jbrowse-plugin-msaview 2.5.1 → 2.5.2

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

@@ -249,37 +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/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)));
         },
     }));
 }