jbrowse-plugin-msaview 2.2.3 → 2.2.4

package/dist/MsaViewPanel/msaCoordToGenomeCoord.js

@@ -1,35 +1,33 @@
-/**
- * Convert gapped MSA column coordinate to ungapped sequence coordinate
- * This is the inverse of ungappedCoordMap
- */
-function gappedToUngappedCoord(seq, gappedPos) {
-    let ungappedPos = 0;
-    for (let i = 0; i < gappedPos && i < seq.length; i++) {
-        if (seq[i] !== '-') {
-            ungappedPos++;
-        }
-    }
-    return ungappedPos;
-}
+import { gappedToUngappedPosition } from './structureConnection';
 export function msaCoordToGenomeCoord({ model, coord: mouseCol, }) {
-    const { querySeqName, transcriptToMsaMap } = model;
-    if (transcriptToMsaMap === undefined) {
+    const { querySeqName, transcriptToMsaMap, mafRegion } = model;
+    // Get the query sequence
+    const queryRow = model.rows.find(f => f[0] === querySeqName);
+    const querySeq = queryRow?.[1];
+    if (!querySeq) {
         return undefined;
     }
-    else {
-        // Get the query sequence
-        const queryRow = model.rows.find(f => f[0] === querySeqName);
-        const querySeq = queryRow?.[1];
-        if (!querySeq) {
-            return undefined;
-        }
-        // Check if the position in the query sequence is a gap
-        if (querySeq[mouseCol] === '-') {
+    // Convert gapped MSA column to ungapped sequence coordinate
+    // Returns undefined if the position is a gap
+    const ungappedPos = gappedToUngappedPosition(querySeq, mouseCol);
+    if (ungappedPos === undefined) {
+        return undefined;
+    }
+    // Handle MAF region mapping
+    if (mafRegion) {
+        const genomePos = mafRegion.start + ungappedPos;
+        // Check if position is within the region
+        if (genomePos >= mafRegion.end) {
             return undefined;
         }
-        // Convert gapped MSA column to ungapped sequence coordinate
-        const ungappedPos = gappedToUngappedCoord(querySeq, mouseCol);
-        // Use the ungapped position to look up in the p2g map
+        return {
+            refName: mafRegion.refName,
+            start: genomePos,
+            end: genomePos + 1,
+        };
+    }
+    // Handle transcript mapping (original behavior)
+    if (transcriptToMsaMap) {
         const { refName, p2g } = transcriptToMsaMap;
         const s = p2g[ungappedPos];
         const e = p2g[ungappedPos + 1];
@@ -41,5 +39,6 @@ export function msaCoordToGenomeCoord({ model, coord: mouseCol, }) {
             }
             : undefined;
     }
+    return undefined;
 }
 //# sourceMappingURL=msaCoordToGenomeCoord.js.map

package/dist/MsaViewPanel/msaCoordToGenomeCoord.js.map

@@ -1 +1 @@
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package/dist/MsaViewPanel/msaCoordToGenomeCoord.test.d.ts

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

package/dist/MsaViewPanel/msaCoordToGenomeCoord.test.js

@@ -0,0 +1,240 @@
+import { describe, expect, test } from 'vitest';
+import { msaCoordToGenomeCoord } from './msaCoordToGenomeCoord';
+describe('msaCoordToGenomeCoord', () => {
+    test('returns undefined when neither transcriptToMsaMap nor mafRegion is defined', () => {
+        const model = {
+            querySeqName: 'QUERY',
+            transcriptToMsaMap: undefined,
+            mafRegion: undefined,
+            rows: [['QUERY', 'MKAA']],
+        };
+        const result = msaCoordToGenomeCoord({ model, coord: 0 });
+        expect(result).toBeUndefined();
+    });
+    test('returns undefined when query row is not found', () => {
+        const model = {
+            querySeqName: 'QUERY',
+            transcriptToMsaMap: {
+                refName: 'chr1',
+                p2g: { 0: 100, 1: 103 },
+            },
+            rows: [['OTHER', 'MKAA']],
+        };
+        const result = msaCoordToGenomeCoord({ model, coord: 0 });
+        expect(result).toBeUndefined();
+    });
+    test('returns undefined when coord is a gap', () => {
+        const model = {
+            querySeqName: 'QUERY',
+            transcriptToMsaMap: {
+                refName: 'chr1',
+                p2g: { 0: 100, 1: 103 },
+            },
+            rows: [['QUERY', 'M-KA']],
+        };
+        // Position 1 is a gap
+        const result = msaCoordToGenomeCoord({ model, coord: 1 });
+        expect(result).toBeUndefined();
+    });
+    test('returns genome region for valid non-gap position', () => {
+        const model = {
+            querySeqName: 'QUERY',
+            transcriptToMsaMap: {
+                refName: 'chr1',
+                p2g: { 0: 100, 1: 103, 2: 106, 3: 109 },
+            },
+            rows: [['QUERY', 'MKAA']],
+        };
+        // Position 0 (M) should map to ungapped 0, genome 100-103
+        const result = msaCoordToGenomeCoord({ model, coord: 0 });
+        expect(result).toEqual({
+            refName: 'chr1',
+            start: 100,
+            end: 103,
+        });
+    });
+    test('handles gapped sequence correctly', () => {
+        const model = {
+            querySeqName: 'QUERY',
+            transcriptToMsaMap: {
+                refName: 'chr1',
+                p2g: { 0: 100, 1: 103, 2: 106, 3: 109 },
+            },
+            rows: [['QUERY', 'M-K-AA']],
+            //                 012345 gapped positions
+            //                 0  1 23 ungapped positions
+        };
+        // Gapped position 2 (K) = ungapped 1
+        const result = msaCoordToGenomeCoord({ model, coord: 2 });
+        expect(result).toEqual({
+            refName: 'chr1',
+            start: 103,
+            end: 106,
+        });
+        // Gapped position 4 (first A) = ungapped 2
+        const result2 = msaCoordToGenomeCoord({ model, coord: 4 });
+        expect(result2).toEqual({
+            refName: 'chr1',
+            start: 106,
+            end: 109,
+        });
+    });
+    test('returns undefined when p2g mapping is incomplete', () => {
+        const model = {
+            querySeqName: 'QUERY',
+            transcriptToMsaMap: {
+                refName: 'chr1',
+                p2g: { 0: 100 }, // Missing entry for position 1
+            },
+            rows: [['QUERY', 'MKAA']],
+        };
+        // Position 0 needs p2g[0] and p2g[1], but p2g[1] is missing
+        const result = msaCoordToGenomeCoord({ model, coord: 0 });
+        expect(result).toBeUndefined();
+    });
+    test('handles reverse strand (start > end in p2g)', () => {
+        const model = {
+            querySeqName: 'QUERY',
+            transcriptToMsaMap: {
+                refName: 'chr1',
+                p2g: { 0: 109, 1: 106, 2: 103, 3: 100 }, // Reverse strand
+            },
+            rows: [['QUERY', 'MKAA']],
+        };
+        // Should return min/max correctly
+        const result = msaCoordToGenomeCoord({ model, coord: 0 });
+        expect(result).toEqual({
+            refName: 'chr1',
+            start: 106, // min(109, 106)
+            end: 109, // max(109, 106)
+        });
+    });
+    test('returns undefined for out of bounds coord', () => {
+        const model = {
+            querySeqName: 'QUERY',
+            transcriptToMsaMap: {
+                refName: 'chr1',
+                p2g: { 0: 100, 1: 103 },
+            },
+            rows: [['QUERY', 'MK']],
+        };
+        // Position 10 is out of bounds
+        const result = msaCoordToGenomeCoord({ model, coord: 10 });
+        expect(result).toBeUndefined();
+    });
+    test('works with multiple rows, uses querySeqName', () => {
+        const model = {
+            querySeqName: 'SEQ2',
+            transcriptToMsaMap: {
+                refName: 'chr1',
+                p2g: { 0: 200, 1: 203 },
+            },
+            rows: [
+                ['SEQ1', 'AAAA'],
+                ['SEQ2', 'MKAA'],
+                ['SEQ3', 'LLLL'],
+            ],
+        };
+        const result = msaCoordToGenomeCoord({ model, coord: 0 });
+        expect(result).toEqual({
+            refName: 'chr1',
+            start: 200,
+            end: 203,
+        });
+    });
+    // MAF region tests
+    describe('mafRegion', () => {
+        test('returns genome position for mafRegion mapping', () => {
+            const model = {
+                querySeqName: 'hg38.chr1',
+                transcriptToMsaMap: undefined,
+                mafRegion: {
+                    refName: 'chr1',
+                    start: 1000,
+                    end: 1010,
+                    assemblyName: 'hg38',
+                },
+                rows: [['hg38.chr1', 'ACGTACGTAC']],
+            };
+            // Position 0 should map to genome 1000
+            const result = msaCoordToGenomeCoord({ model, coord: 0 });
+            expect(result).toEqual({
+                refName: 'chr1',
+                start: 1000,
+                end: 1001,
+            });
+            // Position 5 should map to genome 1005
+            const result2 = msaCoordToGenomeCoord({ model, coord: 5 });
+            expect(result2).toEqual({
+                refName: 'chr1',
+                start: 1005,
+                end: 1006,
+            });
+        });
+        test('handles gaps in mafRegion sequence', () => {
+            const model = {
+                querySeqName: 'hg38.chr1',
+                transcriptToMsaMap: undefined,
+                mafRegion: {
+                    refName: 'chr1',
+                    start: 1000,
+                    end: 1008,
+                    assemblyName: 'hg38',
+                },
+                rows: [['hg38.chr1', 'AC--GTAC']],
+                // Gapped positions: 0  1  2  3  4  5  6  7
+                // Ungapped:         0  1        2  3  4  5
+            };
+            // Position 2 is a gap, should return undefined
+            const result = msaCoordToGenomeCoord({ model, coord: 2 });
+            expect(result).toBeUndefined();
+            // Position 4 (G) = ungapped 2 = genome 1002
+            const result2 = msaCoordToGenomeCoord({ model, coord: 4 });
+            expect(result2).toEqual({
+                refName: 'chr1',
+                start: 1002,
+                end: 1003,
+            });
+        });
+        test('returns undefined when position exceeds mafRegion end', () => {
+            const model = {
+                querySeqName: 'hg38.chr1',
+                transcriptToMsaMap: undefined,
+                mafRegion: {
+                    refName: 'chr1',
+                    start: 1000,
+                    end: 1005,
+                    assemblyName: 'hg38',
+                },
+                rows: [['hg38.chr1', 'ACGTACGTAC']], // 10 chars but region is only 5bp
+            };
+            // Position 8 would be ungapped 8 = genome 1008, but region ends at 1005
+            const result = msaCoordToGenomeCoord({ model, coord: 8 });
+            expect(result).toBeUndefined();
+        });
+        test('mafRegion takes precedence over transcriptToMsaMap', () => {
+            const model = {
+                querySeqName: 'hg38.chr1',
+                transcriptToMsaMap: {
+                    refName: 'chr2',
+                    p2g: { 0: 5000, 1: 5003 },
+                },
+                mafRegion: {
+                    refName: 'chr1',
+                    start: 1000,
+                    end: 1010,
+                    assemblyName: 'hg38',
+                },
+                rows: [['hg38.chr1', 'ACGTACGTAC']],
+            };
+            // Should use mafRegion, not transcriptToMsaMap
+            const result = msaCoordToGenomeCoord({ model, coord: 0 });
+            expect(result).toEqual({
+                refName: 'chr1',
+                start: 1000,
+                end: 1001,
+            });
+        });
+    });
+});
+//# sourceMappingURL=msaCoordToGenomeCoord.test.js.map

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

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/msaDataStore.d.ts

@@ -0,0 +1,14 @@
+export declare function generateDataStoreId(): string;
+export declare function storeMsaData(id: string, data: {
+    msa?: string;
+    tree?: string;
+    treeMetadata?: string;
+}): Promise<boolean>;
+export declare function retrieveMsaData(id: string): Promise<{
+    msa?: string;
+    tree?: string;
+    treeMetadata?: string;
+} | undefined>;
+export declare function deleteMsaData(id: string): Promise<void>;
+export declare function cleanupOldData(maxAgeMs?: number): Promise<number>;
+export declare function isIndexedDBAvailable(): boolean;

package/dist/MsaViewPanel/msaDataStore.js

@@ -0,0 +1,197 @@
+const DB_NAME = 'jbrowse-msaview-data';
+const DB_VERSION = 1;
+const STORE_NAME = 'msa-data';
+let dbPromise;
+let indexedDBAvailable;
+function checkIndexedDBAvailable() {
+    if (indexedDBAvailable !== undefined) {
+        return indexedDBAvailable;
+    }
+    try {
+        // Check if indexedDB exists and is accessible
+        if (typeof indexedDB === 'undefined') {
+            indexedDBAvailable = false;
+            return false;
+        }
+        // Try to open a test database to verify IndexedDB is working
+        // This can fail in private browsing mode in some browsers
+        indexedDBAvailable = true;
+        return true;
+    }
+    catch {
+        indexedDBAvailable = false;
+        return false;
+    }
+}
+async function openDB() {
+    if (!checkIndexedDBAvailable()) {
+        return undefined;
+    }
+    if (dbPromise) {
+        return dbPromise;
+    }
+    dbPromise = new Promise(resolve => {
+        try {
+            const request = indexedDB.open(DB_NAME, DB_VERSION);
+            request.addEventListener('error', () => {
+                // IndexedDB may be blocked in private browsing mode
+                console.warn('IndexedDB unavailable - MSA data will not persist across page refreshes');
+                indexedDBAvailable = false;
+                resolve(undefined);
+            });
+            request.onsuccess = () => {
+                resolve(request.result);
+            };
+            request.onupgradeneeded = event => {
+                const db = event.target.result;
+                if (!db.objectStoreNames.contains(STORE_NAME)) {
+                    const store = db.createObjectStore(STORE_NAME, { keyPath: 'id' });
+                    store.createIndex('timestamp', 'timestamp', { unique: false });
+                }
+            };
+        }
+        catch (e) {
+            console.warn('Failed to open IndexedDB:', e);
+            indexedDBAvailable = false;
+            resolve(undefined);
+        }
+    });
+    return dbPromise;
+}
+export function generateDataStoreId() {
+    return `msa-${Date.now()}-${Math.random().toString(36).slice(2, 11)}`;
+}
+export async function storeMsaData(id, data) {
+    const db = await openDB();
+    if (!db) {
+        // IndexedDB not available, silently skip storage
+        return false;
+    }
+    return new Promise(resolve => {
+        try {
+            const transaction = db.transaction(STORE_NAME, 'readwrite');
+            const store = transaction.objectStore(STORE_NAME);
+            const storedData = {
+                id,
+                msa: data.msa,
+                tree: data.tree,
+                treeMetadata: data.treeMetadata,
+                timestamp: Date.now(),
+            };
+            const request = store.put(storedData);
+            request.addEventListener('error', () => {
+                // Log but don't fail - storage is best-effort
+                console.warn('Failed to store MSA data:', request.error);
+                resolve(false);
+            });
+            request.onsuccess = () => {
+                resolve(true);
+            };
+        }
+        catch (e) {
+            console.warn('Failed to store MSA data:', e);
+            resolve(false);
+        }
+    });
+}
+export async function retrieveMsaData(id) {
+    const db = await openDB();
+    if (!db) {
+        return undefined;
+    }
+    return new Promise(resolve => {
+        try {
+            const transaction = db.transaction(STORE_NAME, 'readonly');
+            const store = transaction.objectStore(STORE_NAME);
+            const request = store.get(id);
+            request.addEventListener('error', () => {
+                console.warn('Failed to retrieve MSA data:', request.error);
+                resolve(undefined);
+            });
+            request.onsuccess = () => {
+                const result = request.result;
+                if (result) {
+                    resolve({
+                        msa: result.msa,
+                        tree: result.tree,
+                        treeMetadata: result.treeMetadata,
+                    });
+                }
+                else {
+                    resolve(undefined);
+                }
+            };
+        }
+        catch (e) {
+            console.warn('Failed to retrieve MSA data:', e);
+            resolve(undefined);
+        }
+    });
+}
+export async function deleteMsaData(id) {
+    const db = await openDB();
+    if (!db) {
+        return;
+    }
+    return new Promise(resolve => {
+        try {
+            const transaction = db.transaction(STORE_NAME, 'readwrite');
+            const store = transaction.objectStore(STORE_NAME);
+            const request = store.delete(id);
+            request.addEventListener('error', () => {
+                console.warn('Failed to delete MSA data:', request.error);
+                resolve();
+            });
+            request.onsuccess = () => {
+                resolve();
+            };
+        }
+        catch (e) {
+            console.warn('Failed to delete MSA data:', e);
+            resolve();
+        }
+    });
+}
+// Clean up entries older than the specified age (default 7 days)
+export async function cleanupOldData(maxAgeMs = 7 * 24 * 60 * 60 * 1000) {
+    const db = await openDB();
+    if (!db) {
+        return 0;
+    }
+    const cutoffTime = Date.now() - maxAgeMs;
+    return new Promise(resolve => {
+        try {
+            const transaction = db.transaction(STORE_NAME, 'readwrite');
+            const store = transaction.objectStore(STORE_NAME);
+            const index = store.index('timestamp');
+            const range = IDBKeyRange.upperBound(cutoffTime);
+            const request = index.openCursor(range);
+            let deletedCount = 0;
+            request.addEventListener('error', () => {
+                console.warn('Failed to cleanup old MSA data:', request.error);
+                resolve(deletedCount);
+            });
+            request.onsuccess = event => {
+                const cursor = event.target
+                    .result;
+                if (cursor) {
+                    cursor.delete();
+                    deletedCount++;
+                    cursor.continue();
+                }
+                else {
+                    resolve(deletedCount);
+                }
+            };
+        }
+        catch (e) {
+            console.warn('Failed to cleanup old MSA data:', e);
+            resolve(0);
+        }
+    });
+}
+// Check if IndexedDB storage is available
+export function isIndexedDBAvailable() {
+    return checkIndexedDBAvailable();
+}
+//# sourceMappingURL=msaDataStore.js.map

package/dist/MsaViewPanel/msaDataStore.js.map

@@ -0,0 +1 @@
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package/dist/MsaViewPanel/pairwiseAlignment.d.ts

@@ -0,0 +1,27 @@
+interface AlignmentResult {
+    alignedSeq1: string;
+    alignedSeq2: string;
+    score: number;
+}
+export interface AlignmentRow {
+    id: string;
+    seq: string;
+}
+export interface PairwiseAlignment {
+    consensus: string;
+    alns: readonly [AlignmentRow, AlignmentRow];
+}
+/**
+ * Needleman-Wunsch global alignment algorithm
+ */
+export declare function needlemanWunsch(seq1: string, seq2: string, gapOpen?: number, gapExtend?: number): AlignmentResult;
+export declare function runPairwiseAlignment(seq1: string, seq2: string): PairwiseAlignment;
+/**
+ * Build coordinate mappings from a pairwise alignment
+ * Maps between ungapped positions in seq1 and seq2
+ */
+export declare function buildAlignmentMaps(pairwiseAlignment: PairwiseAlignment): {
+    seq1ToSeq2: Map<number, number>;
+    seq2ToSeq1: Map<number, number>;
+};
+export {};