jbrowse-plugin-msaview 2.6.0 → 2.6.2

package/dist/LaunchMsaViewExtensionPoint/index.js

@@ -1,34 +1,24 @@
 export default function LaunchMsaViewExtensionPointF(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, }) => {
-        if (!data && !msaFileLocation && !msaTabixLocation) {
+    pluginManager.addToExtensionPoint('LaunchView-MsaView', (args) => {
+        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/dist/MsaViewPanel/afterCreateAutoruns.js

@@ -1,6 +1,6 @@
 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 { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
@@ -116,13 +116,17 @@ export function autoLoadProteinDomains(self) {
         })();
     }
 }
+// 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) {
     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);
                     if (id) {
@@ -137,42 +141,25 @@ export function processInit(self) {
                     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);
+                    self.setMSAFilehandle({ uri: msaUrl, locationType: 'UriLocation' });
                 }
-                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}`);
-                        }
+                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/dist/MsaViewPanel/fetchIndexedMsa.d.ts

@@ -0,0 +1,6 @@
+export declare function fetchIndexedMsa({ location, name, }: {
+    location: {
+        uri: string;
+    };
+    name: string;
+}): Promise<string | undefined>;

package/dist/MsaViewPanel/fetchIndexedMsa.js

@@ -0,0 +1,36 @@
+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, }) {
+    const open = (uri) => openLocation({ uri, locationType: 'UriLocation' });
+    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) => s.replace(/\.\d+$/, '');
+function lookup(idxText, name) {
+    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/dist/MsaViewPanel/types.d.ts

@@ -1,13 +1,10 @@
 export interface MsaViewInitState {
     msaData?: string;
     msaUrl?: string;
-    msaTabixLocation?: {
+    msaIndexedLocation?: {
         uri: string;
     };
-    msaIndexLocation?: {
-        uri: string;
-    };
-    msaId?: string;
+    msaName?: string;
     treeData?: string;
     treeUrl?: string;
     querySeqName?: string;