jbrowse-plugin-msaview 2.4.5 → 2.5.0

package/dist/utils/msa.js

@@ -1,23 +1,24 @@
 import { textfetch, timeout } from './fetch';
 const base = `https://www.ebi.ac.uk/Tools/services/rest`;
+const email = 'colin.diesh@gmail.com';
 const algorithms = {
     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',
     },
@@ -25,10 +26,6 @@ const algorithms = {
 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);
-            onProgress(`Re-checking MSA status in... ${10 - i}`);
-        }
         const result = await textfetch(`${base}/${algorithm}/status/${jobId}`);
         if (result === 'FINISHED') {
             break;
@@ -36,6 +33,10 @@ async function wait({ onProgress, jobId, algorithm, }) {
         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);
+        }
     }
 }
 export async function launchMSA({ algorithm, sequence, onProgress, }) {

package/dist/utils/ncbiBlast.js

@@ -58,16 +58,16 @@ async function initialQuery({ query, blastProgram, blastDatabase, baseUrl, }) {
 async function waitForRid({ rid, onProgress, baseUrl, }) {
     // 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}`);
         const statusMatch = /\s+Status=(\S+)/m.exec(res);
         const status = statusMatch?.[1];
         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;
         }
         if (status === 'FAILED') {

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.4.5";
+export declare const version = "2.5.0";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.4.5';
+export const version = '2.5.0';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.4.5",
+  "version": "2.5.0",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -20,7 +20,7 @@
     "g2p_mapper": "^2.1.5",
     "idb": "^8.0.3",
     "pako-esm2": "^2.0.2",
-    "react-msaview": "^5.0.16",
+    "react-msaview": "^5.1.1",
     "swr": "^2.4.1"
   },
   "devDependencies": {
@@ -28,7 +28,7 @@
     "@eslint/js": "^10.0.1",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
     "@jbrowse/core": "^4.3.0",
-    "@jbrowse/mobx-state-tree": "^5.8.7",
+    "@jbrowse/mobx-state-tree": "^5.10.2",
     "@jbrowse/plugin-linear-genome-view": "^4.3.0",
     "@mui/icons-material": "^7.3.11",
     "@mui/material": "^7.3.11",
@@ -36,19 +36,19 @@
     "@mui/x-data-grid": "^8.28.7",
     "@types/node": "^25.9.1",
     "@types/react": "^19.2.15",
-    "@typescript-eslint/eslint-plugin": "^8.59.4",
-    "@typescript-eslint/parser": "^8.59.4",
+    "@typescript-eslint/eslint-plugin": "^8.60.0",
+    "@typescript-eslint/parser": "^8.60.0",
     "esbuild": "^0.28.0",
     "eslint": "^10.4.0",
     "eslint-plugin-import-x": "^4.16.2",
     "eslint-plugin-react": "^7.37.5",
     "eslint-plugin-react-hooks": "^7.1.1",
     "eslint-plugin-unicorn": "^64.0.0",
-    "mobx": "^6.15.3",
-    "mobx-react": "^9.2.1",
+    "mobx": "^6.15.4",
+    "mobx-react": "^9.2.2",
     "prettier": "^3.8.3",
     "pretty-bytes": "^7.1.0",
-    "puppeteer": "^24.43.1",
+    "puppeteer": "^25.1.0",
     "react": "^19.2.6",
     "react-dom": "^19.2.6",
     "rimraf": "^6.1.3",
@@ -56,7 +56,7 @@
     "serve": "^14.2.6",
     "tss-react": "^4.9.21",
     "typescript": "^6.0.3",
-    "typescript-eslint": "^8.59.4",
+    "typescript-eslint": "^8.60.0",
     "vitest": "^4.1.7"
   },
   "scripts": {

package/src/LaunchMsaView/util.ts

@@ -40,9 +40,7 @@ export function getTranscriptLength(feature: Feature) {
   const cdsLen = sum(
     feature
       .get('subfeatures')
-      ?.filter(
-        f => (f.get('type') as string | undefined)?.toLowerCase() === 'cds',
-      )
+      ?.filter(f => f.get('type') === 'CDS')
       .map(s => s.get('end') - s.get('start')) ?? [],
   )
   return {

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -1,6 +1,7 @@
 import { getSession } from '@jbrowse/core/util'
 
 import { doLaunchBlast } from './doLaunchBlast'
+import { genomeToMSA } from './genomeToMSA'
 import {
   cleanupOldData,
   generateDataStoreId,
@@ -145,6 +146,27 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
   }
 }
 
+/**
+ * Mirror the connected genome view's hover position onto the MSA's hovered
+ * column. Returns the autorun body so it can keep a flag tracking whether the
+ * MSA's mouseCol was set by this sync: that way an unrelated session hover
+ * change clears the column only when the genome put it there, never wiping a
+ * column the user is hovering directly in the MSA.
+ */
+export function syncGenomeHoverToMsaColumn(self: JBrowsePluginMsaViewModel) {
+  let genomeDrivenCol = false
+  return () => {
+    const col = genomeToMSA({ model: self })
+    if (col !== undefined) {
+      self.setMousePos(col)
+      genomeDrivenCol = true
+    } else if (genomeDrivenCol) {
+      self.setMousePos(undefined)
+      genomeDrivenCol = false
+    }
+  }
+}
+
 export function highlightConnectedStructures(self: JBrowsePluginMsaViewModel) {
   const { mouseCol, connectedProteinViews } = self
   if (connectedProteinViews.length === 0) {

package/src/MsaViewPanel/model.ts

@@ -16,14 +16,11 @@ import {
   processInit,
   runCleanup,
   storeDataToIndexedDB,
+  syncGenomeHoverToMsaColumn,
 } from './afterCreateAutoruns'
-import { genomeToMSA } from './genomeToMSA'
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord'
 import { buildAlignmentMaps, runPairwiseAlignment } from './pairwiseAlignment'
-import {
-  getProteinViews,
-  ungappedToGappedPosition,
-} from './structureConnection'
+import { getProteinViews } from './structureConnection'
 import { getCanonicalRefName } from './util'
 
 import type { ProteinView, StructureConnection } from './structureConnection'
@@ -209,41 +206,6 @@ export default function stateModelFactory() {
     }))
 
     .views(self => ({
-      /**
-       * #getter
-       */
-      get structureHoverCol(): number | undefined {
-        for (const conn of self.connectedProteinViews) {
-          const structure = conn.proteinView.structures[conn.structureIdx]
-          const structurePos = structure?.hoverPosition?.structureSeqPos
-          if (structurePos !== undefined) {
-            const msaUngapped = conn.structureToMsa[structurePos]
-            if (msaUngapped !== undefined) {
-              const seq = self.getSequenceByRowName(conn.msaRowName)
-              if (seq) {
-                const globalCol = ungappedToGappedPosition(seq, msaUngapped)
-                if (globalCol !== undefined) {
-                  return self.globalColToVisibleCol(globalCol)
-                }
-              }
-            }
-          }
-        }
-        return undefined
-      },
-    }))
-
-    .views(self => ({
-      /**
-       * #getter
-       */
-      get mouseCol2(): number | undefined {
-        return (
-          self.structureHoverCol ??
-          genomeToMSA({ model: self as JBrowsePluginMsaViewModel })
-        )
-      },
-
       /**
        * #getter
        */
@@ -394,14 +356,13 @@ export default function stateModelFactory() {
           ungappedMsaSequence,
           structureSequence,
         )
-        const { seq1ToSeq2, seq2ToSeq1 } = buildAlignmentMaps(alignment)
+        const { seq1ToSeq2 } = buildAlignmentMaps(alignment)
 
         const connection: StructureConnection = {
           proteinViewId,
           structureIdx,
           msaRowName: rowName,
           msaToStructure: Object.fromEntries(seq1ToSeq2),
-          structureToMsa: Object.fromEntries(seq2ToSeq1),
         }
 
         self.connectedStructures.push(connection)
@@ -503,6 +464,7 @@ export default function stateModelFactory() {
             }),
           )
         }
+        addDisposer(self, autorun(syncGenomeHoverToMsaColumn(self)))
       },
     }))
 }

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/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 = '2.4.5'
+export const version = '2.5.0'