jbrowse-plugin-msaview 2.5.0 → 2.5.1

package/dist/LaunchMsaViewExtensionPoint/index.js

@@ -1,7 +1,7 @@
 export default function LaunchMsaViewExtensionPointF(pluginManager) {
     pluginManager.addToExtensionPoint('LaunchView-MsaView', 
     // @ts-expect-error
-    ({ session, data, msaFileLocation, treeFileLocation, connectedViewId, connectedFeature, displayName, colorSchemeName, colWidth, rowHeight, treeAreaWidth, treeWidth, drawNodeBubbles, labelsAlignRight, showBranchLen, querySeqName, }) => {
+    ({ session, data, msaFileLocation, treeFileLocation, connectedViewId, connectedFeature, displayName, colorSchemeName, colWidth, rowHeight, treeAreaWidth, treeWidth, drawNodeBubbles, labelsAlignRight, showBranchLen, querySeqName, highlightColumns, }) => {
         if (!data && !msaFileLocation) {
             throw new Error('No MSA data or file location provided when launching MSA view');
         }
@@ -18,6 +18,7 @@ export default function LaunchMsaViewExtensionPointF(pluginManager) {
             drawNodeBubbles,
             labelsAlignRight,
             showBranchLen,
+            highlightColumns,
             init: {
                 msaData: data?.msa,
                 treeData: data?.tree,

package/dist/MsaViewPanel/afterCreateAutoruns.d.ts

@@ -2,6 +2,13 @@ import type { JBrowsePluginMsaViewModel } from './model';
 export declare function loadStoredData(self: JBrowsePluginMsaViewModel): void;
 export declare function storeDataToIndexedDB(self: JBrowsePluginMsaViewModel): void;
 export declare function launchBlastIfNeeded(self: JBrowsePluginMsaViewModel): void;
+/**
+ * Once an accession-bearing alignment is present (fresh from BLAST or restored
+ * from cache), fetch NCBI CDD domains for those accessions and overlay them.
+ * Runs once per view; the domainsRequested guard prevents refiring when NCBI
+ * returns no domains (which leaves interProAnnotations undefined).
+ */
+export declare function autoLoadProteinDomains(self: JBrowsePluginMsaViewModel): void;
 export declare function processInit(self: JBrowsePluginMsaViewModel): void;
 /**
  * Mirror the connected genome view's hover position onto the MSA's hovered

package/dist/MsaViewPanel/afterCreateAutoruns.js

@@ -1,6 +1,7 @@
 import { getSession } from '@jbrowse/core/util';
 import { doLaunchBlast } from './doLaunchBlast';
 import { genomeToMSA } from './genomeToMSA';
+import { loadProteinDomains } from './loadProteinDomains';
 import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
 import { gappedToUngappedPosition, getProteinViews, } from './structureConnection';
 import { getUniprotIdFromAlphaFoldUrl } from './util';
@@ -18,6 +19,9 @@ export function loadStoredData(self) {
                     if (storedData.tree) {
                         self.setTree(storedData.tree);
                     }
+                    if (storedData.treeMetadata) {
+                        self.setTreeMetadata(storedData.treeMetadata);
+                    }
                 }
             }
             catch (e) {
@@ -84,6 +88,33 @@ export function launchBlastIfNeeded(self) {
         })();
     }
 }
+/**
+ * Once an accession-bearing alignment is present (fresh from BLAST or restored
+ * from cache), fetch NCBI CDD domains for those accessions and overlay them.
+ * Runs once per view; the domainsRequested guard prevents refiring when NCBI
+ * returns no domains (which leaves interProAnnotations undefined).
+ */
+export function autoLoadProteinDomains(self) {
+    const { rows, domainsRequested, interProAnnotations } = self;
+    const hasAccessions = self.data.treeMetadata?.includes('"Accession"') ?? false;
+    if (rows.length > 0 &&
+        hasAccessions &&
+        !interProAnnotations &&
+        !domainsRequested) {
+        self.setDomainsRequested(true);
+        void (async () => {
+            try {
+                await loadProteinDomains(self);
+            }
+            catch (e) {
+                console.error('[msaview-domains] auto-load failed:', e);
+            }
+            finally {
+                self.setProgress('');
+            }
+        })();
+    }
+}
 export function processInit(self) {
     const { init } = self;
     if (init) {

package/dist/MsaViewPanel/loadProteinDomains.d.ts

@@ -0,0 +1,16 @@
+import type { InterProScanResults } from 'react-msaview';
+interface DomainModel {
+    data: {
+        treeMetadata?: string;
+    };
+    setProgress: (arg: string) => void;
+    setDomains: (data: Record<string, InterProScanResults>) => void;
+}
+/**
+ * Overlay protein domains on the alignment using NCBI's pre-computed CDD
+ * annotations. The BLAST workflow stores each hit's accession in treeMetadata,
+ * so we look those up via efetch and key the results by MSA row name (which is
+ * what react-msaview matches domains against).
+ */
+export declare function loadProteinDomains(self: DomainModel): Promise<void>;
+export {};

package/dist/MsaViewPanel/loadProteinDomains.js

@@ -0,0 +1,33 @@
+import { fetchProteinDomains } from '../utils/ncbiDomains';
+/**
+ * Overlay protein domains on the alignment using NCBI's pre-computed CDD
+ * annotations. The BLAST workflow stores each hit's accession in treeMetadata,
+ * so we look those up via efetch and key the results by MSA row name (which is
+ * what react-msaview matches domains against).
+ */
+export async function loadProteinDomains(self) {
+    const metadataJson = self.data.treeMetadata;
+    if (!metadataJson) {
+        throw new Error('No sequence metadata available to look up domains');
+    }
+    const metadata = JSON.parse(metadataJson);
+    const rowAccessions = Object.entries(metadata)
+        .map(([rowName, meta]) => ({ rowName, accession: meta.Accession }))
+        .filter((r) => !!r.accession);
+    if (rowAccessions.length === 0) {
+        throw new Error('No NCBI accessions found in alignment rows');
+    }
+    self.setProgress(`Fetching protein domains from NCBI for ${rowAccessions.length} sequences...`);
+    const byAccession = await fetchProteinDomains(rowAccessions.map(r => r.accession));
+    const annotations = {};
+    for (const { rowName, accession } of rowAccessions) {
+        const matches = byAccession.get(accession);
+        if (matches && matches.length > 0) {
+            annotations[rowName] = { matches, xref: [{ id: rowName }] };
+        }
+    }
+    if (Object.keys(annotations).length === 0) {
+        throw new Error('No CDD domain annotations found for these proteins');
+    }
+    self.setDomains(annotations);
+}