jbrowse-plugin-msaview 2.7.2 → 2.7.3

package/dist/AddHighlightModel/MsaToGenomeHighlight.js

@@ -11,11 +11,12 @@ const MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({ model, })
     // 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);
+    const highlights = [
+        ...(msaView?.connectedClickHighlights ?? []),
+        ...(hasHoverPosition(hovered)
+            ? []
+            : (msaView?.connectedHoverHighlights ?? [])),
+    ];
     return highlights.length ? (React.createElement(MsaToGenomeHighlightRenderer, { model: model, highlights: highlights })) : null;
 });
 // Inner component: handles the scroll-dependent rendering

package/dist/LaunchMsaView/components/NCBIBlastQuery/CachedBlastResults.js

@@ -68,7 +68,7 @@ const CachedBlastResults = observer(function ({ model, handleClose, feature, })
                     catch (e) {
                         setOperationError(e);
                     }
-                } }, "Clear All")),
+                } }, "Clear results for this gene")),
         React.createElement(List, { dense: true, className: classes.resultList }, results.map(result => (React.createElement(ListItem, { key: result.id, disablePadding: true, secondaryAction: React.createElement(IconButton, { edge: "end", size: "small", onClick: async (e) => {
                     e.stopPropagation();
                     try {

package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.d.ts

@@ -1,5 +1,5 @@
 export declare function useCachedBlastResults(geneIds: string[]): {
-    results: any[];
+    results: import("../../../utils/blastCache").CachedBlastResult[];
     error: any;
     isLoading: boolean;
     handleDelete: (id: string) => Promise<void>;

package/dist/LaunchMsaView/components/NCBIBlastQuery/useCachedBlastResults.js

@@ -1,5 +1,5 @@
 import useSWR from 'swr';
-import { clearAllCachedResults, deleteCachedResult, getAllCachedResults, } from '../../../utils/blastCache';
+import { deleteCachedResult, getAllCachedResults, } from '../../../utils/blastCache';
 import { staticSwrConfig } from '../../../utils/swrConfig';
 export function useCachedBlastResults(geneIds) {
     const { data: results, error, isLoading, mutate, } = useSWR(`cached-blast-${geneIds.join(',')}`, async () => {
@@ -10,8 +10,11 @@ export function useCachedBlastResults(geneIds) {
         await deleteCachedResult(id);
         await mutate(results => results?.filter(result => result.id !== id) ?? [], false);
     };
+    // deletes only what this hook listed, i.e. the results for these gene ids.
+    // The list the user is looking at is gene-scoped, so a store-wide clear here
+    // would silently throw away every other gene's cached alignments too
     const handleClearAll = async () => {
-        await clearAllCachedResults();
+        await Promise.all((results ?? []).map(r => deleteCachedResult(r.id)));
         await mutate([], false);
     };
     return {

package/dist/MsaViewPanel/doLaunchBlast.js

@@ -7,36 +7,26 @@ import { fetchTaxonomyInfo } from '../utils/taxonomyNames';
 export async function doLaunchBlast({ self, }) {
     const { baseUrl, blastDatabase, blastProgram, msaAlgorithm, proteinSequence, selectedTranscript, rid: existingRid, } = self.blastParams;
     const cleanedSeq = cleanProteinSequence(proteinSequence);
-    let hits;
-    let rid;
+    const onProgress = (arg) => {
+        self.setProgress(arg);
+    };
     if (existingRid) {
+        // publish it before the first poll so the view can link out to NCBI while
+        // the job is still running
         self.setRid(existingRid);
-        const result = await queryBlastFromRid({
-            rid: existingRid,
-            baseUrl,
-            onProgress: arg => {
-                self.setProgress(arg);
-            },
-        });
-        hits = result.hits;
-        rid = result.rid;
     }
-    else {
-        const result = await queryBlast({
+    const { hits, rid } = existingRid
+        ? await queryBlastFromRid({ rid: existingRid, baseUrl, onProgress })
+        : await queryBlast({
             query: cleanedSeq,
             blastDatabase,
             blastProgram,
             baseUrl,
-            onProgress: arg => {
-                self.setProgress(arg);
-            },
+            onProgress,
             onRid: r => {
                 self.setRid(r);
             },
         });
-        hits = result.hits;
-        rid = result.rid;
-    }
     self.setProgress('Fetching species taxonomy info...');
     const taxids = hits
         .map(h => h.description[0]?.taxid)
@@ -57,9 +47,7 @@ export async function doLaunchBlast({ self, }) {
     const result = await launchMSA({
         algorithm: msaAlgorithm,
         sequence: [`>QUERY\n${cleanedSeq}`, ...sequences].join('\n'),
-        onProgress: arg => {
-            self.setProgress(arg);
-        },
+        onProgress,
     });
     const treeMetadataJson = JSON.stringify(treeMetadata);
     await saveBlastResult({

package/dist/MsaViewPanel/genomeToMSA.js

@@ -6,18 +6,25 @@ export function genomeToMSA({ model }) {
     if (!connectedView?.initialized || !hasHoverPosition(hovered)) {
         return undefined;
     }
-    const { coord: hoverCoord, refName } = hovered.hoverPosition;
+    const { coord, refName } = hovered.hoverPosition;
+    // hoverPosition.coord is a 1-based display coordinate (core's pxToBp adds the
+    // +1), while g2p and mafRegion are keyed by 0-based genome position
+    const genomePos = coord - 1;
     if (mafRegion) {
         if (refName !== mafRegion.refName ||
             !connectedView.assemblyNames.includes(mafRegion.assemblyName) ||
-            hoverCoord < mafRegion.start ||
-            hoverCoord >= mafRegion.end) {
+            genomePos < mafRegion.start ||
+            genomePos >= mafRegion.end) {
             return undefined;
         }
-        return model.seqPosToVisibleCol(querySeqName, hoverCoord - mafRegion.start);
+        return model.seqPosToVisibleCol(querySeqName, genomePos - mafRegion.start);
     }
-    if (transcriptToMsaMap) {
-        const seqPos = transcriptToMsaMap.g2p[hoverCoord];
+    // session.hovered is global -- set by whichever LinearGenomeView the cursor
+    // was last over, on any assembly -- so the refName gate is load bearing:
+    // without it the same numeric coordinate on an unrelated chromosome matches a
+    // g2p key and lights up a column for a different locus
+    if (refName === transcriptToMsaMap?.refName) {
+        const seqPos = transcriptToMsaMap.g2p[genomePos];
         if (seqPos !== undefined) {
             return model.seqPosToVisibleCol(querySeqName, seqPos);
         }

package/dist/MsaViewPanel/genomeToMSA.test.js

@@ -76,8 +76,9 @@ describe('genomeToMSA', () => {
                 seqPosToVisibleCol: mockSeqPosToVisibleCol,
             };
             const result = genomeToMSA({ model });
-            // coord 1005 - start 1000 = ungapped position 5
-            expect(mockSeqPosToVisibleCol).toHaveBeenCalledWith('hg38.chr1', 5);
+            // hover coord 1005 is 1-based, so the 0-based genome position is 1004,
+            // which is ungapped position 4 of a region starting at 1000
+            expect(mockSeqPosToVisibleCol).toHaveBeenCalledWith('hg38.chr1', 4);
             expect(result).toBe(5);
         });
         test('returns undefined when hover refName does not match mafRegion', () => {
@@ -106,10 +107,11 @@ describe('genomeToMSA', () => {
             expect(result).toBeUndefined();
         });
         test('returns undefined when hover coord is before mafRegion start', () => {
+            // 1-based coord 1000 is the 0-based base 999, one before the region
             mockGetSession.mockReturnValue({
                 hovered: {
                     hoverFeature: {},
-                    hoverPosition: { coord: 999, refName: 'chr1' },
+                    hoverPosition: { coord: 1000, refName: 'chr1' },
                 },
             });
             const model = {
@@ -131,10 +133,11 @@ describe('genomeToMSA', () => {
             expect(result).toBeUndefined();
         });
         test('returns undefined when hover coord is at or after mafRegion end', () => {
+            // 1-based coord 1011 is the 0-based base 1010, one past the region
             mockGetSession.mockReturnValue({
                 hovered: {
                     hoverFeature: {},
-                    hoverPosition: { coord: 1010, refName: 'chr1' },
+                    hoverPosition: { coord: 1011, refName: 'chr1' },
                 },
             });
             const model = {
@@ -193,7 +196,9 @@ describe('genomeToMSA', () => {
             const model = {
                 querySeqName: 'QUERY',
                 transcriptToMsaMap: {
-                    g2p: { 1005: 10 },
+                    refName: 'chr1',
+                    // g2p is keyed by 0-based genome position, the hover coord is 1-based
+                    g2p: { 1004: 10 },
                 },
                 mafRegion: undefined,
                 connectedView: { initialized: true },
@@ -203,6 +208,29 @@ describe('genomeToMSA', () => {
             expect(mockSeqPosToVisibleCol).toHaveBeenCalledWith('QUERY', 10);
             expect(result).toBe(10);
         });
+        test('returns undefined when the hover is on another refName', () => {
+            // session.hovered is global, so a hover on an unrelated chromosome can
+            // carry a coordinate that happens to be a g2p key
+            mockGetSession.mockReturnValue({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1005, refName: 'chr2' },
+                },
+            });
+            const mockSeqPosToVisibleCol = vi.fn();
+            const model = {
+                querySeqName: 'QUERY',
+                transcriptToMsaMap: {
+                    refName: 'chr1',
+                    g2p: { 1004: 10 },
+                },
+                mafRegion: undefined,
+                connectedView: { initialized: true },
+                seqPosToVisibleCol: mockSeqPosToVisibleCol,
+            };
+            expect(genomeToMSA({ model })).toBeUndefined();
+            expect(mockSeqPosToVisibleCol).not.toHaveBeenCalled();
+        });
         test('returns undefined when g2p has no mapping for coord', () => {
             mockGetSession.mockReturnValue({
                 hovered: {
@@ -213,7 +241,8 @@ describe('genomeToMSA', () => {
             const model = {
                 querySeqName: 'QUERY',
                 transcriptToMsaMap: {
-                    g2p: { 1000: 0 }, // No entry for 1005
+                    refName: 'chr1',
+                    g2p: { 1000: 0 }, // No entry for 1004
                 },
                 mafRegion: undefined,
                 connectedView: { initialized: true },

package/dist/MsaViewPanel/model.d.ts

@@ -29,7 +29,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-}, "height" | "id" | "type" | "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles" | "autoTreeAreaWidth" | "bgColor" | "colorSchemeName" | "showColumnStats" | "msaFormat" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "currentAlignment" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & Omit<Omit<Omit<{}, "drawLabels" | "labelsAlignRight" | "treeAreaWidth" | "treeWidth" | "showBranchLen" | "drawTree" | "drawNodeBubbles" | "autoTreeAreaWidth"> & {
+}, "height" | "id" | "type" | "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth" | "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawTree" | "labelsAlignRight" | "showBranchLen" | "treeAreaWidth" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
@@ -38,12 +38,12 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, "bgColor" | "colorSchemeName" | "showColumnStats" | "msaFormat"> & {
+}, "bgColor" | "colorSchemeName" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
-}, "height" | "id" | "type" | "data" | "showDomains" | "hideGaps" | "allowedGappyness" | "subFeatureRows" | "drawMsaLetters" | "scrollZoom" | "rowHeight" | "scrollY" | "scrollX" | "colWidth" | "treeFilehandle" | "msaFilehandle" | "treeMetadataFilehandle" | "gffFilehandle" | "currentAlignment" | "collapsed" | "showOnly" | "turnedOffTracks" | "featureFilters" | "relativeTo" | "highlightColumns"> & {
+}, "height" | "id" | "type" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     hideGaps: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -97,18 +97,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     }, ({
-        locationType: "UriLocation";
-        uri: string;
-    } & Partial<{
-        locationType: "UriLocation";
-        uri: string;
-        baseUri: string | undefined;
-        internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
-            internetAccountType: string;
-            authInfo: any;
-        }> | undefined;
-    }>) | ({
         blobId: string;
         locationType: "BlobLocation";
         name: string;
@@ -130,6 +118,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     } & Partial<{
         locationType: "LocalPathLocation";
         localPath: string;
+    }>) | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
     }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
         locationType: "LocalPathLocation";
         localPath: string;
@@ -191,18 +191,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     }, ({
-        locationType: "UriLocation";
-        uri: string;
-    } & Partial<{
-        locationType: "UriLocation";
-        uri: string;
-        baseUri: string | undefined;
-        internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
-            internetAccountType: string;
-            authInfo: any;
-        }> | undefined;
-    }>) | ({
         blobId: string;
         locationType: "BlobLocation";
         name: string;
@@ -224,6 +212,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     } & Partial<{
         locationType: "LocalPathLocation";
         localPath: string;
+    }>) | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
     }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
         locationType: "LocalPathLocation";
         localPath: string;
@@ -285,18 +285,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     }, ({
-        locationType: "UriLocation";
-        uri: string;
-    } & Partial<{
-        locationType: "UriLocation";
-        uri: string;
-        baseUri: string | undefined;
-        internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
-            internetAccountType: string;
-            authInfo: any;
-        }> | undefined;
-    }>) | ({
         blobId: string;
         locationType: "BlobLocation";
         name: string;
@@ -318,6 +306,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     } & Partial<{
         locationType: "LocalPathLocation";
         localPath: string;
+    }>) | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
     }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
         locationType: "LocalPathLocation";
         localPath: string;
@@ -379,18 +379,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     }, ({
-        locationType: "UriLocation";
-        uri: string;
-    } & Partial<{
-        locationType: "UriLocation";
-        uri: string;
-        baseUri: string | undefined;
-        internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
-            internetAccountType: string;
-            authInfo: any;
-        }> | undefined;
-    }>) | ({
         blobId: string;
         locationType: "BlobLocation";
         name: string;
@@ -412,6 +400,18 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     } & Partial<{
         locationType: "LocalPathLocation";
         localPath: string;
+    }>) | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<{
+        locationType: "UriLocation";
+        uri: string;
+        baseUri: string | undefined;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelCreationType<{
+            internetAccountType: string;
+            authInfo: any;
+        }> | undefined;
     }>)>, import("@jbrowse/core/util/types/mst").LegacyFileLocation | import("@jbrowse/mobx-state-tree").ModelCreationType<{
         locationType: "LocalPathLocation";
         localPath: string;
@@ -581,7 +581,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly noTree: boolean;
     readonly noDomains: boolean;
     menuItems(): never[];
-    readonly treeMetadata: any;
+    readonly treeMetadata: Record<string, Record<string, string> | undefined>;
     readonly MSA: import("react-msaview").MSAParserType | null;
     readonly numColumns: number;
     readonly tree: import("react-msaview").NodeWithIds;
@@ -789,7 +789,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
             accession?: string;
             dbxref?: string;
         } | undefined;
-        treeMetadata: any;
+        treeMetadata: Record<string, string> | undefined;
     };
 } & {
     setHeaderHeight(arg: number): void;
@@ -841,19 +841,21 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
 } & {
     /**
      * #getter
-     * Genome region under the current MSA hover column. Suppressed on the LGV
+     * Genome regions 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;
+    readonly connectedHoverHighlights: IRegion[];
     /**
      * #getter
-     * Genome region under the persistent MSA click selection. Shown
+     * Genome regions under the persistent MSA click selection. Shown
      * regardless of LGV hover, so hovering the genome doesn't hide it.
      */
-    readonly connectedClickHighlight: IRegion | undefined;
+    readonly connectedClickHighlights: IRegion[];
     /**
      * #getter
+     * cross-plugin contract: jbrowse-plugin-mafviewer reads this off the view
+     * to draw the same highlights in its own display
      */
     readonly connectedHighlights: IRegion[];
 } & {
@@ -935,11 +937,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }> & {
-    data: {
-        treeMetadata?: string | undefined;
-        msa?: string | undefined;
-        tree?: string | undefined;
-    };
+    bgColor: boolean;
+    colorSchemeName: string;
+    showColumnStats: boolean;
+    msaFormat: import("react-msaview").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number;
@@ -948,10 +949,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     drawTree: boolean;
     drawNodeBubbles: boolean;
     autoTreeAreaWidth: boolean;
-    bgColor: boolean;
-    colorSchemeName: string;
-    showColumnStats: boolean;
-    msaFormat: import("react-msaview").MSAFormat | undefined;
     id: string;
     showDomains: boolean;
     hideGaps: boolean;
@@ -1052,6 +1049,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     featureFilters: import("mobx").IKeyValueMap<boolean>;
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
+    data: {
+        tree?: string | undefined;
+        msa?: string | undefined;
+        treeMetadata?: string | undefined;
+    };
 } & import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type JBrowsePluginMsaViewStateModel = ReturnType<typeof stateModelFactory>;
 export type JBrowsePluginMsaViewModel = Instance<JBrowsePluginMsaViewStateModel>;

package/dist/MsaViewPanel/model.js

@@ -5,7 +5,7 @@ import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
 import { autorun } from 'mobx';
 import { MSAModelF } from 'react-msaview';
 import { autoLoadProteinDomains, launchBlastIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
-import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
+import { msaCoordToGenomeCoord, msaCoordToGenomeRegions, } from './msaCoordToGenomeCoord';
 /**
  * #stateModel MsaViewPlugin
  * extends
@@ -119,35 +119,37 @@ export default function stateModelFactory() {
         .views(self => ({
         /**
          * #getter
-         * Genome region under the current MSA hover column. Suppressed on the LGV
+         * Genome regions 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() {
+        get connectedHoverHighlights() {
             const { mouseCol } = self;
             return mouseCol === undefined
-                ? undefined
-                : msaCoordToGenomeCoord({ model: self, coord: mouseCol });
+                ? []
+                : msaCoordToGenomeRegions({ model: self, coord: mouseCol });
         },
         /**
          * #getter
-         * Genome region under the persistent MSA click selection. Shown
+         * Genome regions under the persistent MSA click selection. Shown
          * regardless of LGV hover, so hovering the genome doesn't hide it.
          */
-        get connectedClickHighlight() {
+        get connectedClickHighlights() {
             const { mouseClickCol } = self;
             return mouseClickCol === undefined
-                ? undefined
-                : msaCoordToGenomeCoord({ model: self, coord: mouseClickCol });
+                ? []
+                : msaCoordToGenomeRegions({ model: self, coord: mouseClickCol });
         },
         /**
          * #getter
+         * cross-plugin contract: jbrowse-plugin-mafviewer reads this off the view
+         * to draw the same highlights in its own display
          */
         get connectedHighlights() {
             return [
-                this.connectedHoverHighlight,
-                this.connectedClickHighlight,
-            ].filter((r) => r !== undefined);
+                ...this.connectedHoverHighlights,
+                ...this.connectedClickHighlights,
+            ];
         },
     }))
         .actions(self => ({

package/dist/MsaViewPanel/msaCoordToGenomeCoord.d.ts

@@ -1,17 +1,36 @@
 import type { MafRegion } from './types';
-export declare function msaCoordToGenomeCoord({ model, coord: mouseCol, }: {
-    model: {
-        querySeqName: string;
-        transcriptToMsaMap: {
-            refName: string;
-            p2g: Record<number, number>;
-        } | undefined;
-        mafRegion?: MafRegion;
-        rows: string[][];
-    };
-    coord: number;
-}): {
+interface GenomeRegion {
     refName: string;
     start: number;
     end: number;
-} | undefined;
+}
+interface CoordModel {
+    querySeqName: string;
+    transcriptToMsaMap: {
+        refName: string;
+        p2gCodon: Record<number, number[]>;
+    } | undefined;
+    mafRegion?: MafRegion;
+    rows: string[][];
+}
+/**
+ * The genome regions covered by MSA column `coord` of the query row, in 0-based
+ * half-open coordinates (what bpToPx and navTo take).
+ *
+ * Usually one region -- one codon, or one base in a MAF alignment -- but a
+ * codon split across an exon boundary yields one region per contiguous piece,
+ * which is why this returns a list.
+ */
+export declare function msaCoordToGenomeRegions({ model, coord: mouseCol, }: {
+    model: CoordModel;
+    coord: number;
+}): GenomeRegion[];
+/**
+ * A single region spanning the codon at MSA column `coord`, for navigation. For
+ * a codon split across an exon boundary this spans the intervening intron.
+ */
+export declare function msaCoordToGenomeCoord(args: {
+    model: CoordModel;
+    coord: number;
+}): GenomeRegion | undefined;
+export {};