jbrowse-plugin-msaview 2.5.1 → 2.6.0

package/dist/LaunchMsaViewExtensionPoint/index.js

@@ -1,8 +1,8 @@
 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, highlightColumns, }) => {
-        if (!data && !msaFileLocation) {
+    ({ session, data, msaFileLocation, msaTabixLocation, msaIndexLocation, msaId, treeFileLocation, connectedViewId, connectedFeature, displayName, colorSchemeName, colWidth, rowHeight, treeAreaWidth, treeWidth, drawNodeBubbles, labelsAlignRight, showBranchLen, querySeqName, highlightColumns, }) => {
+        if (!data && !msaFileLocation && !msaTabixLocation) {
             throw new Error('No MSA data or file location provided when launching MSA view');
         }
         session.addView('MsaView', {
@@ -23,6 +23,9 @@ export default function LaunchMsaViewExtensionPointF(pluginManager) {
                 msaData: data?.msa,
                 treeData: data?.tree,
                 msaUrl: msaFileLocation?.uri,
+                msaTabixLocation,
+                msaIndexLocation,
+                msaId,
                 treeUrl: treeFileLocation?.uri,
                 querySeqName,
             },

package/dist/MsaViewPanel/afterCreateAutoruns.d.ts

@@ -20,5 +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

@@ -1,5 +1,6 @@
 import { getSession } from '@jbrowse/core/util';
 import { doLaunchBlast } from './doLaunchBlast';
+import { fetchTabixMsa } from './fetchTabixMsa';
 import { genomeToMSA } from './genomeToMSA';
 import { loadProteinDomains } from './loadProteinDomains';
 import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
@@ -121,7 +122,7 @@ export function processInit(self) {
         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);
                     if (id) {
@@ -143,6 +144,25 @@ export function processInit(self) {
                     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) {
                     self.setTree(treeData);
                 }
@@ -249,37 +269,63 @@ 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/fetchTabixMsa.d.ts

@@ -0,0 +1,12 @@
+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

@@ -0,0 +1,33 @@
+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/dist/MsaViewPanel/model.js

@@ -363,13 +363,15 @@ export default function stateModelFactory() {
                 highlightConnectedStructures,
                 autoConnectStructures,
                 autoLoadProteinDomains,
-                observeProteinHighlights,
             ]) {
                 addDisposer(self, autorun(() => {
                     fn(self);
                 }));
             }
+            // 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/dist/MsaViewPanel/types.d.ts

@@ -1,6 +1,13 @@
 export interface MsaViewInitState {
     msaData?: string;
     msaUrl?: string;
+    msaTabixLocation?: {
+        uri: string;
+    };
+    msaIndexLocation?: {
+        uri: string;
+    };
+    msaId?: string;
     treeData?: string;
     treeUrl?: string;
     querySeqName?: string;