jbrowse-plugin-msaview 2.2.2 → 2.2.3

package/dist/out.js

@@ -55142,8 +55142,39 @@ ${seq}`)
        */
       setBlastParams(args) {
         self2.blastParams = args;
+      },
+      /**
+       * #action
+       */
+      handleMsaClick(coord) {
+        const { connectedView, zoomToBaseLevel } = self2;
+        const { assemblyManager } = (0, import_util45.getSession)(self2);
+        const r2 = msaCoordToGenomeCoord({ model: self2, coord });
+        if (!r2 || !connectedView) {
+          return;
+        }
+        if (zoomToBaseLevel) {
+          connectedView.navTo(r2);
+        } else {
+          const r3 = assemblyManager.get(connectedView.assemblyNames[0])?.getCanonicalRefName(r2.refName) ?? r2.refName;
+          connectedView.centerAt(r2.start, r3);
+        }
       }
-    })).views((self2) => ({
+    })).actions((self2) => {
+      const superSetMouseClickPos = self2.setMouseClickPos;
+      return {
+        /**
+         * #action
+         * overrides base setMouseClickPos to trigger navigation
+         */
+        setMouseClickPos(col, row) {
+          superSetMouseClickPos(col, row);
+          if (col !== void 0) {
+            self2.handleMsaClick(col);
+          }
+        }
+      };
+    }).views((self2) => ({
       /**
        * #method
        * overrides base
@@ -55205,23 +55236,6 @@ ${seq}`)
             self2.setConnectedHighlights([r1, r2].filter((f2) => !!f2));
           })
         );
-        (0, import_mobx_state_tree8.addDisposer)(
-          self2,
-          (0, import_mobx7.autorun)(() => {
-            const { connectedView, zoomToBaseLevel, mouseClickCol } = self2;
-            const { assemblyManager } = (0, import_util45.getSession)(self2);
-            const r2 = mouseClickCol === void 0 ? void 0 : msaCoordToGenomeCoord({ model: self2, coord: mouseClickCol });
-            if (!r2 || !connectedView) {
-              return;
-            }
-            if (zoomToBaseLevel) {
-              connectedView.navTo(r2);
-            } else {
-              const r3 = assemblyManager.get(connectedView.assemblyNames[0])?.getCanonicalRefName(r2.refName) ?? r2.refName;
-              connectedView.centerAt(r2.start, r3);
-            }
-          })
-        );
       }
     }));
   }

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "2.2.2",
+  "version": "2.2.3",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "keywords": [

package/src/MsaViewPanel/model.ts

@@ -202,7 +202,46 @@ export default function stateModelFactory() {
       setBlastParams(args?: BlastParams) {
         self.blastParams = args
       },
+      /**
+       * #action
+       */
+      handleMsaClick(coord: number) {
+        const { connectedView, zoomToBaseLevel } = self
+        const { assemblyManager } = getSession(self)
+        const r2 = msaCoordToGenomeCoord({ model: self, coord })
+
+        if (!r2 || !connectedView) {
+          return
+        }
+
+        if (zoomToBaseLevel) {
+          connectedView.navTo(r2)
+        } else {
+          const r =
+            assemblyManager
+              .get(connectedView.assemblyNames[0]!)
+              ?.getCanonicalRefName(r2.refName) ?? r2.refName
+          connectedView.centerAt(r2.start, r)
+        }
+      },
     }))
+    .actions(self => {
+      // store reference to the original action from react-msaview
+      const superSetMouseClickPos = self.setMouseClickPos
+
+      return {
+        /**
+         * #action
+         * overrides base setMouseClickPos to trigger navigation
+         */
+        setMouseClickPos(col?: number, row?: number) {
+          superSetMouseClickPos(col, row)
+          if (col !== undefined) {
+            self.handleMsaClick(col)
+          }
+        },
+      }
+    })
 
     .views(self => ({
       /**
@@ -277,33 +316,6 @@ export default function stateModelFactory() {
             self.setConnectedHighlights([r1, r2].filter(f => !!f))
           }),
         )
-
-        // nav to genome position after click
-        addDisposer(
-          self,
-          autorun(() => {
-            const { connectedView, zoomToBaseLevel, mouseClickCol } = self
-            const { assemblyManager } = getSession(self)
-            const r2 =
-              mouseClickCol === undefined
-                ? undefined
-                : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol })
-
-            if (!r2 || !connectedView) {
-              return
-            }
-
-            if (zoomToBaseLevel) {
-              connectedView.navTo(r2)
-            } else {
-              const r =
-                assemblyManager
-                  .get(connectedView.assemblyNames[0]!)
-                  ?.getCanonicalRefName(r2.refName) ?? r2.refName
-              connectedView.centerAt(r2.start, r)
-            }
-          }),
-        )
       },
     }))
 }

package/src/MsaViewPanel/msaCoordToGenomeCoord.ts

@@ -1,5 +1,3 @@
-import { JBrowsePluginMsaViewModel } from './model'
-
 /**
  * Convert gapped MSA column coordinate to ungapped sequence coordinate
  * This is the inverse of ungappedCoordMap
@@ -18,7 +16,7 @@ export function msaCoordToGenomeCoord({
   model,
   coord: mouseCol,
 }: {
-  model: JBrowsePluginMsaViewModel
+  model: { querySeqName: string; transcriptToMsaMap: any; rows: string[][] }
   coord: number
 }) {
   const { querySeqName, transcriptToMsaMap } = model