jbrowse-plugin-msaview 2.5.0 → 2.5.2

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
@@ -13,5 +20,19 @@ export declare function processInit(self: JBrowsePluginMsaViewModel): void;
 export declare function syncGenomeHoverToMsaColumn(self: JBrowsePluginMsaViewModel): () => void;
 export declare function highlightConnectedStructures(self: JBrowsePluginMsaViewModel): void;
 export declare function autoConnectStructures(self: JBrowsePluginMsaViewModel): void;
-export declare function observeProteinHighlights(self: JBrowsePluginMsaViewModel): void;
+/**
+ * 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 declare function observeProteinHighlights(self: JBrowsePluginMsaViewModel): () => void;
 export declare function runCleanup(): void;

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) {
@@ -218,37 +249,63 @@ export function autoConnectStructures(self) {
         }
     }
 }
+/**
+ * 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) {
-    const { connectedViewId, transcriptToMsaMap, querySeqName } = self;
-    if (!connectedViewId || !transcriptToMsaMap) {
-        return;
-    }
-    const columns = new Set();
-    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 { 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);
+    let proteinDriven = false;
+    return () => {
+        const { connectedViewId, transcriptToMsaMap, querySeqName } = self;
+        if (!connectedViewId || !transcriptToMsaMap) {
+            return;
+        }
+        const columns = new Set();
+        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 { 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 !== undefined);
-    self.setHighlightedColumns(visibleColumns.length > 0 ? visibleColumns : undefined);
+        const visibleColumns = Array.from(columns)
+            .map(col => self.globalColToVisibleCol(col))
+            .filter((col) => 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() {
     cleanupOldData().catch((e) => {

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);
+}