, transcriptToMsaMap, querySeqName } = self
-  if (!transcriptToMsaMap) {
+  if (!transcriptToMsaMap || !hasQueryRow(self)) {
     return []
   }
   const { g2p } = transcriptToMsaMap

package/src/MsaViewPanel/components/ErrorBoundary.tsx

@@ -1,8 +1,9 @@
-import type { ReactNode } from 'react'
 import React, { Component } from 'react'
 
 import { ErrorMessage } from '@jbrowse/core/ui'
 
+import type { ReactNode } from 'react'
+
 interface Props {
   children: ReactNode
 }