jbrowse-plugin-msaview 2.2.8 → 2.3.2

package/dist/MsaViewPanel/msaDataStore.js

@@ -1,197 +1,83 @@
+import { openDB } from 'idb';
 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);
-        }
+async function getDB() {
+    return openDB(DB_NAME, DB_VERSION, {
+        upgrade(db) {
+            if (!db.objectStoreNames.contains(STORE_NAME)) {
+                const store = db.createObjectStore(STORE_NAME, { keyPath: 'id' });
+                store.createIndex('timestamp', 'timestamp', { unique: false });
+            }
+        },
     });
-    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
+    try {
+        const db = await getDB();
+        const storedData = {
+            id,
+            msa: data.msa,
+            tree: data.tree,
+            treeMetadata: data.treeMetadata,
+            timestamp: Date.now(),
+        };
+        await db.put(STORE_NAME, storedData);
+        return true;
+    }
+    catch (e) {
+        console.warn('Failed to store MSA data:', e);
         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);
-                }
+    try {
+        const db = await getDB();
+        const result = (await db.get(STORE_NAME, id));
+        if (result) {
+            return {
+                msa: result.msa,
+                tree: result.tree,
+                treeMetadata: result.treeMetadata,
             };
         }
-        catch (e) {
-            console.warn('Failed to retrieve MSA data:', e);
-            resolve(undefined);
-        }
-    });
+        return undefined;
+    }
+    catch (e) {
+        console.warn('Failed to retrieve MSA data:', e);
+        return undefined;
+    }
 }
 export async function deleteMsaData(id) {
-    const db = await openDB();
-    if (!db) {
-        return;
+    try {
+        const db = await getDB();
+        await db.delete(STORE_NAME, id);
+    }
+    catch (e) {
+        console.warn('Failed to delete MSA data:', e);
     }
-    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) {
+    try {
+        const db = await getDB();
+        const cutoffTime = Date.now() - maxAgeMs;
+        const tx = db.transaction(STORE_NAME, 'readwrite');
+        const index = tx.store.index('timestamp');
+        let cursor = await index.openCursor(IDBKeyRange.upperBound(cutoffTime));
+        let deletedCount = 0;
+        while (cursor) {
+            await cursor.delete();
+            deletedCount++;
+            cursor = await cursor.continue();
+        }
+        return deletedCount;
+    }
+    catch (e) {
+        console.warn('Failed to cleanup old MSA data:', e);
         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

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

@@ -11,15 +11,8 @@ 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>;