jbrowse-plugin-msaview 3.3.0 → 3.4.0

package/src/MsaViewPanel/components/JobLink.tsx

@@ -4,12 +4,17 @@ import { Typography } from '@mui/material'
 
 import ExternalLink from '../../components/ExternalLink'
 import { ebiBlastResultUrl } from '../../utils/ebiBlast'
+import { isPhmmerJobId, phmmerResultUrl } from '../../utils/phmmer'
 
 function JobLink({ jobId }: { jobId: string }) {
+  // read off the job id rather than the launch params, so a link rebuilt for an
+  // old cached job still points at the tool that actually ran it
+  const url = isPhmmerJobId(jobId)
+    ? phmmerResultUrl(jobId)
+    : ebiBlastResultUrl(jobId)
   return (
     <Typography>
-      Job {jobId} (
-      <ExternalLink href={ebiBlastResultUrl(jobId)}>see status</ExternalLink>)
+      Job {jobId} (<ExternalLink href={url}>see status</ExternalLink>)
     </Typography>
   )
 }

package/src/MsaViewPanel/components/LaunchProgress.tsx

@@ -0,0 +1,62 @@
+import React from 'react'
+
+import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
+import { Typography } from '@mui/material'
+import { observer } from 'mobx-react'
+import { makeStyles } from 'tss-react/mui'
+
+import JobLink from './JobLink'
+
+import type { JBrowsePluginMsaViewModel } from '../model'
+
+const useStyles = makeStyles()({
+  margin: {
+    padding: 20,
+  },
+})
+
+/**
+ * What a view shows while it is still building its alignment, and what it shows
+ * when that fails.
+ *
+ * Every launch that resolves something leaves its request on the model until it
+ * succeeds -- `blastParams`, `orthologParams`, `init` -- so one still being
+ * there IS "no alignment yet", and the error a failed launch records is only
+ * readable here. This used to key on `blastParams` alone, which left an ortholog
+ * launch rendering an empty MSAView for the minutes its alignment takes and, on
+ * failure, forever: the error was set and nothing drew it.
+ */
+const LaunchProgress = observer(function LaunchProgress2({
+  model,
+}: {
+  model: JBrowsePluginMsaViewModel
+}) {
+  const { blastParams, orthologParams, progress, rid, error } = model
+  const { classes } = useStyles()
+  const message = blastParams
+    ? 'Running EBI BLAST'
+    : orthologParams
+      ? 'Building ortholog alignment'
+      : 'Loading alignment'
+  return (
+    <div className={classes.margin}>
+      {error ? (
+        <>
+          <Typography variant="h5">{message} failed</Typography>
+          {/* the job outlives the browser, so its link is worth keeping next to
+              the failure -- EBI's own page says more about a job than we can */}
+          {rid ? <JobLink jobId={rid} /> : null}
+          <ErrorMessage error={error} />
+        </>
+      ) : (
+        <>
+          <LoadingEllipses message={message} variant="h5" />
+          {rid ? <JobLink jobId={rid} /> : null}
+          <Typography>{progress || 'Initializing'}</Typography>
+        </>
+      )}
+    </div>
+  )
+})
+
+export default LaunchProgress

package/src/MsaViewPanel/components/MsaViewPanel.test.tsx

@@ -0,0 +1,83 @@
+// @vitest-environment jsdom
+import React from 'react'
+
+import { cleanup, render, screen } from '@testing-library/react'
+import { afterEach, expect, test, vi } from 'vitest'
+
+import MsaViewPanel from './MsaViewPanel'
+
+import type { JBrowsePluginMsaViewModel } from '../model'
+
+// react-msaview's MSAView is the "nothing is launching" branch and wants a real
+// MST model; a marker is enough to say the panel reached it
+vi.mock('react-msaview', () => ({
+  MSAView: () => <div>the alignment</div>,
+}))
+
+function panel(model: Partial<JBrowsePluginMsaViewModel>) {
+  return render(<MsaViewPanel model={model as JBrowsePluginMsaViewModel} />)
+}
+
+afterEach(() => {
+  cleanup()
+})
+
+test('an alignment with no pending launch draws itself', () => {
+  panel({ progress: '' })
+  expect(screen.getByText('the alignment')).toBeTruthy()
+})
+
+test('a running BLAST shows its progress, not an empty alignment', () => {
+  panel({
+    blastParams: { proteinSequence: 'MKV' } as never,
+    progress: 'Submitting query',
+  })
+  expect(screen.queryByText('the alignment')).toBeNull()
+  expect(screen.getByText(/Running EBI BLAST/)).toBeTruthy()
+  expect(screen.getByText('Submitting query')).toBeTruthy()
+})
+
+// the bug this file was written for: an ortholog launch sets orthologParams
+// rather than blastParams, and the panel keyed on blastParams alone -- so it
+// rendered an empty MSAView for the minutes the alignment takes, and drew
+// nothing at all when the launch failed
+test('a running ortholog launch shows its progress', () => {
+  panel({
+    orthologParams: { taxId: 9606 } as never,
+    progress: 'Resolving orthologs',
+  })
+  expect(screen.queryByText('the alignment')).toBeNull()
+  expect(screen.getByText(/Building ortholog alignment/)).toBeTruthy()
+  expect(screen.getByText('Resolving orthologs')).toBeTruthy()
+})
+
+test('a failed ortholog launch shows why', () => {
+  panel({
+    orthologParams: { taxId: 9606 } as never,
+    progress: '',
+    error: new Error('Only 1 ortholog(s) found for this gene'),
+  })
+  expect(screen.getByText(/Only 1 ortholog\(s\) found/)).toBeTruthy()
+})
+
+test('a failed init shows why', () => {
+  panel({
+    init: { msaName: 'ENST00000288602' },
+    progress: '',
+    error: new Error('No alignment named ENST00000288602 in msa.fa.gz'),
+  })
+  expect(screen.queryByText('the alignment')).toBeNull()
+  expect(screen.getByText(/No alignment named ENST00000288602/)).toBeTruthy()
+})
+
+test('a running job links out to it', () => {
+  panel({
+    blastParams: { proteinSequence: 'MKV' } as never,
+    progress: 'Re-checking BLAST status in... 7',
+    rid: 'ncbiblast-R20260826-123456-0001-abc',
+  })
+  const link = screen.getByRole('link')
+  expect(link.getAttribute('href')).toContain(
+    'jobId=ncbiblast-R20260826-123456-0001-abc',
+  )
+})

package/src/MsaViewPanel/components/MsaViewPanel.tsx

@@ -6,7 +6,7 @@ import { MSAView } from 'react-msaview'
 import { makeStyles } from 'tss-react/mui'
 
 import { ErrorBoundary } from './ErrorBoundary'
-import LoadingBLAST from './LoadingBLAST'
+import LaunchProgress from './LaunchProgress'
 
 import type { JBrowsePluginMsaViewModel } from '../model'
 
@@ -22,12 +22,15 @@ const MsaViewPanel = observer(function MsaViewPanel2({
   model: JBrowsePluginMsaViewModel
 }) {
   const { classes } = useStyles()
-  const { blastParams, loadingStoredData } = model
+  const { blastParams, orthologParams, init, loadingStoredData } = model
+  // an unresolved launch request means there is no alignment to draw yet, so all
+  // three gate the same panel -- see LaunchProgress
+  const launching = !!(blastParams ?? orthologParams ?? init)
   return (
     <ErrorBoundary>
       <div>
-        {blastParams ? (
-          <LoadingBLAST model={model} />
+        {launching ? (
+          <LaunchProgress model={model} />
         ) : loadingStoredData ? (
           <div className={classes.loadingContainer}>
             <LoadingEllipses message="Loading MSA data" variant="h6" />

package/src/MsaViewPanel/doLaunchBlast.ts

@@ -2,45 +2,112 @@ import { makeId, strip } from '../LaunchMsaView/components/util'
 import { cleanProteinSequence } from '../LaunchMsaView/util'
 import { saveBlastResult } from '../utils/blastCache'
 import { queryEbiBlast } from '../utils/ebiBlast'
-import { launchMSA } from '../utils/msa'
+import { launchMSA, launchTree } from '../utils/msa'
+import { buildPhmmerMsa, buildRowMetadata } from '../utils/msaRows'
+import { queryPhmmer } from '../utils/phmmer'
 import { fetchTaxonomyInfo } from '../utils/taxonomyNames'
 
+import type {
+  BlastDatabase,
+  MsaAlgorithm,
+  PhmmerDatabase,
+} from '../LaunchMsaView/components/BlastQuery/consts'
 import type { JBrowsePluginMsaViewModel } from './model'
-import type { TaxonomyInfo } from '../utils/taxonomyNames'
-import type { BlastHitDescription } from '../utils/types'
+
+type TreeMetadata = Record<string, Record<string, string>>
 
 export async function doLaunchBlast({
   self,
 }: {
   self: JBrowsePluginMsaViewModel
 }) {
-  const { blastDatabase, msaAlgorithm, proteinSequence, selectedTranscript } =
-    self.blastParams!
-  const cleanedSeq = cleanProteinSequence(proteinSequence)
+  // kept whole rather than destructured: the database's type depends on
+  // searchProgram, and pulling the two apart loses the link between them
+  const params = self.blastParams!
+  const { selectedTranscript } = params
+  const cleanedSeq = cleanProteinSequence(params.proteinSequence)
 
   const onProgress = (arg: string) => {
     self.setProgress(arg)
   }
+  // publish the job id before the first poll so the view can link out while the
+  // job is still running
+  const onRid = (r: string) => {
+    self.setRid(r)
+  }
+
+  const { msa, tree, treeMetadata, rid } =
+    params.searchProgram === 'phmmer'
+      ? await runPhmmer({
+          query: cleanedSeq,
+          database: params.blastDatabase,
+          onProgress,
+          onRid,
+        })
+      : await runBlast({
+          query: cleanedSeq,
+          blastDatabase: params.blastDatabase,
+          msaAlgorithm: params.msaAlgorithm,
+          onProgress,
+          onRid,
+        })
+
+  const treeMetadataJson = JSON.stringify(treeMetadata)
+
+  await saveBlastResult({
+    proteinSequence: cleanedSeq,
+    blastDatabase: params.blastDatabase,
+    msaAlgorithm: params.msaAlgorithm,
+    searchProgram: params.searchProgram,
+    msa,
+    tree,
+    treeMetadata: treeMetadataJson,
+    rid,
+    geneId: selectedTranscript?.get('parentId'),
+    transcriptId: selectedTranscript?.id(),
+    transcriptName:
+      selectedTranscript?.get('name') ?? selectedTranscript?.get('id'),
+    geneName:
+      selectedTranscript?.get('gene_name') ??
+      selectedTranscript?.get('parentId'),
+  })
 
+  return { msa, tree, treeMetadata: treeMetadataJson }
+}
+
+/**
+ * BLAST returns each hit already aligned to the query, but pairwise and one hit
+ * at a time, so the alignments are stripped back off and every hit is realigned
+ * together by a dedicated aligner.
+ */
+async function runBlast({
+  query,
+  blastDatabase,
+  msaAlgorithm,
+  onProgress,
+  onRid,
+}: {
+  query: string
+  blastDatabase: BlastDatabase
+  msaAlgorithm: MsaAlgorithm
+  onProgress: (arg: string) => void
+  onRid: (arg: string) => void
+}) {
   const { hits, rid } = await queryEbiBlast({
-    query: cleanedSeq,
+    query,
     blastDatabase,
     onProgress,
-    // publish the job id before the first poll so the view can link out while
-    // the job is still running
-    onRid: r => {
-      self.setRid(r)
-    },
+    onRid,
   })
 
-  self.setProgress('Fetching species taxonomy info...')
-  const taxids = hits
-    .map(h => h.description[0]?.taxid)
-    .filter((t): t is number => t !== undefined)
-  const taxonomyInfo = await fetchTaxonomyInfo(taxids)
-
-  const treeMetadata: Record<string, Record<string, string>> = {}
+  onProgress('Fetching species taxonomy info...')
+  const taxonomyInfo = await fetchTaxonomyInfo(
+    hits
+      .map(h => h.description[0]?.taxid)
+      .filter((t): t is number => t !== undefined),
+  )
 
+  const treeMetadata: TreeMetadata = {}
   const sequences = hits.map(h => {
     const desc = h.description[0] ?? {
       accession: 'unknown',
@@ -48,66 +115,57 @@ export async function doLaunchBlast({
       sciname: 'unknown',
     }
     const rowName = makeId(desc, taxonomyInfo)
-    const seq = strip(h.hsps[0]?.hseq ?? '')
-
     treeMetadata[rowName] = buildRowMetadata(desc, taxonomyInfo)
-
-    return `>${rowName}\n${seq}`
+    return `>${rowName}\n${strip(h.hsps[0]?.hseq ?? '')}`
   })
 
   const result = await launchMSA({
     algorithm: msaAlgorithm,
-    sequence: [`>QUERY\n${cleanedSeq}`, ...sequences].join('\n'),
+    sequence: [`>QUERY\n${query}`, ...sequences].join('\n'),
     onProgress,
   })
+  return { ...result, treeMetadata, rid }
+}
 
-  const treeMetadataJson = JSON.stringify(treeMetadata)
-
-  await saveBlastResult({
-    proteinSequence: cleanedSeq,
-    blastDatabase,
-    msaAlgorithm,
-    msa: result.msa,
-    tree: result.tree,
-    treeMetadata: treeMetadataJson,
-    rid,
-    geneId: selectedTranscript?.get('parentId'),
-    transcriptId: selectedTranscript?.id(),
-    transcriptName:
-      selectedTranscript?.get('name') ?? selectedTranscript?.get('id'),
-    geneName:
-      selectedTranscript?.get('gene_name') ??
-      selectedTranscript?.get('parentId'),
+/**
+ * phmmer aligns every hit to a profile of the query as it searches, so its own
+ * output is the MSA and there is no realignment step — the hits keep the
+ * placement HMMER gave them, and the query row is derived from the alignment's
+ * match columns rather than being aligned back in afterwards. That leaves no
+ * aligner run to take a tree from, so the tree is built from this alignment.
+ */
+async function runPhmmer({
+  query,
+  database,
+  onProgress,
+  onRid,
+}: {
+  query: string
+  database: PhmmerDatabase
+  onProgress: (arg: string) => void
+  onRid: (arg: string) => void
+}) {
+  const { rows, queryRow, rid } = await queryPhmmer({
+    query,
+    database,
+    onProgress,
+    onRid,
   })
 
-  return {
-    ...result,
-    treeMetadata: treeMetadataJson,
-  }
-}
-
-function buildRowMetadata(
-  desc: BlastHitDescription,
-  taxonomyInfo: Map<number, TaxonomyInfo>,
-) {
-  const metadata: Record<string, string> = {}
-  const taxInfo = desc.taxid ? taxonomyInfo.get(desc.taxid) : undefined
+  onProgress('Fetching species taxonomy info...')
+  const taxonomyInfo = await fetchTaxonomyInfo(
+    rows.map(r => r.taxid).filter((t): t is number => t !== undefined),
+  )
 
-  if (taxInfo?.sciname) {
-    metadata['Scientific name'] = taxInfo.sciname
-  }
-  if (taxInfo?.commonName) {
-    metadata['Common name'] = taxInfo.commonName
-  }
-  if (desc.accession) {
-    metadata.Accession = desc.accession
-  }
-  if (desc.id) {
-    metadata.ID = desc.id
-  }
-  if (desc.title) {
-    metadata.Description = desc.title
+  const { msa, treeMetadata } = buildPhmmerMsa({
+    rows,
+    queryRow,
+    taxonomyInfo,
+  })
+  return {
+    msa,
+    tree: await launchTree({ alignment: msa, onProgress }),
+    treeMetadata,
+    rid,
   }
-
-  return metadata
 }

package/src/MsaViewPanel/doLaunchOrthologs.test.ts

@@ -1,6 +1,5 @@
 import { beforeEach, describe, expect, test, vi } from 'vitest'
 
-import { doLaunchOrthologs } from './doLaunchOrthologs'
 import { launchMSA } from '../utils/msa'
 import {
   defaultMaxSpecies,
@@ -10,9 +9,10 @@ import {
 } from '../utils/ncbiOrthologs'
 import { fetchPantherOrthologs } from '../utils/pantherOrthologs'
 import { fetchTaxonomyInfo } from '../utils/taxonomyNames'
+import { doLaunchOrthologs } from './doLaunchOrthologs'
 
-import type { JBrowsePluginMsaViewModel } from './model'
 import type { OrthologRow } from '../utils/ncbiOrthologs'
+import type { JBrowsePluginMsaViewModel } from './model'
 
 // Every network call is mocked and nothing else is. What is under test is the
 // argument shaping either side of those calls -- which species get asked for,

package/src/MsaViewPanel/doLaunchOrthologs.ts

@@ -9,8 +9,8 @@ import {
 import { fetchPantherOrthologs } from '../utils/pantherOrthologs'
 import { fetchTaxonomyInfo } from '../utils/taxonomyNames'
 
-import type { JBrowsePluginMsaViewModel } from './model'
 import type { OrthologRow } from '../utils/ncbiOrthologs'
+import type { JBrowsePluginMsaViewModel } from './model'
 
 interface Representative {
   accession: string

package/src/MsaViewPanel/genomeToMSA.test.ts

@@ -25,6 +25,7 @@ describe('genomeToMSA', () => {
 
     const model = {
       querySeqName: 'hg38.chr1',
+      rows: [['hg38.chr1', 'ACGTACGTAC']],
       transcriptToMsaMap: undefined,
       mafRegion: {
         refName: 'chr1',
@@ -47,6 +48,7 @@ describe('genomeToMSA', () => {
 
     const model = {
       querySeqName: 'hg38.chr1',
+      rows: [['hg38.chr1', 'ACGTACGTAC']],
       transcriptToMsaMap: undefined,
       mafRegion: {
         refName: 'chr1',
@@ -75,6 +77,7 @@ describe('genomeToMSA', () => {
 
       const model = {
         querySeqName: 'hg38.chr1',
+        rows: [['hg38.chr1', 'ACGTACGTAC']],
         transcriptToMsaMap: undefined,
         mafRegion: {
           refName: 'chr1',
@@ -107,6 +110,7 @@ describe('genomeToMSA', () => {
 
       const model = {
         querySeqName: 'hg38.chr1',
+        rows: [['hg38.chr1', 'ACGTACGTAC']],
         transcriptToMsaMap: undefined,
         mafRegion: {
           refName: 'chr1',
@@ -136,6 +140,7 @@ describe('genomeToMSA', () => {
 
       const model = {
         querySeqName: 'hg38.chr1',
+        rows: [['hg38.chr1', 'ACGTACGTAC']],
         transcriptToMsaMap: undefined,
         mafRegion: {
           refName: 'chr1',
@@ -165,6 +170,7 @@ describe('genomeToMSA', () => {
 
       const model = {
         querySeqName: 'hg38.chr1',
+        rows: [['hg38.chr1', 'ACGTACGTAC']],
         transcriptToMsaMap: undefined,
         mafRegion: {
           refName: 'chr1',
@@ -193,6 +199,7 @@ describe('genomeToMSA', () => {
 
       const model = {
         querySeqName: 'hg38.chr1',
+        rows: [['hg38.chr1', 'ACGTACGTAC']],
         transcriptToMsaMap: undefined,
         mafRegion: {
           refName: 'chr1',
@@ -225,6 +232,7 @@ describe('genomeToMSA', () => {
 
       const model = {
         querySeqName: 'QUERY',
+        rows: [['QUERY', 'MKVLTAEEK']],
         transcriptToMsaMap: {
           refName: 'chr1',
           // g2p is keyed by 0-based genome position, the hover coord is 1-based
@@ -254,6 +262,7 @@ describe('genomeToMSA', () => {
       const mockSeqPosToVisibleCol = vi.fn()
       const model = {
         querySeqName: 'QUERY',
+        rows: [['QUERY', 'MKVLTAEEK']],
         transcriptToMsaMap: {
           refName: 'chr1',
           g2p: { 1004: 10 },
@@ -277,6 +286,7 @@ describe('genomeToMSA', () => {
 
       const model = {
         querySeqName: 'QUERY',
+        rows: [['QUERY', 'MKVLTAEEK']],
         transcriptToMsaMap: {
           refName: 'chr1',
           g2p: { 1000: 0 }, // No entry for 1004
@@ -301,6 +311,7 @@ describe('genomeToMSA', () => {
 
     const model = {
       querySeqName: 'QUERY',
+      rows: [['QUERY', 'MKVLTAEEK']],
       transcriptToMsaMap: undefined,
       mafRegion: undefined,
       connectedView: { initialized: true },
@@ -310,4 +321,30 @@ describe('genomeToMSA', () => {
     const result = genomeToMSA({ model })
     expect(result).toBeUndefined()
   })
+
+  // seqPosToVisibleCol answers 0 for a row name it does not know, so without a
+  // guard an alignment whose query row is missing -- the default 'QUERY' on an
+  // uploaded file, or the empty name the manual panel leaves when it matches
+  // nothing -- lights column 0 on every genome hover
+  test('returns undefined when querySeqName names no row here', () => {
+    mockGetSession.mockReturnValue({
+      hovered: {
+        hoverFeature: {},
+        hoverPosition: { coord: 1005, refName: 'chr1' },
+      },
+    } as any)
+
+    const seqPosToVisibleCol = vi.fn(() => 0)
+    const model = {
+      querySeqName: 'QUERY',
+      rows: [['some_other_row', 'MKVLTAEEK']],
+      transcriptToMsaMap: { refName: 'chr1', g2p: { 1004: 3 } },
+      mafRegion: undefined,
+      connectedView: { initialized: true },
+      seqPosToVisibleCol,
+    } as any
+
+    expect(genomeToMSA({ model })).toBeUndefined()
+    expect(seqPosToVisibleCol).not.toHaveBeenCalled()
+  })
 })

package/src/MsaViewPanel/genomeToMSA.ts

@@ -1,6 +1,6 @@
 import { getSession } from '@jbrowse/core/util'
 
-import { hasHoverPosition } from './util'
+import { hasHoverPosition, hasQueryRow } from './util'
 
 import type { JBrowsePluginMsaViewModel } from './model'
 
@@ -8,7 +8,11 @@ export function genomeToMSA({ model }: { model: JBrowsePluginMsaViewModel }) {
   const { hovered } = getSession(model)
   const { querySeqName, transcriptToMsaMap, connectedView, mafRegion } = model
 
-  if (!connectedView?.initialized || !hasHoverPosition(hovered)) {
+  if (
+    !connectedView?.initialized ||
+    !hasHoverPosition(hovered) ||
+    !hasQueryRow(model)
+  ) {
     return undefined
   }
 

package/src/MsaViewPanel/model.ts

@@ -25,11 +25,12 @@ import {
   msaCoordToGenomeRegions,
 } from './msaCoordToGenomeCoord'
 
-import type { MafRegion, MsaViewInitState } from './types'
 import type {
   BlastDatabase,
   MsaAlgorithm,
+  PhmmerDatabase,
 } from '../LaunchMsaView/components/BlastQuery/consts'
+import type { MafRegion, MsaViewInitState } from './types'
 import type { Feature } from '@jbrowse/core/util'
 import type { Instance } from '@jbrowse/mobx-state-tree'
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -44,12 +45,34 @@ export interface IRegion {
   end: number
 }
 
-export interface BlastParams {
-  blastDatabase: BlastDatabase
-  msaAlgorithm: MsaAlgorithm
+/**
+ * A search to run, discriminated by the program that runs it: the two arms
+ * differ in which databases they name and in whether an aligner runs at all, so
+ * splitting them is what lets doLaunchBlast read the database without asserting
+ * whose it is.
+ *
+ * The field is still `blastDatabase` rather than `database`: it is persisted in
+ * session snapshots and in the IndexedDB result cache, so renaming it would
+ * orphan every row already written.
+ */
+export type BlastParams = {
   selectedTranscript?: Feature
   proteinSequence: string
-}
+} & (
+  | {
+      /** absent on params written before phmmer existed, which were all blastp */
+      searchProgram?: 'blastp'
+      blastDatabase: BlastDatabase
+      msaAlgorithm: MsaAlgorithm
+    }
+  | {
+      searchProgram: 'phmmer'
+      /** phmmer names its databases its own way: `swissprot`, not `uniprotkb_swissprot` */
+      blastDatabase: PhmmerDatabase
+      /** phmmer aligns as it searches, so there is no aligner to choose */
+      msaAlgorithm?: undefined
+    }
+)
 
 /**
  * Where the ortholog set comes from. NCBI's sets cover vertebrates and

package/src/MsaViewPanel/observeProteinHighlights.test.ts

@@ -30,6 +30,7 @@ function makeModel({ highlightColumns }: { highlightColumns?: number[] } = {}) {
   const calls: (number[] | undefined)[] = []
   const model = {
     querySeqName: 'query',
+    rows: [['query', 'MKVLTAEEK']],
     connectedViewId: CONNECTED,
     // g2p is indexed by genome coord; identity keeps the arithmetic out of the way
     transcriptToMsaMap: {
@@ -249,6 +250,18 @@ describe('scope and redundant writes', () => {
     expect(calls).toEqual([])
   })
 
+  // seqPosToGlobalCol answers 0 for a row name it does not know, so without a
+  // guard a structure hover would light column 0 of whatever row is first
+  test('a query row this alignment does not have contributes no column', () => {
+    const { model, calls } = makeModel()
+    Object.assign(model, { rows: [['some_other_row', 'MKVLTAEEK']] })
+    const run = observeProteinHighlights(model)
+
+    session({ hover: [{ start: 10, end: 12 }] })
+    run()
+    expect(calls).toEqual([])
+  })
+
   test('nothing happens until the view is connected and mapped', () => {
     const { calls } = makeModel()
     const bare = {