jbrowse-plugin-msaview 2.4.3 → 2.4.5

package/dist/MsaViewPanel/model.js

@@ -1,11 +1,11 @@
 import { lazy } from 'react';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes';
 import { getSession } from '@jbrowse/core/util';
-import { addDisposer, cast, types } from '@jbrowse/mobx-state-tree';
+import { addDisposer, types } from '@jbrowse/mobx-state-tree';
 import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
 import { autorun } from 'mobx';
 import { MSAModelF } from 'react-msaview';
-import { autoConnectStructures, highlightConnectedStructures, launchBlastIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, updateGenomeHighlights, } from './afterCreateAutoruns';
+import { autoConnectStructures, highlightConnectedStructures, launchBlastIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, } from './afterCreateAutoruns';
 import { genomeToMSA } from './genomeToMSA';
 import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
 import { buildAlignmentMaps, runPairwiseAlignment } from './pairwiseAlignment';
@@ -31,11 +31,6 @@ export default function stateModelFactory() {
         /**
          * #property
          */
-        connectedHighlights: types.array(types.model({
-            refName: types.string,
-            start: types.number,
-            end: types.number,
-        })),
         /**
          * #property
          */
@@ -165,11 +160,22 @@ export default function stateModelFactory() {
          * #getter
          */
         get mouseCol2() {
-            const structureCol = self.structureHoverCol;
-            if (structureCol !== undefined) {
-                return structureCol;
-            }
-            return genomeToMSA({ model: self });
+            return (self.structureHoverCol ??
+                genomeToMSA({ model: self }));
+        },
+        /**
+         * #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);
         },
     }))
         .actions(self => ({
@@ -197,24 +203,6 @@ export default function stateModelFactory() {
         setRid(arg) {
             self.rid = arg;
         },
-        /**
-         * #action
-         */
-        setConnectedHighlights(r) {
-            self.connectedHighlights = cast(r);
-        },
-        /**
-         * #action
-         */
-        addToConnectedHighlights(r) {
-            self.connectedHighlights.push(r);
-        },
-        /**
-         * #action
-         */
-        clearConnectedHighlights() {
-            self.connectedHighlights = cast([]);
-        },
         /**
          * #action
          */
@@ -396,7 +384,6 @@ export default function stateModelFactory() {
                 storeDataToIndexedDB,
                 launchBlastIfNeeded,
                 processInit,
-                updateGenomeHighlights,
                 highlightConnectedStructures,
                 autoConnectStructures,
                 observeProteinHighlights,
@@ -408,4 +395,6 @@ export default function stateModelFactory() {
         },
     }));
 }
-//# sourceMappingURL=model.js.map
+export function isMsaView(view) {
+    return view.type === 'MsaView';
+}

package/dist/MsaViewPanel/msaCoordToGenomeCoord.js

@@ -1,44 +1,27 @@
 import { gappedToUngappedPosition } from './structureConnection';
 export function msaCoordToGenomeCoord({ model, coord: mouseCol, }) {
     const { querySeqName, transcriptToMsaMap, mafRegion } = model;
-    // Get the query sequence
-    const queryRow = model.rows.find(f => f[0] === querySeqName);
-    const querySeq = queryRow?.[1];
+    const querySeq = model.rows.find(f => f[0] === querySeqName)?.[1];
     if (!querySeq) {
         return undefined;
     }
-    // Convert gapped MSA column to ungapped sequence coordinate
-    // Returns undefined if the position is a gap
     const ungappedPos = gappedToUngappedPosition(querySeq, mouseCol);
     if (ungappedPos === undefined) {
         return undefined;
     }
-    // Handle MAF region mapping
     if (mafRegion) {
         const genomePos = mafRegion.start + ungappedPos;
-        // Check if position is within the region
-        if (genomePos >= mafRegion.end) {
-            return undefined;
-        }
-        return {
-            refName: mafRegion.refName,
-            start: genomePos,
-            end: genomePos + 1,
-        };
+        return genomePos < mafRegion.end
+            ? { refName: mafRegion.refName, start: genomePos, end: genomePos + 1 }
+            : undefined;
     }
-    // Handle transcript mapping (original behavior)
     if (transcriptToMsaMap) {
         const { refName, p2g } = transcriptToMsaMap;
         const s = p2g[ungappedPos];
         const e = p2g[ungappedPos + 1];
         return s !== undefined && e !== undefined
-            ? {
-                refName,
-                start: Math.min(s, e),
-                end: Math.max(s, e),
-            }
+            ? { refName, start: Math.min(s, e), end: Math.max(s, e) }
             : undefined;
     }
     return undefined;
 }
-//# sourceMappingURL=msaCoordToGenomeCoord.js.map

package/dist/MsaViewPanel/msaCoordToGenomeCoord.test.js

@@ -237,4 +237,3 @@ describe('msaCoordToGenomeCoord', () => {
         });
     });
 });
-//# sourceMappingURL=msaCoordToGenomeCoord.test.js.map

package/dist/MsaViewPanel/msaDataStore.js

@@ -71,4 +71,3 @@ export async function cleanupOldData(maxAgeMs = 7 * 24 * 60 * 60 * 1000) {
         return 0;
     }
 }
-//# sourceMappingURL=msaDataStore.js.map

package/dist/MsaViewPanel/pairwiseAlignment.js

@@ -143,4 +143,3 @@ export function buildAlignmentMaps(pairwiseAlignment) {
     }
     return { seq1ToSeq2, seq2ToSeq1 };
 }
-//# sourceMappingURL=pairwiseAlignment.js.map

package/dist/MsaViewPanel/pairwiseAlignment.test.js

@@ -109,4 +109,3 @@ describe('buildAlignmentMaps', () => {
         expect(seq1ToSeq2.size).toBeLessThanOrEqual(structureSeq.length);
     });
 });
-//# sourceMappingURL=pairwiseAlignment.test.js.map

package/dist/MsaViewPanel/structureConnection.js

@@ -43,4 +43,3 @@ export function ungappedToGappedPosition(sequence, ungappedPosition) {
     }
     return undefined;
 }
-//# sourceMappingURL=structureConnection.js.map

package/dist/MsaViewPanel/structureConnection.test.js

@@ -101,4 +101,3 @@ describe('gappedToUngappedPosition and ungappedToGappedPosition are inverses', (
         }
     });
 });
-//# sourceMappingURL=structureConnection.test.js.map

package/dist/MsaViewPanel/types.js

@@ -1,2 +1 @@
 export {};
-//# sourceMappingURL=types.js.map

package/dist/MsaViewPanel/util.d.ts

@@ -1,6 +1,4 @@
-import type { Feature } from '@jbrowse/core/util';
-export declare function checkHovered(hovered: unknown): hovered is {
-    hoverFeature: Feature;
+export declare function hasHoverPosition(hovered: unknown): hovered is {
     hoverPosition: {
         coord: number;
         refName: string;

package/dist/MsaViewPanel/util.js

@@ -1,7 +1,6 @@
-export function checkHovered(hovered) {
+export function hasHoverPosition(hovered) {
     return (!!hovered &&
         typeof hovered === 'object' &&
-        'hoverFeature' in hovered &&
         'hoverPosition' in hovered &&
         !!hovered.hoverPosition);
 }
@@ -22,4 +21,3 @@ export function getUniprotIdFromAlphaFoldUrl(url) {
     const match = /AF-([A-Z0-9]+)-F\d+/.exec(url);
     return match?.[1];
 }
-//# sourceMappingURL=util.js.map

package/dist/components/ExternalLink.js

@@ -8,4 +8,3 @@ export default function ExternalLink(props) {
         " ",
         React.createElement(OpenInNewIcon, { fontSize: "small" })));
 }
-//# sourceMappingURL=ExternalLink.js.map

package/dist/components/ReadOnlyTextField2.js

@@ -17,4 +17,3 @@ export default function ReadOnlyTextField2({ value }) {
             },
         } }));
 }
-//# sourceMappingURL=ReadOnlyTextField2.js.map

package/dist/components/TextField2.js

@@ -5,4 +5,3 @@ function TextField2({ children, ...rest }) {
         React.createElement(TextField, { ...rest }, children)));
 }
 export default TextField2;
-//# sourceMappingURL=TextField2.js.map

package/dist/index.js

@@ -55,4 +55,3 @@ export default class MsaViewPlugin extends Plugin {
         }
     }
 }
-//# sourceMappingURL=index.js.map