jbrowse-plugin-msaview 2.6.4 → 2.6.6

package/dist/AddHighlightModel/MsaToGenomeHighlight.js

@@ -8,10 +8,15 @@ const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, })
     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 ? (React.createElement(MsaToGenomeHighlightRenderer, { model: model, highlights: highlights })) : null;
+    // 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 !== undefined);
+    return highlights.length ? (React.createElement(MsaToGenomeHighlightRenderer, { model: model, highlights: highlights })) : null;
 });
 // Inner component: handles the scroll-dependent rendering
 const MsaToGenomeHighlightRenderer = observer(function ({ model, highlights, }) {

package/dist/MsaViewPanel/model.d.ts

@@ -384,43 +384,92 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }>;
     readonly tidyInterProAnnotations: {
         id: string;
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }[];
     readonly tidyFilteredInterProAnnotations: {
         id: string;
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }[];
     readonly tidyFilteredGatheredInterProAnnotations: Record<string, {
         id: string;
         name: string;
         accession: string;
         description: string;
+        featureType: string | undefined;
         start: number;
         end: number;
+        strand: number | undefined;
     }[]>;
 } & {
     readonly showVerticalScrollbar: boolean;
 } & {
     readonly verticalScrollbarWidth: 0 | 20;
+    readonly segmentDomainTypes: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
+    readonly categoricalDomainTypes: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
     readonly fillPalette: {
-        [k: string]: string;
+        [x: string]: string;
     };
     readonly strokePalette: {
         [k: string]: string;
     };
+    readonly segmentLabels: Map<string, string>;
+    readonly visibleDomainTypes: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
+    readonly mouseOverDomains: {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        featureType: string | undefined;
+        start: number;
+        end: number;
+        strand: number | undefined;
+    }[];
     getRowData(name: string): {
         data: {
             name?: string;
@@ -477,6 +526,19 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      */
     readonly connectedView: MaybeLGV;
 } & {
+    /**
+     * #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).
+     */
+    readonly connectedHoverHighlight: IRegion | undefined;
+    /**
+     * #getter
+     * Genome region under the persistent MSA click selection. Shown
+     * regardless of LGV hover, so hovering the genome doesn't hide it.
+     */
+    readonly connectedClickHighlight: IRegion | undefined;
     /**
      * #getter
      */

package/dist/MsaViewPanel/model.js

@@ -111,19 +111,34 @@ 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() {
+            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() {
+            const { mouseClickCol } = self;
+            return mouseClickCol === undefined
+                ? undefined
+                : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol });
+        },
         /**
          * #getter
          */
         get connectedHighlights() {
-            const { mouseCol, mouseClickCol } = self;
-            return [
-                mouseCol === undefined
-                    ? undefined
-                    : msaCoordToGenomeCoord({ model: self, coord: mouseCol }),
-                mouseClickCol === undefined
-                    ? undefined
-                    : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol }),
-            ].filter((r) => r !== undefined);
+            return [this.connectedHoverHighlight, this.connectedClickHighlight].filter((r) => r !== undefined);
         },
     }))
         .actions(self => ({