jbrowse-plugin-msaview 2.6.4 → 2.6.6

package/dist/utils/ncbiDomains.d.ts

@@ -11,11 +11,13 @@ export declare function parseCddDomains(xml: string): Map<string, {
             name: string;
             description: string;
             accession: string;
+            featureType?: string;
         };
     };
     locations: {
         start: number;
         end: number;
+        strand?: number;
     }[];
 }[]>;
 /**
@@ -30,10 +32,12 @@ export declare function fetchProteinDomains(accessions: string[]): Promise<Map<s
             name: string;
             description: string;
             accession: string;
+            featureType?: string;
         };
     };
     locations: {
         start: number;
         end: number;
+        strand?: number;
     }[];
 }[]>>;

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "2.6.4";
+export declare const version = "2.6.6";

package/dist/version.js

@@ -1 +1 @@
-export const version = '2.6.4';
+export const version = '2.6.6';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.6.4",
+  "version": "2.6.6",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -21,7 +21,7 @@
     "g2p_mapper": "^2.1.5",
     "idb": "^8.0.3",
     "pako-esm2": "^2.0.2",
-    "react-msaview": "^5.4.1",
+    "react-msaview": "^5.5.0",
     "swr": "^2.4.2"
   },
   "devDependencies": {
@@ -47,7 +47,7 @@
     "eslint-plugin-unicorn": "^64.0.0",
     "mobx": "^6.16.1",
     "mobx-react": "^9.2.2",
-    "msa-parsers": "5.4.1",
+    "msa-parsers": "^5.5.0",
     "pixelmatch": "^7.2.0",
     "pngjs": "^7.0.0",
     "prettier": "^3.8.4",

package/src/AddHighlightModel/MsaToGenomeHighlight.tsx

@@ -19,11 +19,20 @@ const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({
   const msaView = views
     .filter(isMsaView)
     .find(v => v.connectedViewId === model.id)
-  const highlights = msaView?.connectedHighlights
 
-  // Suppress codon highlight while hovering the LGV — GenomeMouseoverHighlight
-  // handles the single-bp display in that case
-  return !hasHoverPosition(hovered) && highlights?.length ? (
+  // The persistent click selection always shows. The hover codon is suppressed
+  // while hovering the LGV — GenomeMouseoverHighlight handles the single-bp
+  // display in that case, so we don't stack a wider codon band on top of it.
+  const clickHighlight = msaView?.connectedClickHighlight
+  const hoverHighlight = hasHoverPosition(hovered)
+    ? undefined
+    : msaView?.connectedHoverHighlight
+  const highlights = [clickHighlight, hoverHighlight].filter(
+    (r): r is { refName: string; start: number; end: number } =>
+      r !== undefined,
+  )
+
+  return highlights.length ? (
     <MsaToGenomeHighlightRenderer model={model} highlights={highlights} />
   ) : null
 })

package/src/MsaViewPanel/model.ts

@@ -180,19 +180,36 @@ export default function stateModelFactory() {
     }))
 
     .views(self => ({
+      /**
+       * #getter
+       * Genome region under the current MSA hover column. Suppressed on the LGV
+       * while it's being hovered (GenomeMouseoverHighlight shows the crisp 1bp
+       * marker there instead of this wider codon band).
+       */
+      get connectedHoverHighlight(): IRegion | undefined {
+        const { mouseCol } = self
+        return mouseCol === undefined
+          ? undefined
+          : msaCoordToGenomeCoord({ model: self, coord: mouseCol })
+      },
+      /**
+       * #getter
+       * Genome region under the persistent MSA click selection. Shown
+       * regardless of LGV hover, so hovering the genome doesn't hide it.
+       */
+      get connectedClickHighlight(): IRegion | undefined {
+        const { mouseClickCol } = self
+        return mouseClickCol === undefined
+          ? undefined
+          : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
+      },
       /**
        * #getter
        */
       get connectedHighlights(): IRegion[] {
-        const { mouseCol, mouseClickCol } = self
-        return [
-          mouseCol === undefined
-            ? undefined
-            : msaCoordToGenomeCoord({ model: self, coord: mouseCol }),
-          mouseClickCol === undefined
-            ? undefined
-            : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol }),
-        ].filter((r): r is IRegion => r !== undefined)
+        return [this.connectedHoverHighlight, this.connectedClickHighlight].filter(
+          (r): r is IRegion => r !== undefined,
+        )
       },
     }))
 

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.6.4'
+export const version = '2.6.6'