jbrowse-plugin-msaview 2.4.5 → 2.5.0

package/dist/LaunchMsaView/util.js

@@ -26,7 +26,7 @@ export function getTranscriptFeatures(feature) {
 export function getTranscriptLength(feature) {
     const cdsLen = sum(feature
         .get('subfeatures')
-        ?.filter(f => f.get('type')?.toLowerCase() === 'cds')
+        ?.filter(f => f.get('type') === 'CDS')
         .map(s => s.get('end') - s.get('start')) ?? []);
     return {
         len: Math.floor(cdsLen / 3),

package/dist/MsaViewPanel/afterCreateAutoruns.d.ts

@@ -3,6 +3,14 @@ export declare function loadStoredData(self: JBrowsePluginMsaViewModel): void;
 export declare function storeDataToIndexedDB(self: JBrowsePluginMsaViewModel): void;
 export declare function launchBlastIfNeeded(self: JBrowsePluginMsaViewModel): void;
 export declare function processInit(self: JBrowsePluginMsaViewModel): void;
+/**
+ * Mirror the connected genome view's hover position onto the MSA's hovered
+ * column. Returns the autorun body so it can keep a flag tracking whether the
+ * MSA's mouseCol was set by this sync: that way an unrelated session hover
+ * change clears the column only when the genome put it there, never wiping a
+ * column the user is hovering directly in the MSA.
+ */
+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;

package/dist/MsaViewPanel/afterCreateAutoruns.js

@@ -1,5 +1,6 @@
 import { getSession } from '@jbrowse/core/util';
 import { doLaunchBlast } from './doLaunchBlast';
+import { genomeToMSA } from './genomeToMSA';
 import { cleanupOldData, generateDataStoreId, retrieveMsaData, storeMsaData, } from './msaDataStore';
 import { gappedToUngappedPosition, getProteinViews, } from './structureConnection';
 import { getUniprotIdFromAlphaFoldUrl } from './util';
@@ -131,6 +132,27 @@ export function processInit(self) {
         })();
     }
 }
+/**
+ * Mirror the connected genome view's hover position onto the MSA's hovered
+ * column. Returns the autorun body so it can keep a flag tracking whether the
+ * MSA's mouseCol was set by this sync: that way an unrelated session hover
+ * change clears the column only when the genome put it there, never wiping a
+ * column the user is hovering directly in the MSA.
+ */
+export function syncGenomeHoverToMsaColumn(self) {
+    let genomeDrivenCol = false;
+    return () => {
+        const col = genomeToMSA({ model: self });
+        if (col !== undefined) {
+            self.setMousePos(col);
+            genomeDrivenCol = true;
+        }
+        else if (genomeDrivenCol) {
+            self.setMousePos(undefined);
+            genomeDrivenCol = false;
+        }
+    };
+}
 export function highlightConnectedStructures(self) {
     const { mouseCol, connectedProteinViews } = self;
     if (connectedProteinViews.length === 0) {