jbrowse-plugin-msaview 2.7.2 → 2.7.4

package/dist/MsaViewPanel/model.d.ts

@@ -20,6 +20,17 @@ export interface BlastParams {
     proteinSequence: string;
     rid?: string;
 }
+export interface OrthologParams {
+    /** NCBI taxon id of the assembly the query gene came from */
+    taxId: number;
+    /** taxon ids to include as rows (the query taxon is represented by QUERY) */
+    taxa: number[];
+    /** candidate gene identifiers off the feature, tried in order */
+    geneCandidates: string[];
+    msaAlgorithm: MsaAlgorithm;
+    selectedTranscript?: Feature;
+    proteinSequence: string;
+}
 /**
  * #stateModel MsaViewPlugin
  * extends
@@ -29,7 +40,7 @@ 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 +49,12 @@ 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"> & {
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
+}, "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 +108,6 @@ 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 +129,18 @@ 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 +202,6 @@ 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 +223,18 @@ 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 +296,6 @@ 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 +317,18 @@ 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 +390,6 @@ 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 +411,18 @@ 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;
@@ -456,10 +467,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     featureFilters: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
-}, "init" | "querySeqName" | "zoomToBaseLevel" | "connectedViewId" | "connectedFeature" | "blastParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
+}, "init" | "querySeqName" | "zoomToBaseLevel" | "connectedViewId" | "connectedFeature" | "blastParams" | "orthologParams" | "uniprotId" | "dataStoreId" | "mafRegion"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
     blastParams: import("@jbrowse/mobx-state-tree").IType<BlastParams | undefined, BlastParams | undefined, BlastParams | undefined>;
+    orthologParams: import("@jbrowse/mobx-state-tree").IType<OrthologParams | undefined, OrthologParams | undefined, OrthologParams | undefined>;
     querySeqName: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
     uniprotId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     zoomToBaseLevel: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -495,7 +507,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setColorSchemeName(name: string): void;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
-    setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
+    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
     status: {
@@ -581,8 +593,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly noTree: boolean;
     readonly noDomains: boolean;
     menuItems(): never[];
-    readonly treeMetadata: any;
-    readonly MSA: import("react-msaview").MSAParserType | null;
+    readonly treeMetadata: Record<string, Record<string, string> | undefined>;
+    readonly MSA: import("msa-parsers").MSAParserType | null;
     readonly numColumns: number;
     readonly tree: import("react-msaview").NodeWithIds;
     readonly rowNames: string[];
@@ -789,7 +801,7 @@ 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 +853,21 @@ 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[];
 } & {
@@ -877,6 +891,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setBlastParams(args?: BlastParams): void;
+    /**
+     * #action
+     */
+    setOrthologParams(args?: OrthologParams): void;
     /**
      * #action
      */
@@ -935,11 +953,10 @@ 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("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number;
@@ -948,10 +965,6 @@ 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 +1065,11 @@ 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

@@ -4,8 +4,8 @@ import { addDisposer, types } from '@jbrowse/mobx-state-tree';
 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 { autoLoadProteinDomains, launchBlastIfNeeded, launchOrthologsIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
+import { msaCoordToGenomeCoord, msaCoordToGenomeRegions, } from './msaCoordToGenomeCoord';
 /**
  * #stateModel MsaViewPlugin
  * extends
@@ -26,6 +26,10 @@ export default function stateModelFactory() {
          * #property
          */
         blastParams: types.frozen(),
+        /**
+         * #property
+         */
+        orthologParams: types.frozen(),
         /**
          * #property
          */
@@ -119,35 +123,37 @@ 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 => ({
@@ -181,6 +187,12 @@ export default function stateModelFactory() {
         setBlastParams(args) {
             self.blastParams = args;
         },
+        /**
+         * #action
+         */
+        setOrthologParams(args) {
+            self.orthologParams = args;
+        },
         /**
          * #action
          */
@@ -287,6 +299,7 @@ export default function stateModelFactory() {
                 loadStoredData,
                 storeDataToIndexedDB,
                 launchBlastIfNeeded,
+                launchOrthologsIfNeeded,
                 processInit,
                 autoLoadProteinDomains,
             ]) {

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 {};

package/dist/MsaViewPanel/msaCoordToGenomeCoord.js

@@ -1,27 +1,56 @@
+import { getCodonRanges } from 'g2p_mapper';
 import { gappedToUngappedPosition } from './structureConnection';
-export function msaCoordToGenomeCoord({ model, coord: mouseCol, }) {
-    const { querySeqName, transcriptToMsaMap, mafRegion } = model;
-    const querySeq = model.rows.find(f => f[0] === querySeqName)?.[1];
+/**
+ * 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 function msaCoordToGenomeRegions({ model, coord: mouseCol, }) {
+    const { querySeqName, transcriptToMsaMap, mafRegion, rows } = model;
+    const querySeq = rows.find(f => f[0] === querySeqName)?.[1];
     if (!querySeq) {
-        return undefined;
+        return [];
     }
     const ungappedPos = gappedToUngappedPosition(querySeq, mouseCol);
     if (ungappedPos === undefined) {
-        return undefined;
+        return [];
     }
     if (mafRegion) {
         const genomePos = mafRegion.start + ungappedPos;
         return genomePos < mafRegion.end
-            ? { refName: mafRegion.refName, start: genomePos, end: genomePos + 1 }
-            : undefined;
+            ? [{ refName: mafRegion.refName, start: genomePos, end: genomePos + 1 }]
+            : [];
     }
     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) }
-            : undefined;
+        const { refName, p2gCodon } = transcriptToMsaMap;
+        // p2gCodon holds every genomic base of the codon, so the range is exact on
+        // either strand. Deriving it from consecutive p2g entries instead
+        // (p2g[pos]..p2g[pos+1]) was off by one base on the reverse strand -- where
+        // p2g stores the codon's *highest* coordinate -- dropped the final residue,
+        // whose successor has no p2g entry, and spanned the whole intron for a
+        // codon split across an exon boundary.
+        return (getCodonRanges(p2gCodon, ungappedPos)?.map(([start, end]) => ({
+            refName,
+            start,
+            end,
+        })) ?? []);
     }
-    return undefined;
+    return [];
+}
+/**
+ * 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 function msaCoordToGenomeCoord(args) {
+    const regions = msaCoordToGenomeRegions(args);
+    const first = regions[0];
+    const last = regions.at(-1);
+    // getCodonRanges returns ranges sorted ascending, so first.start..last.end
+    // bounds the codon
+    return first && last
+        ? { refName: first.refName, start: first.start, end: last.end }
+        : undefined;
 }