jbrowse-plugin-msaview 2.2.3 → 2.2.4

package/dist/MsaViewPanel/genomeToMSA.js

@@ -1,16 +1,46 @@
 import { getSession } from '@jbrowse/core/util';
 import { checkHovered } from './util';
+/**
+ * Convert a genome coordinate from session.hovered to a visible MSA column.
+ *
+ * @param model - The MSA view model
+ * @returns The visible column index, or undefined if no mapping exists
+ */
 export function genomeToMSA({ model }) {
     const { hovered } = getSession(model);
-    const { querySeqName, transcriptToMsaMap, connectedView } = model;
-    if (connectedView?.initialized &&
-        transcriptToMsaMap &&
-        checkHovered(hovered)) {
-        const { coord: hoverCoord } = hovered.hoverPosition;
+    const { querySeqName, transcriptToMsaMap, connectedView, mafRegion } = model;
+    if (!connectedView?.initialized || !checkHovered(hovered)) {
+        return undefined;
+    }
+    const { coord: hoverCoord, refName } = hovered.hoverPosition;
+    // Handle MAF region mapping
+    if (mafRegion) {
+        // Check if the hover is on the same refName as the MAF region
+        if (refName !== mafRegion.refName) {
+            return undefined;
+        }
+        // Check if we're on the same assembly (if assembly info is available)
+        const viewAssemblies = connectedView.assemblyNames;
+        if (!viewAssemblies.includes(mafRegion.assemblyName)) {
+            return undefined;
+        }
+        // Check if the hover coordinate is within the MAF region
+        if (hoverCoord < mafRegion.start || hoverCoord >= mafRegion.end) {
+            return undefined;
+        }
+        // Calculate the ungapped position relative to the region start
+        const ungappedPos = hoverCoord - mafRegion.start;
+        // Convert to visible column using the query sequence
+        return model.seqPosToVisibleCol(querySeqName, ungappedPos);
+    }
+    // Handle transcript mapping (original behavior)
+    if (transcriptToMsaMap) {
         const { g2p } = transcriptToMsaMap;
-        const ret = g2p[hoverCoord];
-        if (ret !== undefined) {
-            return model.seqCoordToRowSpecificGlobalCoord(querySeqName, ret + 1);
+        // g2p maps genome coordinate to sequence position (0-based)
+        const seqPos = g2p[hoverCoord];
+        if (seqPos !== undefined) {
+            // Convert sequence position to visible column
+            return model.seqPosToVisibleCol(querySeqName, seqPos);
         }
     }
     return undefined;

package/dist/MsaViewPanel/genomeToMSA.js.map

@@ -1 +1 @@
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+{"version":3,"file":"genomeToMSA.js","sourceRoot":"","sources":["../../src/MsaViewPanel/genomeToMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAG/C,OAAO,EAAE,YAAY,EAAE,MAAM,QAAQ,CAAA;AAErC;;;;;GAKG;AACH,MAAM,UAAU,WAAW,CAAC,EAAE,KAAK,EAAwC;IACzE,MAAM,EAAE,OAAO,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACrC,MAAM,EAAE,YAAY,EAAE,kBAAkB,EAAE,aAAa,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAE5E,IAAI,CAAC,aAAa,EAAE,WAAW,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,EAAE,CAAC;QAC1D,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,aAAa,CAAA;IAE5D,4BAA4B;IAC5B,IAAI,SAAS,EAAE,CAAC;QACd,8DAA8D;QAC9D,IAAI,OAAO,KAAK,SAAS,CAAC,OAAO,EAAE,CAAC;YAClC,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,sEAAsE;QACtE,MAAM,cAAc,GAAG,aAAa,CAAC,aAAa,CAAA;QAClD,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,SAAS,CAAC,YAAY,CAAC,EAAE,CAAC;YACrD,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,yDAAyD;QACzD,IAAI,UAAU,GAAG,SAAS,CAAC,KAAK,IAAI,UAAU,IAAI,SAAS,CAAC,GAAG,EAAE,CAAC;YAChE,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,+DAA+D;QAC/D,MAAM,WAAW,GAAG,UAAU,GAAG,SAAS,CAAC,KAAK,CAAA;QAChD,qDAAqD;QACrD,OAAO,KAAK,CAAC,kBAAkB,CAAC,YAAY,EAAE,WAAW,CAAC,CAAA;IAC5D,CAAC;IAED,gDAAgD;IAChD,IAAI,kBAAkB,EAAE,CAAC;QACvB,MAAM,EAAE,GAAG,EAAE,GAAG,kBAAkB,CAAA;QAClC,4DAA4D;QAC5D,MAAM,MAAM,GAAG,GAAG,CAAC,UAAU,CAAC,CAAA;QAC9B,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,8CAA8C;YAC9C,OAAO,KAAK,CAAC,kBAAkB,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;QACvD,CAAC;IACH,CAAC;IAED,OAAO,SAAS,CAAA;AAClB,CAAC"}

package/dist/MsaViewPanel/genomeToMSA.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/MsaViewPanel/genomeToMSA.test.js

@@ -0,0 +1,244 @@
+import { getSession } from '@jbrowse/core/util';
+import { beforeEach, describe, expect, test, vi } from 'vitest';
+import { genomeToMSA } from './genomeToMSA';
+// Mock getSession
+vi.mock('@jbrowse/core/util', () => ({
+    getSession: vi.fn(),
+}));
+const mockGetSession = vi.mocked(getSession);
+describe('genomeToMSA', () => {
+    beforeEach(() => {
+        vi.clearAllMocks();
+    });
+    test('returns undefined when connectedView is not initialized', () => {
+        mockGetSession.mockReturnValue({
+            hovered: {
+                hoverFeature: {},
+                hoverPosition: { coord: 1005, refName: 'chr1' },
+            },
+        });
+        const model = {
+            querySeqName: 'hg38.chr1',
+            transcriptToMsaMap: undefined,
+            mafRegion: {
+                refName: 'chr1',
+                start: 1000,
+                end: 1010,
+                assemblyName: 'hg38',
+            },
+            connectedView: { initialized: false },
+            seqPosToVisibleCol: vi.fn(),
+        };
+        const result = genomeToMSA({ model });
+        expect(result).toBeUndefined();
+    });
+    test('returns undefined when hovered is not valid', () => {
+        mockGetSession.mockReturnValue({
+            hovered: null,
+        });
+        const model = {
+            querySeqName: 'hg38.chr1',
+            transcriptToMsaMap: undefined,
+            mafRegion: {
+                refName: 'chr1',
+                start: 1000,
+                end: 1010,
+                assemblyName: 'hg38',
+            },
+            connectedView: { initialized: true },
+            seqPosToVisibleCol: vi.fn(),
+        };
+        const result = genomeToMSA({ model });
+        expect(result).toBeUndefined();
+    });
+    describe('mafRegion mapping', () => {
+        test('returns visible column for valid hover within mafRegion', () => {
+            mockGetSession.mockReturnValue({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1005, refName: 'chr1' },
+                },
+            });
+            const mockSeqPosToVisibleCol = vi.fn().mockReturnValue(5);
+            const model = {
+                querySeqName: 'hg38.chr1',
+                transcriptToMsaMap: undefined,
+                mafRegion: {
+                    refName: 'chr1',
+                    start: 1000,
+                    end: 1010,
+                    assemblyName: 'hg38',
+                },
+                connectedView: {
+                    initialized: true,
+                    assemblyNames: ['hg38'],
+                },
+                seqPosToVisibleCol: mockSeqPosToVisibleCol,
+            };
+            const result = genomeToMSA({ model });
+            // coord 1005 - start 1000 = ungapped position 5
+            expect(mockSeqPosToVisibleCol).toHaveBeenCalledWith('hg38.chr1', 5);
+            expect(result).toBe(5);
+        });
+        test('returns undefined when hover refName does not match mafRegion', () => {
+            mockGetSession.mockReturnValue({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1005, refName: 'chr2' },
+                },
+            });
+            const model = {
+                querySeqName: 'hg38.chr1',
+                transcriptToMsaMap: undefined,
+                mafRegion: {
+                    refName: 'chr1',
+                    start: 1000,
+                    end: 1010,
+                    assemblyName: 'hg38',
+                },
+                connectedView: {
+                    initialized: true,
+                    assemblyNames: ['hg38'],
+                },
+                seqPosToVisibleCol: vi.fn(),
+            };
+            const result = genomeToMSA({ model });
+            expect(result).toBeUndefined();
+        });
+        test('returns undefined when hover coord is before mafRegion start', () => {
+            mockGetSession.mockReturnValue({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 999, refName: 'chr1' },
+                },
+            });
+            const model = {
+                querySeqName: 'hg38.chr1',
+                transcriptToMsaMap: undefined,
+                mafRegion: {
+                    refName: 'chr1',
+                    start: 1000,
+                    end: 1010,
+                    assemblyName: 'hg38',
+                },
+                connectedView: {
+                    initialized: true,
+                    assemblyNames: ['hg38'],
+                },
+                seqPosToVisibleCol: vi.fn(),
+            };
+            const result = genomeToMSA({ model });
+            expect(result).toBeUndefined();
+        });
+        test('returns undefined when hover coord is at or after mafRegion end', () => {
+            mockGetSession.mockReturnValue({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1010, refName: 'chr1' },
+                },
+            });
+            const model = {
+                querySeqName: 'hg38.chr1',
+                transcriptToMsaMap: undefined,
+                mafRegion: {
+                    refName: 'chr1',
+                    start: 1000,
+                    end: 1010,
+                    assemblyName: 'hg38',
+                },
+                connectedView: {
+                    initialized: true,
+                    assemblyNames: ['hg38'],
+                },
+                seqPosToVisibleCol: vi.fn(),
+            };
+            const result = genomeToMSA({ model });
+            expect(result).toBeUndefined();
+        });
+        test('returns undefined when assembly does not match', () => {
+            mockGetSession.mockReturnValue({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1005, refName: 'chr1' },
+                },
+            });
+            const model = {
+                querySeqName: 'hg38.chr1',
+                transcriptToMsaMap: undefined,
+                mafRegion: {
+                    refName: 'chr1',
+                    start: 1000,
+                    end: 1010,
+                    assemblyName: 'hg38',
+                },
+                connectedView: {
+                    initialized: true,
+                    assemblyNames: ['mm39'], // Different assembly
+                },
+                seqPosToVisibleCol: vi.fn(),
+            };
+            const result = genomeToMSA({ model });
+            expect(result).toBeUndefined();
+        });
+    });
+    describe('transcriptToMsaMap mapping (original behavior)', () => {
+        test('returns visible column using g2p mapping', () => {
+            mockGetSession.mockReturnValue({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1005, refName: 'chr1' },
+                },
+            });
+            const mockSeqPosToVisibleCol = vi.fn().mockReturnValue(10);
+            const model = {
+                querySeqName: 'QUERY',
+                transcriptToMsaMap: {
+                    g2p: { 1005: 10 },
+                },
+                mafRegion: undefined,
+                connectedView: { initialized: true },
+                seqPosToVisibleCol: mockSeqPosToVisibleCol,
+            };
+            const result = genomeToMSA({ model });
+            expect(mockSeqPosToVisibleCol).toHaveBeenCalledWith('QUERY', 10);
+            expect(result).toBe(10);
+        });
+        test('returns undefined when g2p has no mapping for coord', () => {
+            mockGetSession.mockReturnValue({
+                hovered: {
+                    hoverFeature: {},
+                    hoverPosition: { coord: 1005, refName: 'chr1' },
+                },
+            });
+            const model = {
+                querySeqName: 'QUERY',
+                transcriptToMsaMap: {
+                    g2p: { 1000: 0 }, // No entry for 1005
+                },
+                mafRegion: undefined,
+                connectedView: { initialized: true },
+                seqPosToVisibleCol: vi.fn(),
+            };
+            const result = genomeToMSA({ model });
+            expect(result).toBeUndefined();
+        });
+    });
+    test('returns undefined when neither mafRegion nor transcriptToMsaMap is set', () => {
+        mockGetSession.mockReturnValue({
+            hovered: {
+                hoverFeature: {},
+                hoverPosition: { coord: 1005, refName: 'chr1' },
+            },
+        });
+        const model = {
+            querySeqName: 'QUERY',
+            transcriptToMsaMap: undefined,
+            mafRegion: undefined,
+            connectedView: { initialized: true },
+            seqPosToVisibleCol: vi.fn(),
+        };
+        const result = genomeToMSA({ model });
+        expect(result).toBeUndefined();
+    });
+});
+//# sourceMappingURL=genomeToMSA.test.js.map

package/dist/MsaViewPanel/genomeToMSA.test.js.map

@@ -0,0 +1 @@
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