jbrowse-plugin-msaview 2.5.1 → 2.6.0

package/dist/utils/ncbiDomains.js

@@ -73,7 +73,9 @@ function parseFeature(featureXml) {
             : noteName || quals.site_type || 'site';
         const accession = isDomain ? cddId : `${cddId}:${name}`;
         return {
-            signature: { entry: { name, description: quals.note ?? name, accession } },
+            signature: {
+                entry: { name, description: quals.note ?? name, accession },
+            },
             locations: [span],
         };
     }

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.5.1";
+export declare const version = "2.6.0";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.5.1';
+export const version = '2.6.0';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.5.1",
+  "version": "2.6.0",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -17,41 +17,42 @@
   ],
   "dependencies": {
     "@emotion/styled": "^11.14.1",
+    "@gmod/tabix": "^3.0.1",
     "g2p_mapper": "^2.1.5",
     "idb": "^8.0.3",
     "pako-esm2": "^2.0.2",
     "react-msaview": "^5.4.1",
-    "swr": "^2.4.1"
+    "swr": "^2.4.2"
   },
   "devDependencies": {
     "@emotion/react": "^11.14.0",
     "@eslint/js": "^10.0.1",
     "@fal-works/esbuild-plugin-global-externals": "^2.1.2",
     "@jbrowse/core": "^4.3.0",
-    "@jbrowse/mobx-state-tree": "^5.10.8",
+    "@jbrowse/mobx-state-tree": "^5.11.1",
     "@jbrowse/plugin-linear-genome-view": "^4.3.0",
     "@mui/icons-material": "^7.3.11",
     "@mui/material": "^7.3.11",
     "@mui/system": "^7.3.11",
-    "@mui/x-data-grid": "^8.28.7",
-    "@types/node": "^25.9.1",
-    "@types/react": "^19.2.16",
-    "@typescript-eslint/eslint-plugin": "^8.60.1",
-    "@typescript-eslint/parser": "^8.60.1",
-    "esbuild": "^0.28.0",
-    "eslint": "^10.4.1",
-    "eslint-plugin-import-x": "^4.16.2",
+    "@mui/x-data-grid": "^8.29.1",
+    "@types/node": "^25.9.4",
+    "@types/react": "^19.2.17",
+    "@typescript-eslint/eslint-plugin": "^8.62.0",
+    "@typescript-eslint/parser": "^8.62.0",
+    "esbuild": "^0.28.1",
+    "eslint": "^10.5.0",
+    "eslint-plugin-import-x": "^4.17.0",
     "eslint-plugin-react": "^7.37.5",
     "eslint-plugin-react-hooks": "^7.1.1",
     "eslint-plugin-unicorn": "^64.0.0",
-    "mobx": "^6.15.4",
+    "mobx": "^6.16.1",
     "mobx-react": "^9.2.2",
     "msa-parsers": "5.4.1",
     "pixelmatch": "^7.2.0",
     "pngjs": "^7.0.0",
-    "prettier": "^3.8.3",
+    "prettier": "^3.8.4",
     "pretty-bytes": "^7.1.0",
-    "puppeteer": "^25.1.0",
+    "puppeteer": "^25.2.1",
     "react": "^19.2.7",
     "react-dom": "^19.2.7",
     "rimraf": "^6.1.3",
@@ -59,8 +60,8 @@
     "serve": "^14.2.6",
     "tss-react": "^4.9.21",
     "typescript": "^6.0.3",
-    "typescript-eslint": "^8.60.1",
-    "vitest": "^4.1.8"
+    "typescript-eslint": "^8.62.0",
+    "vitest": "^4.1.9"
   },
   "scripts": {
     "clean": "rimraf dist",

package/src/LaunchMsaViewExtensionPoint/index.ts

@@ -11,6 +11,9 @@ export default function LaunchMsaViewExtensionPointF(
       session,
       data,
       msaFileLocation,
+      msaTabixLocation,
+      msaIndexLocation,
+      msaId,
       treeFileLocation,
       connectedViewId,
       connectedFeature,
@@ -29,6 +32,9 @@ export default function LaunchMsaViewExtensionPointF(
       session: AbstractSessionModel
       data?: { msa: string; tree?: string }
       msaFileLocation?: { uri: string }
+      msaTabixLocation?: { uri: string }
+      msaIndexLocation?: { uri: string }
+      msaId?: string
       treeFileLocation?: { uri: string }
       connectedViewId?: string
       connectedFeature?: Record<string, unknown>
@@ -44,7 +50,7 @@ export default function LaunchMsaViewExtensionPointF(
       querySeqName?: string
       highlightColumns?: number[]
     }) => {
-      if (!data && !msaFileLocation) {
+      if (!data && !msaFileLocation && !msaTabixLocation) {
         throw new Error(
           'No MSA data or file location provided when launching MSA view',
         )
@@ -68,6 +74,9 @@ export default function LaunchMsaViewExtensionPointF(
           msaData: data?.msa,
           treeData: data?.tree,
           msaUrl: msaFileLocation?.uri,
+          msaTabixLocation,
+          msaIndexLocation,
+          msaId,
           treeUrl: treeFileLocation?.uri,
           querySeqName,
         },

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -1,6 +1,7 @@
 import { getSession } from '@jbrowse/core/util'
 
 import { doLaunchBlast } from './doLaunchBlast'
+import { fetchTabixMsa } from './fetchTabixMsa'
 import { genomeToMSA } from './genomeToMSA'
 import { loadProteinDomains } from './loadProteinDomains'
 import {
@@ -133,7 +134,16 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
     void (async () => {
       try {
         self.setError(undefined)
-        const { msaData, msaUrl, treeData, treeUrl, querySeqName } = init
+        const {
+          msaData,
+          msaUrl,
+          msaTabixLocation,
+          msaIndexLocation,
+          msaId,
+          treeData,
+          treeUrl,
+          querySeqName,
+        } = init
 
         if (msaUrl) {
           const id = getUniprotIdFromAlphaFoldUrl(msaUrl)
@@ -156,6 +166,25 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
           }
           const data = await response.text()
           self.setMSA(data)
+        } else if (msaTabixLocation) {
+          const feature = self.connectedFeature
+          if (feature) {
+            const fasta = await fetchTabixMsa({
+              location: msaTabixLocation,
+              indexLocation: msaIndexLocation,
+              msaId: msaId ?? String(feature.name),
+              refName: String(feature.refName),
+              start: Number(feature.start),
+              end: Number(feature.end),
+            })
+            if (fasta) {
+              self.setMSA(fasta)
+            } else {
+              throw new Error(
+                `No alignment for ${msaId ?? String(feature.name)} in ${msaTabixLocation.uri}`,
+              )
+            }
+          }
         }
 
         if (treeData) {
@@ -282,46 +311,71 @@ export function autoConnectStructures(self: JBrowsePluginMsaViewModel) {
   }
 }
 
+/**
+ * Mirror a connected 3D protein view's hovered residue onto the MSA's
+ * highlighted columns. Returns the autorun body and keeps a flag tracking
+ * whether the current highlight was set by THIS sync: when a protein hover ends
+ * we restore the declarative highlightColumns seed (or clear) rather than
+ * blindly wiping it.
+ *
+ * Without the flag this autorun fires once on creation — with the view connected
+ * to a *genome* LGV but no 3D protein structure attached — computes zero columns,
+ * and calls setHighlightedColumns(undefined), clobbering the seed that
+ * MSAModelF.afterCreate just set from the declarative `highlightColumns`. That is
+ * the bug that made the BRAF/TP53 genome-browser links open with no V600/R248
+ * column lit (SRC has no highlightColumns, so nothing was there to wipe).
+ */
 export function observeProteinHighlights(self: JBrowsePluginMsaViewModel) {
-  const { connectedViewId, transcriptToMsaMap, querySeqName } = self
+  let proteinDriven = false
+  return () => {
+    const { connectedViewId, transcriptToMsaMap, querySeqName } = self
 
-  if (!connectedViewId || !transcriptToMsaMap) {
-    return
-  }
+    if (!connectedViewId || !transcriptToMsaMap) {
+      return
+    }
 
-  const columns = new Set<number>()
+    const columns = new Set<number>()
 
-  for (const view of getProteinViews(getSession(self).views)) {
-    for (const structure of view.structures) {
-      if (structure.connectedViewId !== connectedViewId) {
-        continue
-      }
+    for (const view of getProteinViews(getSession(self).views)) {
+      for (const structure of view.structures) {
+        if (structure.connectedViewId !== connectedViewId) {
+          continue
+        }
 
-      const highlights = structure.hoverGenomeHighlights
-      if (!highlights || highlights.length === 0) {
-        continue
-      }
+        const highlights = structure.hoverGenomeHighlights
+        if (!highlights || highlights.length === 0) {
+          continue
+        }
 
-      const { g2p } = transcriptToMsaMap
-      for (const highlight of highlights) {
-        for (let coord = highlight.start; coord < highlight.end; coord++) {
-          const proteinPos = g2p[coord]
-          if (proteinPos !== undefined) {
-            const col = self.seqPosToGlobalCol(querySeqName, proteinPos)
-            columns.add(col)
+        const { g2p } = transcriptToMsaMap
+        for (const highlight of highlights) {
+          for (let coord = highlight.start; coord < highlight.end; coord++) {
+            const proteinPos = g2p[coord]
+            if (proteinPos !== undefined) {
+              const col = self.seqPosToGlobalCol(querySeqName, proteinPos)
+              columns.add(col)
+            }
           }
         }
       }
     }
-  }
-
-  const visibleColumns = Array.from(columns)
-    .map(col => self.globalColToVisibleCol(col))
-    .filter((col): col is number => col !== undefined)
 
-  self.setHighlightedColumns(
-    visibleColumns.length > 0 ? visibleColumns : undefined,
-  )
+    const visibleColumns = Array.from(columns)
+      .map(col => self.globalColToVisibleCol(col))
+      .filter((col): col is number => col !== undefined)
+
+    if (visibleColumns.length > 0) {
+      self.setHighlightedColumns(visibleColumns)
+      proteinDriven = true
+    } else if (proteinDriven) {
+      // our protein-hover highlight ended — fall back to the declarative seed
+      // instead of wiping a column the URL/user asked to keep lit
+      self.setHighlightedColumns(
+        self.highlightColumns?.length ? self.highlightColumns : undefined,
+      )
+      proteinDriven = false
+    }
+  }
 }
 
 export function runCleanup() {

package/src/MsaViewPanel/fetchTabixMsa.ts

@@ -0,0 +1,50 @@
+import { TabixIndexedFile } from '@gmod/tabix'
+import { openLocation } from '@jbrowse/core/util/io'
+
+// Pull one transcript's whole multiple-alignment out of a locus-keyed tabix
+// file. Each line is `refName<TAB>start<TAB>end<TAB>msaId<TAB>packed`, where
+// `packed` is `name:SEQ;name:SEQ;...` — no newlines, so the alignment survives
+// as a single tabix column. We query the transcript's genomic locus, then pick
+// the line whose msaId matches, and rebuild a FASTA string.
+export async function fetchTabixMsa({
+  location,
+  indexLocation,
+  msaId,
+  refName,
+  start,
+  end,
+}: {
+  location: { uri: string }
+  indexLocation?: { uri: string }
+  msaId: string
+  refName: string
+  start: number
+  end: number
+}) {
+  const uri = (loc: { uri: string }) =>
+    openLocation({ uri: loc.uri, locationType: 'UriLocation' as const })
+  const file = new TabixIndexedFile({
+    filehandle: uri(location),
+    csiFilehandle: uri(indexLocation ?? { uri: `${location.uri}.csi` }),
+  })
+  const lines: string[] = []
+  await file.getLines(refName, start, end, {
+    lineCallback: line => {
+      lines.push(line)
+    },
+  })
+  const line = lines.find(l => l.split('\t')[3] === msaId)
+  return line ? unpack(line) : undefined
+}
+
+function unpack(line: string) {
+  const packed = line.split('\t')[4] ?? ''
+  return packed
+    .split(';')
+    .filter(Boolean)
+    .map(pair => {
+      const colon = pair.indexOf(':')
+      return `>${pair.slice(0, colon)}\n${pair.slice(colon + 1)}`
+    })
+    .join('\n')
+}

package/src/MsaViewPanel/model.ts

@@ -471,7 +471,6 @@ export default function stateModelFactory() {
           highlightConnectedStructures,
           autoConnectStructures,
           autoLoadProteinDomains,
-          observeProteinHighlights,
         ]) {
           addDisposer(
             self,
@@ -480,7 +479,10 @@ export default function stateModelFactory() {
             }),
           )
         }
+        // these two keep per-reaction state across runs (a "did I set it?" flag),
+        // so they're factories returning the autorun body rather than plain fns
         addDisposer(self, autorun(syncGenomeHoverToMsaColumn(self)))
+        addDisposer(self, autorun(observeProteinHighlights(self)))
       },
     }))
 }

package/src/MsaViewPanel/types.ts

@@ -1,6 +1,14 @@
 export interface MsaViewInitState {
   msaData?: string
   msaUrl?: string
+  // a tabix file keyed by genomic locus, where each line packs one transcript's
+  // whole multiple-alignment (`name:SEQ;name:SEQ;...`). The transcript's locus
+  // comes from the view's connectedFeature, and `msaId` (default the feature's
+  // name) selects its line. Lets one genome-scale alignment serve any gene
+  // without per-gene files. See react-msaview's gene-explorer.
+  msaTabixLocation?: { uri: string }
+  msaIndexLocation?: { uri: string }
+  msaId?: string
   treeData?: string
   treeUrl?: string
   querySeqName?: string

package/src/utils/domainCache.ts

@@ -26,8 +26,7 @@ export async function getCachedDomains(accessions: string[]) {
   const tx = db.transaction(STORE_NAME, 'readonly')
   const results = await Promise.all(
     accessions.map(
-      accession =>
-        tx.store.get(accession) as Promise<CachedDomain | undefined>,
+      accession => tx.store.get(accession) as Promise<CachedDomain | undefined>,
     ),
   )
   await tx.done

package/src/utils/ncbiDomains.ts

@@ -83,7 +83,9 @@ function parseFeature(featureXml: string): DomainMatch | undefined {
       : noteName || quals.site_type || 'site'
     const accession = isDomain ? cddId : `${cddId}:${name}`
     return {
-      signature: { entry: { name, description: quals.note ?? name, accession } },
+      signature: {
+        entry: { name, description: quals.note ?? name, accession },
+      },
       locations: [span],
     }
   }

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.5.1'
+export const version = '2.6.0'