jbrowse-plugin-msaview 2.6.0 → 2.6.2

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.6.0";
+export declare const version = "2.6.2";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.6.0';
+export const version = '2.6.2';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.6.0",
+  "version": "2.6.2",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -17,7 +17,7 @@
   ],
   "dependencies": {
     "@emotion/styled": "^11.14.1",
-    "@gmod/tabix": "^3.0.1",
+    "@gmod/bgzf-filehandle": "^6.2.0",
     "g2p_mapper": "^2.1.5",
     "idb": "^8.0.3",
     "pako-esm2": "^2.0.2",

package/src/LaunchMsaViewExtensionPoint/index.ts

@@ -1,86 +1,68 @@
 import type PluginManager from '@jbrowse/core/PluginManager'
 import type { AbstractSessionModel } from '@jbrowse/core/util'
 
+interface LaunchMsaViewArgs {
+  session: AbstractSessionModel
+  data?: { msa: string; tree?: string }
+  msaFileLocation?: { uri: string }
+  msaIndexedLocation?: { uri: string }
+  msaName?: string
+  treeFileLocation?: { uri: string }
+  connectedViewId?: string
+  connectedFeature?: Record<string, unknown>
+  displayName?: string
+  colorSchemeName?: string
+  colWidth?: number
+  rowHeight?: number
+  treeAreaWidth?: number
+  treeWidth?: number
+  drawNodeBubbles?: boolean
+  labelsAlignRight?: boolean
+  showBranchLen?: boolean
+  querySeqName?: string
+  highlightColumns?: number[]
+}
+
 export default function LaunchMsaViewExtensionPointF(
   pluginManager: PluginManager,
 ) {
   pluginManager.addToExtensionPoint(
     'LaunchView-MsaView',
-    // @ts-expect-error
-    ({
-      session,
-      data,
-      msaFileLocation,
-      msaTabixLocation,
-      msaIndexLocation,
-      msaId,
-      treeFileLocation,
-      connectedViewId,
-      connectedFeature,
-      displayName,
-      colorSchemeName,
-      colWidth,
-      rowHeight,
-      treeAreaWidth,
-      treeWidth,
-      drawNodeBubbles,
-      labelsAlignRight,
-      showBranchLen,
-      querySeqName,
-      highlightColumns,
-    }: {
-      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>
-      displayName?: string
-      colorSchemeName?: string
-      colWidth?: number
-      rowHeight?: number
-      treeAreaWidth?: number
-      treeWidth?: number
-      drawNodeBubbles?: boolean
-      labelsAlignRight?: boolean
-      showBranchLen?: boolean
-      querySeqName?: string
-      highlightColumns?: number[]
-    }) => {
-      if (!data && !msaFileLocation && !msaTabixLocation) {
+    (args: LaunchMsaViewArgs) => {
+      const {
+        session,
+        data,
+        msaFileLocation,
+        msaIndexedLocation,
+        msaName,
+        treeFileLocation,
+        querySeqName,
+        ...rest
+      } = args
+
+      if (!data && !msaFileLocation && !msaIndexedLocation) {
         throw new Error(
           'No MSA data or file location provided when launching MSA view',
         )
       }
 
+      // all data sources flow through `init` so processInit is the single place
+      // that resolves them (AlphaFold detection, native filehandle loading, etc.)
       session.addView('MsaView', {
         type: 'MsaView',
-        displayName,
-        connectedViewId,
-        connectedFeature,
-        colorSchemeName,
-        colWidth,
-        rowHeight,
-        treeAreaWidth,
-        treeWidth,
-        drawNodeBubbles,
-        labelsAlignRight,
-        showBranchLen,
-        highlightColumns,
+        ...rest,
         init: {
           msaData: data?.msa,
           treeData: data?.tree,
           msaUrl: msaFileLocation?.uri,
-          msaTabixLocation,
-          msaIndexLocation,
-          msaId,
+          msaIndexedLocation,
+          msaName,
           treeUrl: treeFileLocation?.uri,
           querySeqName,
         },
       })
+
+      return args
     },
   )
 }

package/src/MsaViewPanel/afterCreateAutoruns.ts

@@ -1,7 +1,7 @@
 import { getSession } from '@jbrowse/core/util'
 
 import { doLaunchBlast } from './doLaunchBlast'
-import { fetchTabixMsa } from './fetchTabixMsa'
+import { fetchIndexedMsa } from './fetchIndexedMsa'
 import { genomeToMSA } from './genomeToMSA'
 import { loadProteinDomains } from './loadProteinDomains'
 import {
@@ -128,22 +128,25 @@ export function autoLoadProteinDomains(self: JBrowsePluginMsaViewModel) {
   }
 }
 
+// Resolve the declarative `init` launch contract once. Inline strings go straight
+// to the data model; URLs are handed to react-msaview's native filehandle loaders
+// (openLocation + progress + abort + CORS-proxy) rather than a hand-rolled fetch;
+// the bgzip name-indexed block is the one source with no native loader.
 export function processInit(self: JBrowsePluginMsaViewModel) {
   const { init } = self
   if (init) {
+    const {
+      msaData,
+      msaUrl,
+      msaIndexedLocation,
+      msaName,
+      treeData,
+      treeUrl,
+      querySeqName,
+    } = init
     void (async () => {
       try {
         self.setError(undefined)
-        const {
-          msaData,
-          msaUrl,
-          msaTabixLocation,
-          msaIndexLocation,
-          msaId,
-          treeData,
-          treeUrl,
-          querySeqName,
-        } = init
 
         if (msaUrl) {
           const id = getUniprotIdFromAlphaFoldUrl(msaUrl)
@@ -152,7 +155,6 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
             self.setQuerySeqName('query')
           }
         }
-
         if (querySeqName) {
           self.setQuerySeqName(querySeqName)
         }
@@ -160,42 +162,25 @@ export function processInit(self: JBrowsePluginMsaViewModel) {
         if (msaData) {
           self.setMSA(msaData)
         } else if (msaUrl) {
-          const response = await fetch(msaUrl)
-          if (!response.ok) {
-            throw new Error(`Failed to fetch MSA: ${response.status}`)
-          }
-          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}`,
-              )
-            }
+          self.setMSAFilehandle({ uri: msaUrl, locationType: 'UriLocation' })
+        } else if (msaIndexedLocation && msaName) {
+          const fasta = await fetchIndexedMsa({
+            location: msaIndexedLocation,
+            name: msaName,
+          })
+          if (fasta) {
+            self.setMSA(fasta)
+          } else {
+            throw new Error(
+              `No alignment named ${msaName} in ${msaIndexedLocation.uri}`,
+            )
           }
         }
 
         if (treeData) {
           self.setTree(treeData)
         } else if (treeUrl) {
-          const response = await fetch(treeUrl)
-          if (!response.ok) {
-            throw new Error(`Failed to fetch tree: ${response.status}`)
-          }
-          const data = await response.text()
-          self.setTree(data)
+          self.setTreeFilehandle({ uri: treeUrl, locationType: 'UriLocation' })
         }
 
         self.setInit(undefined)

package/src/MsaViewPanel/fetchIndexedMsa.ts

@@ -0,0 +1,47 @@
+import { BgzfFilehandle } from '@gmod/bgzf-filehandle'
+import { openLocation } from '@jbrowse/core/util/io'
+
+// Pull one transcript's whole multiple-alignment out of a single bgzip file
+// keyed by NAME. Given the `.fa.gz` uri, the bgzip index (`.gzi`) and name index
+// (`.idx`, a TSV `name<TAB>offset<TAB>length` of each block's uncompressed byte
+// offset + length) are found by suffix. We fetch the small `.idx` once, look up
+// the name, and random-read just that block — already valid FASTA
+// (`>hg38\nSEQ\n>panTro4\nSEQ\n...`). One genome-scale alignment serves any gene
+// with no per-gene files or coordinates. See react-msaview's gene-explorer.
+export async function fetchIndexedMsa({
+  location,
+  name,
+}: {
+  location: { uri: string }
+  name: string
+}) {
+  const open = (uri: string) =>
+    openLocation({ uri, locationType: 'UriLocation' as const })
+
+  const idxText = await open(`${location.uri}.idx`).readFile('utf8')
+  const entry = lookup(idxText, name)
+  if (entry) {
+    const fh = new BgzfFilehandle({
+      filehandle: open(location.uri),
+      gziFilehandle: open(`${location.uri}.gzi`),
+    })
+    const bytes = await fh.read(entry.length, entry.offset)
+    return new TextDecoder().decode(bytes).trim()
+  }
+  return undefined
+}
+
+// ids are matched versionless, so version drift between the alignment build and
+// the live annotation never breaks the lookup
+const versionless = (s: string) => s.replace(/\.\d+$/, '')
+
+function lookup(idxText: string, name: string) {
+  const want = versionless(name)
+  for (const line of idxText.split('\n')) {
+    const [id, offset, length] = line.split('\t')
+    if (id && versionless(id) === want) {
+      return { offset: Number(offset), length: Number(length) }
+    }
+  }
+  return undefined
+}

package/src/MsaViewPanel/types.ts

@@ -1,14 +1,16 @@
+// Declarative launch contract, resolved once by processInit. This is also a
+// cross-repo contract: jbrowse-plugin-protein3d builds an MsaView snapshot
+// directly with `init: { msaUrl }`, so these keys must stay stable.
 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
+  // a single bgzip `.fa.gz` of per-transcript FASTA blocks; its `.gzi` and name
+  // index `.idx` (name<TAB>offset<TAB>length) are found by suffix. `msaName`
+  // selects one transcript's block by name (a random read), so one genome-scale
+  // alignment serves any gene without per-gene files or coordinates. See
+  // react-msaview's gene-explorer.
+  msaIndexedLocation?: { uri: string }
+  msaName?: string
   treeData?: string
   treeUrl?: string
   querySeqName?: string

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.6.0'
+export const version = '2.6.2'

package/dist/MsaViewPanel/fetchTabixMsa.d.ts

@@ -1,12 +0,0 @@
-export declare function fetchTabixMsa({ location, indexLocation, msaId, refName, start, end, }: {
-    location: {
-        uri: string;
-    };
-    indexLocation?: {
-        uri: string;
-    };
-    msaId: string;
-    refName: string;
-    start: number;
-    end: number;
-}): Promise<string | undefined>;

package/dist/MsaViewPanel/fetchTabixMsa.js

@@ -1,33 +0,0 @@
-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, }) {
-    const uri = (loc) => openLocation({ uri: loc.uri, locationType: 'UriLocation' });
-    const file = new TabixIndexedFile({
-        filehandle: uri(location),
-        csiFilehandle: uri(indexLocation ?? { uri: `${location.uri}.csi` }),
-    });
-    const lines = [];
-    await file.getLines(refName, start, end, {
-        lineCallback: line => {
-            lines.push(line);
-        },
-    });
-    const line = lines.find(l => l.split('\t')[3] === msaId);
-    return line ? unpack(line) : undefined;
-}
-function unpack(line) {
-    const packed = line.split('\t')[4] ?? '';
-    return packed
-        .split(';')
-        .filter(Boolean)
-        .map(pair => {
-        const colon = pair.indexOf(':');
-        return `>${pair.slice(0, colon)}\n${pair.slice(colon + 1)}`;
-    })
-        .join('\n');
-}

package/src/MsaViewPanel/fetchTabixMsa.ts

@@ -1,50 +0,0 @@
-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')
-}