jbrowse-plugin-msaview 2.7.1 → 2.7.3

package/src/LaunchMsaView/components/geneticCodes.ts

@@ -0,0 +1,298 @@
+// NCBI translation tables (genetic codes), copied verbatim from
+// jbrowse-components packages/core/src/util/geneticCodes.ts, which parses them
+// from NCBI's authoritative gc.prt. `ncbieaa` gives the amino acid for each of
+// the 64 codons in a fixed base order; `sncbieaa` marks valid start codons.
+//
+// Vendored rather than imported: core exports this only on main, and the msaview
+// bundle has to translate the same way on every host a config names, back to
+// v4.0.0. Replace the whole file with a re-export of
+// `@jbrowse/core/util/geneticCodes` once a release ships it -- that path is not
+// in ReExports, so it bundles rather than binding to the host.
+export interface NcbiGeneticCode {
+  id: number
+  name: string
+  ncbieaa: string
+  sncbieaa: string
+}
+
+export const ncbiGeneticCodes: NcbiGeneticCode[] = [
+  {
+    id: 1,
+    name: 'Standard',
+    ncbieaa: 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------**--*----M---------------M----------------------------',
+  },
+  {
+    id: 2,
+    name: 'Vertebrate Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**--------------------MMMM----------**---M------------',
+  },
+  {
+    id: 3,
+    name: 'Yeast Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**----------------------MM---------------M------------',
+  },
+  {
+    id: 4,
+    name: 'Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '--MM------**-------M------------MMMM---------------M------------',
+  },
+  {
+    id: 5,
+    name: 'Invertebrate Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------**--------------------MMMM---------------M------------',
+  },
+  {
+    id: 6,
+    name: 'Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear',
+    ncbieaa: 'FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '--------------*--------------------M----------------------------',
+  },
+  {
+    id: 9,
+    name: 'Echinoderm Mitochondrial; Flatworm Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**-----------------------M---------------M------------',
+  },
+  {
+    id: 10,
+    name: 'Euplotid Nuclear',
+    ncbieaa: 'FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**-----------------------M----------------------------',
+  },
+  {
+    id: 11,
+    name: 'Bacterial, Archaeal and Plant Plastid',
+    ncbieaa: 'FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------**--*----M------------MMMM---------------M------------',
+  },
+  {
+    id: 12,
+    name: 'Alternative Yeast Nuclear',
+    ncbieaa: 'FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**--*----M---------------M----------------------------',
+  },
+  {
+    id: 13,
+    name: 'Ascidian Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------**----------------------MM---------------M------------',
+  },
+  {
+    id: 14,
+    name: 'Alternative Flatworm Mitochondrial',
+    ncbieaa: 'FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '-----------*-----------------------M----------------------------',
+  },
+  {
+    id: 15,
+    name: 'Blepharisma Macronuclear',
+    ncbieaa: 'FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------*---*--------------------M----------------------------',
+  },
+  {
+    id: 16,
+    name: 'Chlorophycean Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------*---*--------------------M----------------------------',
+  },
+  {
+    id: 21,
+    name: 'Trematode Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**-----------------------M---------------M------------',
+  },
+  {
+    id: 22,
+    name: 'Scenedesmus obliquus Mitochondrial',
+    ncbieaa: 'FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '------*---*---*--------------------M----------------------------',
+  },
+  {
+    id: 23,
+    name: 'Thraustochytrium Mitochondrial',
+    ncbieaa: 'FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '--*-------**--*-----------------M--M---------------M------------',
+  },
+  {
+    id: 24,
+    name: 'Rhabdopleuridae Mitochondrial',
+    ncbieaa: 'FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------**-------M---------------M---------------M------------',
+  },
+  {
+    id: 25,
+    name: 'Candidate Division SR1 and Gracilibacteria',
+    ncbieaa: 'FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------**-----------------------M---------------M------------',
+  },
+  {
+    id: 26,
+    name: 'Pachysolen tannophilus Nuclear',
+    ncbieaa: 'FFLLSSSSYY**CC*WLLLAPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**--*----M---------------M----------------------------',
+  },
+  {
+    id: 27,
+    name: 'Karyorelict Nuclear',
+    ncbieaa: 'FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '--------------*--------------------M----------------------------',
+  },
+  {
+    id: 28,
+    name: 'Condylostoma Nuclear',
+    ncbieaa: 'FFLLSSSSYYQQCCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**--*--------------------M----------------------------',
+  },
+  {
+    id: 29,
+    name: 'Mesodinium Nuclear',
+    ncbieaa: 'FFLLSSSSYYYYCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '--------------*--------------------M----------------------------',
+  },
+  {
+    id: 30,
+    name: 'Peritrich Nuclear',
+    ncbieaa: 'FFLLSSSSYYEECC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '--------------*--------------------M----------------------------',
+  },
+  {
+    id: 31,
+    name: 'Blastocrithidia Nuclear',
+    ncbieaa: 'FFLLSSSSYYEECCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '----------**-----------------------M----------------------------',
+  },
+  {
+    id: 32,
+    name: 'Balanophoraceae Plastid',
+    ncbieaa: 'FFLLSSSSYY*WCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M------*---*----M------------MMMM---------------M------------',
+  },
+  {
+    id: 33,
+    name: 'Cephalodiscidae Mitochondrial',
+    ncbieaa: 'FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG',
+    sncbieaa:
+      '---M-------*-------M---------------M---------------M------------',
+  },
+]
+
+// The codon order shared by every NCBI table -- the Base1/Base2/Base3 comment
+// rows in gc.prt. codon i = BASE1[i] + BASE2[i] + BASE3[i].
+const BASE1 = 'TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG'
+const BASE2 = 'TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG'
+const BASE3 = 'TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG'
+
+const CODONS = Array.from(
+  { length: 64 },
+  (_, i) => BASE1[i]! + BASE2[i]! + BASE3[i]!,
+)
+
+const ncbiCodeById = new Map(ncbiGeneticCodes.map(t => [t.id, t]))
+
+export interface GeneticCode {
+  id: number
+  name: string
+  // case-insensitive codon -> amino acid letter, '*' for a stop codon
+  codonTable: Record<string, string>
+  // valid start codons (uppercase)
+  starts: string[]
+}
+
+// Expand an uppercase codon map so every case combination of a triplet resolves,
+// which is what callers reading raw sequence need.
+function caseExpand(table: Record<string, string>) {
+  const out: Record<string, string> = {}
+  for (const [codon, aa] of Object.entries(table)) {
+    const cases = (i: number) => {
+      const n = codon.charAt(i)
+      return [n.toUpperCase(), n.toLowerCase()]
+    }
+    for (const n0 of cases(0)) {
+      for (const n1 of cases(1)) {
+        for (const n2 of cases(2)) {
+          out[n0 + n1 + n2] = aa
+        }
+      }
+    }
+  }
+  return out
+}
+
+function buildGeneticCode(id: number): GeneticCode {
+  const def = ncbiCodeById.get(id)
+  if (!def && id !== 1) {
+    console.warn(
+      `Unknown genetic code (transl_table=${id}); using standard code`,
+    )
+  }
+  const {
+    id: resolvedId,
+    name,
+    ncbieaa,
+    sncbieaa,
+  } = def ?? ncbiCodeById.get(1)!
+  const table: Record<string, string> = {}
+  const starts: string[] = []
+  for (const [i, codon] of CODONS.entries()) {
+    table[codon] = ncbieaa[i]!
+    if (sncbieaa[i] === 'M') {
+      starts.push(codon)
+    }
+  }
+  return { id: resolvedId, name, codonTable: caseExpand(table), starts }
+}
+
+const geneticCodeCache = new Map<number, GeneticCode>()
+
+// Resolves the codon map + start set for an NCBI translation-table id, falling
+// back to the standard code (1) for an unrecognized id. Memoized: there are only
+// ~27 tables and each result is immutable.
+export function getGeneticCode(id = 1): GeneticCode {
+  let code = geneticCodeCache.get(id)
+  if (!code) {
+    code = buildGeneticCode(id)
+    geneticCodeCache.set(id, code)
+  }
+  return code
+}
+
+// Parses a GFF/GenBank `transl_table` attribute value into an NCBI table id. The
+// GFF adapter yields a string (or an array if the attribute repeated), so this
+// normalizes both; returns undefined for a missing or non-positive-integer value
+// so callers fall back to their default code.
+export function parseTranslTable(value: unknown): number | undefined {
+  const raw = Array.isArray(value) ? value[0] : value
+  const n = Number(raw)
+  return Number.isInteger(n) && n > 0 ? n : undefined
+}

package/src/LaunchMsaView/components/types.ts

@@ -2,6 +2,9 @@ export interface Feat {
   start: number
   end: number
   type?: string
+  // GFF phase of the first coding base; convertCodingSequenceToPeptides reads it
+  // off cds[0] to start translation in the right frame
+  phase?: number
 }
 
 export interface SeqState {

package/src/LaunchMsaView/index.ts

@@ -15,8 +15,9 @@ function isDisplay(elt: { name: string }): elt is DisplayType {
 }
 
 // The canvas LinearBasicDisplay (JBrowse >=4.3) exposes the right-clicked
-// feature via contextMenuInfo + async fetchFullFeature rather than a synchronous
-// feature object.
+// feature via contextMenuInfo + async fetchFullFeature. Hosts before that -- and
+// the v3.7.0 in the wild that shipped configs still name -- expose it
+// synchronously as contextMenuFeature, and only have that one.
 interface ContextMenuInfo {
   item: { featureId: string; type?: string }
   displayedRegionIndex: number
@@ -25,13 +26,16 @@ interface ContextMenuInfo {
 interface DisplayModel {
   contextMenuItems: () => MenuItem[]
   contextMenuInfo?: ContextMenuInfo
-  isGeneLike: boolean
-  fetchFullFeature: (
+  isGeneLike?: boolean
+  fetchFullFeature?: (
     featureId: string,
     displayedRegionIndex: number,
   ) => Promise<Feature | undefined>
+  contextMenuFeature?: Feature
 }
 
+const GENE_LIKE_TYPES = new Set(['gene', 'mRNA', 'transcript'])
+
 function extendStateModel(stateModel: IAnyModelType) {
   return stateModel.views((self: DisplayModel) => {
     const superContextMenuItems = self.contextMenuItems
@@ -39,40 +43,45 @@ function extendStateModel(stateModel: IAnyModelType) {
       contextMenuItems() {
         const track = getContainingTrack(self)
         const session = getSession(track)
+        const launch = (feature: Feature) => {
+          session.queueDialog(handleClose => [
+            LaunchMsaViewDialog,
+            { model: track, handleClose, feature },
+          ])
+        }
+
         const info = self.contextMenuInfo
-        const showMsaMenuItem = info && self.isGeneLike
+        const fetchFullFeature = self.fetchFullFeature
+        const legacyFeature = self.contextMenuFeature
+        const onClick =
+          info && fetchFullFeature && self.isGeneLike
+            ? () => {
+                fetchFullFeature(info.item.featureId, info.displayedRegionIndex)
+                  .then(feature => {
+                    if (feature) {
+                      launch(feature)
+                    } else {
+                      session.notify(
+                        'Could not load feature for MSA view',
+                        'warning',
+                      )
+                    }
+                  })
+                  .catch((e: unknown) => {
+                    session.notifyError(`${e}`, e)
+                  })
+              }
+            : legacyFeature &&
+                GENE_LIKE_TYPES.has(String(legacyFeature.get('type')))
+              ? () => {
+                  launch(legacyFeature)
+                }
+              : undefined
+
         return [
           ...superContextMenuItems(),
-          ...(showMsaMenuItem
-            ? [
-                {
-                  label: 'Launch MSA view',
-                  icon: AddIcon,
-                  onClick: () => {
-                    self
-                      .fetchFullFeature(
-                        info.item.featureId,
-                        info.displayedRegionIndex,
-                      )
-                      .then(feature => {
-                        if (feature) {
-                          session.queueDialog(handleClose => [
-                            LaunchMsaViewDialog,
-                            { model: track, handleClose, feature },
-                          ])
-                        } else {
-                          session.notify(
-                            'Could not load feature for MSA view',
-                            'warning',
-                          )
-                        }
-                      })
-                      .catch((e: unknown) => {
-                        session.notifyError(`${e}`, e)
-                      })
-                  },
-                },
-              ]
+          ...(onClick
+            ? [{ label: 'Launch MSA view', icon: AddIcon, onClick }]
             : []),
         ]
       },

package/src/MsaViewPanel/doLaunchBlast.ts

@@ -25,36 +25,29 @@ export async function doLaunchBlast({
   } = self.blastParams!
   const cleanedSeq = cleanProteinSequence(proteinSequence)
 
-  let hits
-  let rid: string
+  const onProgress = (arg: string) => {
+    self.setProgress(arg)
+  }
+
   if (existingRid) {
+    // publish it before the first poll so the view can link out to NCBI while
+    // the job is still running
     self.setRid(existingRid)
-    const result = await queryBlastFromRid({
-      rid: existingRid,
-      baseUrl,
-      onProgress: arg => {
-        self.setProgress(arg)
-      },
-    })
-    hits = result.hits
-    rid = result.rid
-  } else {
-    const result = await queryBlast({
-      query: cleanedSeq,
-      blastDatabase,
-      blastProgram,
-      baseUrl,
-      onProgress: arg => {
-        self.setProgress(arg)
-      },
-      onRid: r => {
-        self.setRid(r)
-      },
-    })
-    hits = result.hits
-    rid = result.rid
   }
 
+  const { hits, rid } = existingRid
+    ? await queryBlastFromRid({ rid: existingRid, baseUrl, onProgress })
+    : await queryBlast({
+        query: cleanedSeq,
+        blastDatabase,
+        blastProgram,
+        baseUrl,
+        onProgress,
+        onRid: r => {
+          self.setRid(r)
+        },
+      })
+
   self.setProgress('Fetching species taxonomy info...')
   const taxids = hits
     .map(h => h.description[0]?.taxid)
@@ -80,9 +73,7 @@ export async function doLaunchBlast({
   const result = await launchMSA({
     algorithm: msaAlgorithm,
     sequence: [`>QUERY\n${cleanedSeq}`, ...sequences].join('\n'),
-    onProgress: arg => {
-      self.setProgress(arg)
-    },
+    onProgress,
   })
 
   const treeMetadataJson = JSON.stringify(treeMetadata)

package/src/MsaViewPanel/genomeToMSA.test.ts

@@ -91,8 +91,9 @@ describe('genomeToMSA', () => {
 
       const result = genomeToMSA({ model })
 
-      // coord 1005 - start 1000 = ungapped position 5
-      expect(mockSeqPosToVisibleCol).toHaveBeenCalledWith('hg38.chr1', 5)
+      // hover coord 1005 is 1-based, so the 0-based genome position is 1004,
+      // which is ungapped position 4 of a region starting at 1000
+      expect(mockSeqPosToVisibleCol).toHaveBeenCalledWith('hg38.chr1', 4)
       expect(result).toBe(5)
     })
 
@@ -125,10 +126,11 @@ describe('genomeToMSA', () => {
     })
 
     test('returns undefined when hover coord is before mafRegion start', () => {
+      // 1-based coord 1000 is the 0-based base 999, one before the region
       mockGetSession.mockReturnValue({
         hovered: {
           hoverFeature: {},
-          hoverPosition: { coord: 999, refName: 'chr1' },
+          hoverPosition: { coord: 1000, refName: 'chr1' },
         },
       } as any)
 
@@ -153,10 +155,11 @@ describe('genomeToMSA', () => {
     })
 
     test('returns undefined when hover coord is at or after mafRegion end', () => {
+      // 1-based coord 1011 is the 0-based base 1010, one past the region
       mockGetSession.mockReturnValue({
         hovered: {
           hoverFeature: {},
-          hoverPosition: { coord: 1010, refName: 'chr1' },
+          hoverPosition: { coord: 1011, refName: 'chr1' },
         },
       } as any)
 
@@ -223,7 +226,9 @@ describe('genomeToMSA', () => {
       const model = {
         querySeqName: 'QUERY',
         transcriptToMsaMap: {
-          g2p: { 1005: 10 },
+          refName: 'chr1',
+          // g2p is keyed by 0-based genome position, the hover coord is 1-based
+          g2p: { 1004: 10 },
         },
         mafRegion: undefined,
         connectedView: { initialized: true },
@@ -236,6 +241,32 @@ describe('genomeToMSA', () => {
       expect(result).toBe(10)
     })
 
+    test('returns undefined when the hover is on another refName', () => {
+      // session.hovered is global, so a hover on an unrelated chromosome can
+      // carry a coordinate that happens to be a g2p key
+      mockGetSession.mockReturnValue({
+        hovered: {
+          hoverFeature: {},
+          hoverPosition: { coord: 1005, refName: 'chr2' },
+        },
+      } as any)
+
+      const mockSeqPosToVisibleCol = vi.fn()
+      const model = {
+        querySeqName: 'QUERY',
+        transcriptToMsaMap: {
+          refName: 'chr1',
+          g2p: { 1004: 10 },
+        },
+        mafRegion: undefined,
+        connectedView: { initialized: true },
+        seqPosToVisibleCol: mockSeqPosToVisibleCol,
+      } as any
+
+      expect(genomeToMSA({ model })).toBeUndefined()
+      expect(mockSeqPosToVisibleCol).not.toHaveBeenCalled()
+    })
+
     test('returns undefined when g2p has no mapping for coord', () => {
       mockGetSession.mockReturnValue({
         hovered: {
@@ -247,7 +278,8 @@ describe('genomeToMSA', () => {
       const model = {
         querySeqName: 'QUERY',
         transcriptToMsaMap: {
-          g2p: { 1000: 0 }, // No entry for 1005
+          refName: 'chr1',
+          g2p: { 1000: 0 }, // No entry for 1004
         },
         mafRegion: undefined,
         connectedView: { initialized: true },

package/src/MsaViewPanel/genomeToMSA.ts

@@ -12,22 +12,30 @@ export function genomeToMSA({ model }: { model: JBrowsePluginMsaViewModel }) {
     return undefined
   }
 
-  const { coord: hoverCoord, refName } = hovered.hoverPosition
+  const { coord, refName } = hovered.hoverPosition
+
+  // hoverPosition.coord is a 1-based display coordinate (core's pxToBp adds the
+  // +1), while g2p and mafRegion are keyed by 0-based genome position
+  const genomePos = coord - 1
 
   if (mafRegion) {
     if (
       refName !== mafRegion.refName ||
       !connectedView.assemblyNames.includes(mafRegion.assemblyName) ||
-      hoverCoord < mafRegion.start ||
-      hoverCoord >= mafRegion.end
+      genomePos < mafRegion.start ||
+      genomePos >= mafRegion.end
     ) {
       return undefined
     }
-    return model.seqPosToVisibleCol(querySeqName, hoverCoord - mafRegion.start)
+    return model.seqPosToVisibleCol(querySeqName, genomePos - mafRegion.start)
   }
 
-  if (transcriptToMsaMap) {
-    const seqPos = transcriptToMsaMap.g2p[hoverCoord]
+  // session.hovered is global -- set by whichever LinearGenomeView the cursor
+  // was last over, on any assembly -- so the refName gate is load bearing:
+  // without it the same numeric coordinate on an unrelated chromosome matches a
+  // g2p key and lights up a column for a different locus
+  if (refName === transcriptToMsaMap?.refName) {
+    const seqPos = transcriptToMsaMap.g2p[genomePos]
     if (seqPos !== undefined) {
       return model.seqPosToVisibleCol(querySeqName, seqPos)
     }

package/src/MsaViewPanel/model.ts

@@ -19,7 +19,10 @@ import {
   storeDataToIndexedDB,
   syncGenomeHoverToMsaColumn,
 } from './afterCreateAutoruns'
-import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord'
+import {
+  msaCoordToGenomeCoord,
+  msaCoordToGenomeRegions,
+} from './msaCoordToGenomeCoord'
 
 import type { MafRegion, MsaViewInitState } from './types'
 import type {
@@ -188,35 +191,37 @@ export default function stateModelFactory() {
     .views(self => ({
       /**
        * #getter
-       * Genome region under the current MSA hover column. Suppressed on the LGV
+       * Genome regions under the current MSA hover column. Suppressed on the LGV
        * while it's being hovered (GenomeMouseoverHighlight shows the crisp 1bp
        * marker there instead of this wider codon band).
        */
-      get connectedHoverHighlight(): IRegion | undefined {
+      get connectedHoverHighlights(): IRegion[] {
         const { mouseCol } = self
         return mouseCol === undefined
-          ? undefined
-          : msaCoordToGenomeCoord({ model: self, coord: mouseCol })
+          ? []
+          : msaCoordToGenomeRegions({ model: self, coord: mouseCol })
       },
       /**
        * #getter
-       * Genome region under the persistent MSA click selection. Shown
+       * Genome regions under the persistent MSA click selection. Shown
        * regardless of LGV hover, so hovering the genome doesn't hide it.
        */
-      get connectedClickHighlight(): IRegion | undefined {
+      get connectedClickHighlights(): IRegion[] {
         const { mouseClickCol } = self
         return mouseClickCol === undefined
-          ? undefined
-          : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
+          ? []
+          : msaCoordToGenomeRegions({ model: self, coord: mouseClickCol })
       },
       /**
        * #getter
+       * cross-plugin contract: jbrowse-plugin-mafviewer reads this off the view
+       * to draw the same highlights in its own display
        */
       get connectedHighlights(): IRegion[] {
         return [
-          this.connectedHoverHighlight,
-          this.connectedClickHighlight,
-        ].filter((r): r is IRegion => r !== undefined)
+          ...this.connectedHoverHighlights,
+          ...this.connectedClickHighlights,
+        ]
       },
     }))