jbrowse-plugin-msaview 2.4.4 → 2.5.0

package/src/MsaViewPanel/pairwiseAlignment.ts

@@ -128,13 +128,8 @@ function buildConsensus(alignedSeq1: string, alignedSeq2: string) {
   for (let i = 0; i < alignedSeq1.length; i++) {
     const a = alignedSeq1[i]!
     const b = alignedSeq2[i]!
-    if (a === '-' || b === '-') {
-      consensus += ' '
-    } else if (a.toUpperCase() === b.toUpperCase()) {
-      consensus += '|'
-    } else {
-      consensus += ' '
-    }
+    const match = a !== '-' && b !== '-' && a.toUpperCase() === b.toUpperCase()
+    consensus += match ? '|' : ' '
   }
   return consensus
 }

package/src/MsaViewPanel/structureConnection.test.ts

@@ -1,9 +1,6 @@
 import { describe, expect, test } from 'vitest'
 
-import {
-  gappedToUngappedPosition,
-  ungappedToGappedPosition,
-} from './structureConnection'
+import { gappedToUngappedPosition } from './structureConnection'
 
 describe('gappedToUngappedPosition', () => {
   test('returns correct ungapped position for non-gap character', () => {
@@ -63,60 +60,3 @@ describe('gappedToUngappedPosition', () => {
     expect(gappedToUngappedPosition(seq, 2)).toBeUndefined()
   })
 })
-
-describe('ungappedToGappedPosition', () => {
-  test('returns correct gapped position', () => {
-    const seq = 'M-KA-A'
-    //           0 12 34  (gapped)
-    //           0  1  23 (ungapped)
-    expect(ungappedToGappedPosition(seq, 0)).toBe(0) // M
-    expect(ungappedToGappedPosition(seq, 1)).toBe(2) // K
-    expect(ungappedToGappedPosition(seq, 2)).toBe(3) // A
-    expect(ungappedToGappedPosition(seq, 3)).toBe(5) // A
-  })
-
-  test('returns undefined for out-of-bounds ungapped position', () => {
-    const seq = 'M-KA'
-    expect(ungappedToGappedPosition(seq, 4)).toBeUndefined()
-    expect(ungappedToGappedPosition(seq, 100)).toBeUndefined()
-  })
-
-  test('handles sequence with no gaps', () => {
-    const seq = 'MKAA'
-    expect(ungappedToGappedPosition(seq, 0)).toBe(0)
-    expect(ungappedToGappedPosition(seq, 1)).toBe(1)
-    expect(ungappedToGappedPosition(seq, 2)).toBe(2)
-    expect(ungappedToGappedPosition(seq, 3)).toBe(3)
-  })
-
-  test('handles sequence with leading gaps', () => {
-    const seq = '--MKA'
-    expect(ungappedToGappedPosition(seq, 0)).toBe(2) // M
-    expect(ungappedToGappedPosition(seq, 1)).toBe(3) // K
-    expect(ungappedToGappedPosition(seq, 2)).toBe(4) // A
-  })
-
-  test('handles empty sequence', () => {
-    expect(ungappedToGappedPosition('', 0)).toBeUndefined()
-  })
-
-  test('handles all-gap sequence', () => {
-    const seq = '---'
-    expect(ungappedToGappedPosition(seq, 0)).toBeUndefined()
-  })
-})
-
-describe('gappedToUngappedPosition and ungappedToGappedPosition are inverses', () => {
-  test('round-trip conversion works', () => {
-    const seq = 'M-KA--YL-S'
-    // For each non-gap position, converting to ungapped and back should return original
-    for (let i = 0; i < seq.length; i++) {
-      if (seq[i] !== '-') {
-        const ungapped = gappedToUngappedPosition(seq, i)
-        expect(ungapped).toBeDefined()
-        const backToGapped = ungappedToGappedPosition(seq, ungapped!)
-        expect(backToGapped).toBe(i)
-      }
-    }
-  })
-})

package/src/MsaViewPanel/structureConnection.ts

@@ -40,8 +40,6 @@ export interface StructureConnection {
   msaRowName: string
   /** Map from MSA ungapped position to structure sequence position */
   msaToStructure: Record<number, number>
-  /** Map from structure sequence position to MSA ungapped position */
-  structureToMsa: Record<number, number>
 }
 
 /**
@@ -69,23 +67,3 @@ export function gappedToUngappedPosition(
 
   return ungapped
 }
-
-/**
- * Helper to convert ungapped position to gapped MSA column for a specific row
- */
-export function ungappedToGappedPosition(
-  sequence: string,
-  ungappedPosition: number,
-): number | undefined {
-  let ungapped = 0
-  for (let i = 0; i < sequence.length; i++) {
-    const element = sequence[i]
-    if (element !== '-') {
-      if (ungapped === ungappedPosition) {
-        return i
-      }
-      ungapped++
-    }
-  }
-  return undefined
-}

package/src/MsaViewPanel/syncGenomeHoverToMsaColumn.test.ts

@@ -0,0 +1,112 @@
+import { getSession } from '@jbrowse/core/util'
+import { beforeEach, describe, expect, test, vi } from 'vitest'
+
+import { syncGenomeHoverToMsaColumn } from './afterCreateAutoruns'
+
+import type { JBrowsePluginMsaViewModel } from './model'
+
+// Mock only getSession; keep the rest of the util module real so the
+// afterCreateAutoruns import graph still loads.
+vi.mock('@jbrowse/core/util', async importOriginal => ({
+  ...(await importOriginal<Record<string, unknown>>()),
+  getSession: vi.fn(),
+}))
+
+const mockGetSession = vi.mocked(getSession)
+
+const mafRegion = {
+  refName: 'chr1',
+  start: 1000,
+  end: 1010,
+  assemblyName: 'hg38',
+}
+
+// A model wired through the real genomeToMSA path: a connected genome view
+// over a maf region, with seqPosToVisibleCol as identity so the asserted
+// column equals the ungapped offset into the region.
+function makeModel() {
+  const calls: (number | undefined)[] = []
+  const model = {
+    querySeqName: 'hg38.chr1',
+    transcriptToMsaMap: undefined,
+    mafRegion,
+    connectedView: { initialized: true, assemblyNames: ['hg38'] },
+    seqPosToVisibleCol: (_name: string, pos: number) => pos,
+    setMousePos: (col?: number) => {
+      calls.push(col)
+    },
+  } as unknown as JBrowsePluginMsaViewModel
+  return { model, calls }
+}
+
+function hoverGenome(coord: number) {
+  mockGetSession.mockReturnValue({
+    hovered: { hoverFeature: {}, hoverPosition: { coord, refName: 'chr1' } },
+  } as unknown as ReturnType<typeof getSession>)
+}
+
+function clearGenomeHover() {
+  mockGetSession.mockReturnValue({
+    hovered: null,
+  } as unknown as ReturnType<typeof getSession>)
+}
+
+describe('syncGenomeHoverToMsaColumn (real genomeToMSA mapping)', () => {
+  beforeEach(() => {
+    vi.clearAllMocks()
+  })
+
+  test('genome hover at coord 1005 highlights MSA column 5', () => {
+    const { model, calls } = makeModel()
+    const run = syncGenomeHoverToMsaColumn(model)
+
+    hoverGenome(1005) // 1005 - mafRegion.start(1000) = ungapped 5
+    run()
+    expect(calls).toEqual([5])
+  })
+
+  test('moving the genome hover moves the highlighted column', () => {
+    const { model, calls } = makeModel()
+    const run = syncGenomeHoverToMsaColumn(model)
+
+    hoverGenome(1002)
+    run()
+    hoverGenome(1007)
+    run()
+    expect(calls).toEqual([2, 7])
+  })
+
+  test('leaving the genome clears the column it set', () => {
+    const { model, calls } = makeModel()
+    const run = syncGenomeHoverToMsaColumn(model)
+
+    hoverGenome(1004)
+    run()
+    clearGenomeHover()
+    run()
+    expect(calls).toEqual([4, undefined])
+  })
+
+  test('a hover outside the maf region clears a previously-set column once', () => {
+    const { model, calls } = makeModel()
+    const run = syncGenomeHoverToMsaColumn(model)
+
+    hoverGenome(1004)
+    run()
+    hoverGenome(5000) // outside [1000,1010) -> genomeToMSA returns undefined
+    run()
+    run()
+    expect(calls).toEqual([4, undefined])
+  })
+
+  test('never touches mouseCol when the genome never provides a column, so a direct MSA hover survives unrelated session hovers', () => {
+    const { model, calls } = makeModel()
+    const run = syncGenomeHoverToMsaColumn(model)
+
+    clearGenomeHover()
+    run()
+    hoverGenome(9999) // unrelated/out-of-range hover elsewhere
+    run()
+    expect(calls).toEqual([])
+  })
+})

package/src/MsaViewPanel/util.ts

@@ -1,13 +1,9 @@
-import type { Feature } from '@jbrowse/core/util'
-
-export function checkHovered(hovered: unknown): hovered is {
-  hoverFeature: Feature
-  hoverPosition: { coord: number; refName: string }
-} {
+export function hasHoverPosition(
+  hovered: unknown,
+): hovered is { hoverPosition: { coord: number; refName: string } } {
   return (
     !!hovered &&
     typeof hovered === 'object' &&
-    'hoverFeature' in hovered &&
     'hoverPosition' in hovered &&
     !!hovered.hoverPosition
   )

package/src/utils/blastCache.ts

@@ -46,10 +46,8 @@ function createCacheKey(
   blastProgram: BlastProgram,
   transcriptId?: string,
 ) {
-  if (transcriptId) {
-    return `${blastDatabase}:${blastProgram}:${transcriptId}:${proteinSequence}`
-  }
-  return `${blastDatabase}:${blastProgram}:${proteinSequence}`
+  const idPart = transcriptId ? `:${transcriptId}` : ''
+  return `${blastDatabase}:${blastProgram}${idPart}:${proteinSequence}`
 }
 
 export async function saveBlastResult({

package/src/utils/msa.ts

@@ -3,6 +3,7 @@ import { textfetch, timeout } from './fetch'
 import type { MsaAlgorithm } from '../LaunchMsaView/components/NCBIBlastQuery/consts'
 
 const base = `https://www.ebi.ac.uk/Tools/services/rest`
+const email = 'colin.diesh@gmail.com'
 
 const algorithms: Record<
   MsaAlgorithm,
@@ -13,22 +14,22 @@ const algorithms: Record<
   }
 > = {
   clustalo: {
-    params: { email: 'colin.diesh@gmail.com' },
+    params: { email },
     msaResult: 'aln-clustal_num',
     treeResult: 'phylotree',
   },
   muscle: {
-    params: { email: 'colin.diesh@gmail.com', format: 'clw', tree: 'tree1' },
+    params: { email, format: 'clw', tree: 'tree1' },
     msaResult: 'fa',
     treeResult: 'phylotree',
   },
   kalign: {
-    params: { email: 'colin.diesh@gmail.com', stype: 'protein' },
+    params: { email, stype: 'protein' },
     msaResult: 'fa',
     treeResult: 'phylotree',
   },
   mafft: {
-    params: { email: 'colin.diesh@gmail.com', stype: 'protein' },
+    params: { email, stype: 'protein' },
     msaResult: 'fa',
     treeResult: 'phylotree',
   },
@@ -45,10 +46,6 @@ async function wait({
 }) {
   // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
   while (true) {
-    for (let i = 0; i < 10; i++) {
-      await timeout(1000)
-      onProgress(`Re-checking MSA status in... ${10 - i}`)
-    }
     const result = await textfetch(`${base}/${algorithm}/status/${jobId}`)
 
     if (result === 'FINISHED') {
@@ -56,6 +53,11 @@ async function wait({
     } else if (result.includes('FAILURE')) {
       throw new Error(`Failed to run: jobId ${jobId}`)
     }
+
+    for (let i = 0; i < 10; i++) {
+      onProgress(`Re-checking MSA status in... ${10 - i}`)
+      await timeout(1000)
+    }
   }
 }
 

package/src/utils/ncbiBlast.ts

@@ -112,12 +112,6 @@ async function waitForRid({
 }) {
   // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
   while (true) {
-    const iter = 20
-    for (let i = 0; i < iter; i++) {
-      await timeout(1000)
-      onProgress(`Re-checking BLAST status in... ${iter - i}`)
-    }
-
     const res = await textfetch(
       `${baseUrl}?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=${rid}`,
     )
@@ -126,6 +120,11 @@ async function waitForRid({
     const hasHits = /\s+ThereAreHits=yes/m.test(res)
 
     if (status === 'WAITING') {
+      const iter = 20
+      for (let i = 0; i < iter; i++) {
+        onProgress(`Re-checking BLAST status in... ${iter - i}`)
+        await timeout(1000)
+      }
       continue
     }
 

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.4.4'
+export const version = '2.5.0'

package/dist/AddHighlightModel/GenomeMouseoverHighlight.js.map

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package/dist/AddHighlightModel/HighlightComponents.js.map

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package/dist/AddHighlightModel/MsaToGenomeHighlight.js.map

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package/dist/AddHighlightModel/index.js.map

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package/dist/AddHighlightModel/util.js.map

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package/dist/BgzipFastaMsaAdapter/BgzipFastaMsaAdapter.js.map

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package/dist/LaunchMsaView/components/LaunchPanelContent.js.map

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package/dist/LaunchMsaView/components/ManualMSALoader/fetchGeneList.js.map

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package/dist/LaunchMsaView/components/ManualMSALoader/launchView.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/MsaAlgorithmSelect.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastAutomaticPanel.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastManualPanel.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastMethodSelector.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastPanel.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBIBlastRIDPanel.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/NCBISettingsDialog.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/blastLaunchView.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/consts.js.map

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package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js.map

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package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js.map

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package/dist/LaunchMsaView/components/PreLoadedMSA/fetchMSAData.js.map

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package/dist/LaunchMsaView/components/PreLoadedMSA/preCalculatedLaunchView.js.map

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package/dist/LaunchMsaView/components/PreLoadedMSA/types.js.map

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package/dist/LaunchMsaView/components/SubmitCancelActions.js.map

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package/dist/LaunchMsaView/components/TabPanel.js.map

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package/dist/LaunchMsaView/components/TranscriptSelector.js.map

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package/dist/LaunchMsaView/components/calculateProteinSequence.js.map

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package/dist/LaunchMsaView/components/fetchSeq.js.map

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