Preserve cached alignment downloads

lib/controller.ts

@@ -66,7 +66,7 @@ export class BRIGController {
   private parserWorker?: Worker;
   private alignmentWorkers: Worker[] = [];
   private progressCallback?: (update: ProgressUpdate) => void;
-  private alignmentCache: Map<string, AlignmentResult> = new Map();
+  private alignmentCache: Map<string, { result: AlignmentResult; rawOutput: string }> = new Map();
 
   async initialize(): Promise<void> {
     console.log('[Controller] Starting initialization...');
@@ -532,8 +532,7 @@ export class BRIGController {
 
           if (!params.forceAlignment && this.alignmentCache.has(cacheKey)) {
             console.log(`[Controller] Using cached alignment for ${query.name}`);
-            const cachedResult = this.alignmentCache.get(cacheKey)!;
-            result = { result: cachedResult, rawOutput: '' };
+            result = this.alignmentCache.get(cacheKey)!;
           } else {
             console.log(`[Controller] Aligning ${query.name} (${query.length} bp)`);
             try {
@@ -550,7 +549,7 @@ export class BRIGController {
               const message = error instanceof Error ? error.message : String(error);
               throw new Error(`Alignment failed for ${query.name}: ${message}`);
             }
-            this.alignmentCache.set(cacheKey, result.result);
+            this.alignmentCache.set(cacheKey, result);
           }
 
           alignmentResults[ringIndex] = result;

tests/e2e/brigx.spec.ts

@@ -411,7 +411,9 @@ test.describe('BRIGX e2e — circular genome plot', () => {
     })
 
     const pageErrors: Error[] = []
+    const consoleMessages: string[] = []
     page.on('pageerror', error => pageErrors.push(error))
+    page.on('console', message => consoleMessages.push(message.text()))
     await page.goto('/app')
 
     await page.getByLabel('Reference genome file').setInputFiles(REFERENCE)
@@ -439,6 +441,25 @@ test.describe('BRIGX e2e — circular genome plot', () => {
     await page.getByRole('button', { name: 'Run Alignments' }).click()
     await Promise.all(assetResponses)
     await expect(page.getByText('Alignments completed successfully!')).toBeVisible({ timeout: 30_000 })
+
+    const downloadAlignment = async () => {
+      const downloadPromise = page.waitForEvent('download')
+      await page.getByRole('button', { name: 'Download', exact: true }).click()
+      const download = await downloadPromise
+      const downloadPath = await download.path()
+      expect(downloadPath).not.toBeNull()
+      return fs.readFile(downloadPath!, 'utf8')
+    }
+    await expect(page.getByRole('button', { name: 'Download', exact: true })).toHaveCount(1)
+    const freshAlignment = await downloadAlignment()
+    expect(freshAlignment).toContain('#query\tsubject\t%identity')
+
+    await page.getByRole('button', { name: 'Run Alignments' }).click()
+    await expect.poll(() => consoleMessages.some(message => message.includes('Using cached alignment'))).toBe(true)
+    await expect(page.getByRole('button', { name: 'Download', exact: true })).toHaveCount(1)
+    const cachedAlignment = await downloadAlignment()
+    expect(cachedAlignment).toBe(freshAlignment)
+
     for (const moduleName of ['formatdb', 'blastall']) {
       const jsRequests = requestedAssets.filter(pathname => pathname.endsWith(`/wasm/blast/${moduleName}.js`))
       const wasmRequests = requestedAssets.filter(pathname => pathname.endsWith(`/wasm/blast/${moduleName}.wasm`))