jbrowse-plugin-msaview 2.7.1 → 2.7.3

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 {};

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;
 }

package/dist/MsaViewPanel/msaCoordToGenomeCoord.test.js

@@ -1,5 +1,14 @@
+import { genomeToTranscriptSeqMapping } from 'g2p_mapper';
 import { describe, expect, test } from 'vitest';
-import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
+import { msaCoordToGenomeCoord, msaCoordToGenomeRegions, } from './msaCoordToGenomeCoord';
+// codon at protein position i covers three consecutive genome bases starting at
+// 100 + i * 3, i.e. a single-exon forward-strand transcript
+function forwardCodons(n) {
+    return Object.fromEntries(Array.from({ length: n }, (_, i) => [
+        i,
+        [100 + i * 3, 101 + i * 3, 102 + i * 3],
+    ]));
+}
 describe('msaCoordToGenomeCoord', () => {
     test('returns undefined when neither transcriptToMsaMap nor mafRegion is defined', () => {
         const model = {
@@ -16,7 +25,7 @@ describe('msaCoordToGenomeCoord', () => {
             querySeqName: 'QUERY',
             transcriptToMsaMap: {
                 refName: 'chr1',
-                p2g: { 0: 100, 1: 103 },
+                p2gCodon: forwardCodons(2),
             },
             rows: [['OTHER', 'MKAA']],
         };
@@ -28,7 +37,7 @@ describe('msaCoordToGenomeCoord', () => {
             querySeqName: 'QUERY',
             transcriptToMsaMap: {
                 refName: 'chr1',
-                p2g: { 0: 100, 1: 103 },
+                p2gCodon: forwardCodons(2),
             },
             rows: [['QUERY', 'M-KA']],
         };
@@ -41,7 +50,7 @@ describe('msaCoordToGenomeCoord', () => {
             querySeqName: 'QUERY',
             transcriptToMsaMap: {
                 refName: 'chr1',
-                p2g: { 0: 100, 1: 103, 2: 106, 3: 109 },
+                p2gCodon: forwardCodons(4),
             },
             rows: [['QUERY', 'MKAA']],
         };
@@ -58,7 +67,7 @@ describe('msaCoordToGenomeCoord', () => {
             querySeqName: 'QUERY',
             transcriptToMsaMap: {
                 refName: 'chr1',
-                p2g: { 0: 100, 1: 103, 2: 106, 3: 109 },
+                p2gCodon: forwardCodons(4),
             },
             rows: [['QUERY', 'M-K-AA']],
             //                 012345 gapped positions
@@ -79,34 +88,33 @@ describe('msaCoordToGenomeCoord', () => {
             end: 109,
         });
     });
-    test('returns undefined when p2g mapping is incomplete', () => {
+    test('returns undefined when the position has no codon mapping', () => {
         const model = {
             querySeqName: 'QUERY',
             transcriptToMsaMap: {
                 refName: 'chr1',
-                p2g: { 0: 100 }, // Missing entry for position 1
+                p2gCodon: forwardCodons(1),
             },
             rows: [['QUERY', 'MKAA']],
         };
-        // Position 0 needs p2g[0] and p2g[1], but p2g[1] is missing
-        const result = msaCoordToGenomeCoord({ model, coord: 0 });
+        // ungapped position 1 has no entry in p2gCodon
+        const result = msaCoordToGenomeCoord({ model, coord: 1 });
         expect(result).toBeUndefined();
     });
-    test('handles reverse strand (start > end in p2g)', () => {
+    test('maps the final residue, whose codon has no successor', () => {
         const model = {
             querySeqName: 'QUERY',
             transcriptToMsaMap: {
                 refName: 'chr1',
-                p2g: { 0: 109, 1: 106, 2: 103, 3: 100 }, // Reverse strand
+                p2gCodon: forwardCodons(4),
             },
             rows: [['QUERY', 'MKAA']],
         };
-        // Should return min/max correctly
-        const result = msaCoordToGenomeCoord({ model, coord: 0 });
+        const result = msaCoordToGenomeCoord({ model, coord: 3 });
         expect(result).toEqual({
             refName: 'chr1',
-            start: 106, // min(109, 106)
-            end: 109, // max(109, 106)
+            start: 109,
+            end: 112,
         });
     });
     test('returns undefined for out of bounds coord', () => {
@@ -114,7 +122,7 @@ describe('msaCoordToGenomeCoord', () => {
             querySeqName: 'QUERY',
             transcriptToMsaMap: {
                 refName: 'chr1',
-                p2g: { 0: 100, 1: 103 },
+                p2gCodon: forwardCodons(2),
             },
             rows: [['QUERY', 'MK']],
         };
@@ -127,7 +135,7 @@ describe('msaCoordToGenomeCoord', () => {
             querySeqName: 'SEQ2',
             transcriptToMsaMap: {
                 refName: 'chr1',
-                p2g: { 0: 200, 1: 203 },
+                p2gCodon: { 0: [200, 201, 202], 1: [203, 204, 205] },
             },
             rows: [
                 ['SEQ1', 'AAAA'],
@@ -142,6 +150,88 @@ describe('msaCoordToGenomeCoord', () => {
             end: 203,
         });
     });
+    // The mapping comes from the real g2p_mapper rather than hand-written
+    // fixtures: on the reverse strand p2g stores the codon's *highest*
+    // coordinate, which is what the old p2g[pos]..p2g[pos+1] arithmetic got wrong
+    describe('real g2p_mapper mappings', () => {
+        test('forward strand, single exon', () => {
+            const { p2gCodon, refName } = genomeToTranscriptSeqMapping({
+                refName: 'chr1',
+                start: 100,
+                end: 112,
+                strand: 1,
+                subfeatures: [{ refName: 'chr1', type: 'CDS', start: 100, end: 112 }],
+            });
+            const model = {
+                querySeqName: 'QUERY',
+                transcriptToMsaMap: { refName, p2gCodon },
+                rows: [['QUERY', 'MKAA']],
+            };
+            expect(msaCoordToGenomeCoord({ model, coord: 0 })).toEqual({
+                refName: 'chr1',
+                start: 100,
+                end: 103,
+            });
+            expect(msaCoordToGenomeCoord({ model, coord: 3 })).toEqual({
+                refName: 'chr1',
+                start: 109,
+                end: 112,
+            });
+        });
+        test('reverse strand codon covers the last three bases of the CDS', () => {
+            const { p2gCodon, refName } = genomeToTranscriptSeqMapping({
+                refName: 'chr1',
+                start: 100,
+                end: 112,
+                strand: -1,
+                subfeatures: [{ refName: 'chr1', type: 'CDS', start: 100, end: 112 }],
+            });
+            const model = {
+                querySeqName: 'QUERY',
+                transcriptToMsaMap: { refName, p2gCodon },
+                rows: [['QUERY', 'MKAA']],
+            };
+            // the first residue is translated from the 3' end of the genome region
+            expect(msaCoordToGenomeCoord({ model, coord: 0 })).toEqual({
+                refName: 'chr1',
+                start: 109,
+                end: 112,
+            });
+            expect(msaCoordToGenomeCoord({ model, coord: 3 })).toEqual({
+                refName: 'chr1',
+                start: 100,
+                end: 103,
+            });
+        });
+        test('codon split across an exon boundary yields one region per piece', () => {
+            // exon 1 contributes 4 bases, so residue 1 straddles the intron
+            const { p2gCodon, refName } = genomeToTranscriptSeqMapping({
+                refName: 'chr1',
+                start: 100,
+                end: 210,
+                strand: 1,
+                subfeatures: [
+                    { refName: 'chr1', type: 'CDS', start: 100, end: 104 },
+                    { refName: 'chr1', type: 'CDS', start: 200, end: 202 },
+                ],
+            });
+            const model = {
+                querySeqName: 'QUERY',
+                transcriptToMsaMap: { refName, p2gCodon },
+                rows: [['QUERY', 'MK']],
+            };
+            expect(msaCoordToGenomeRegions({ model, coord: 1 })).toEqual([
+                { refName: 'chr1', start: 103, end: 104 },
+                { refName: 'chr1', start: 200, end: 202 },
+            ]);
+            // the single-region form bounds the pieces, for navigation
+            expect(msaCoordToGenomeCoord({ model, coord: 1 })).toEqual({
+                refName: 'chr1',
+                start: 103,
+                end: 202,
+            });
+        });
+    });
     // MAF region tests
     describe('mafRegion', () => {
         test('returns genome position for mafRegion mapping', () => {
@@ -217,7 +307,7 @@ describe('msaCoordToGenomeCoord', () => {
                 querySeqName: 'hg38.chr1',
                 transcriptToMsaMap: {
                     refName: 'chr2',
-                    p2g: { 0: 5000, 1: 5003 },
+                    p2gCodon: { 0: [5000, 5001, 5002], 1: [5003, 5004, 5005] },
                 },
                 mafRegion: {
                     refName: 'chr1',