feat: Implement Assemble by Parts flow with part DNA locking and scrambler settings

- Added `applyPartLock` function to lock DNA encoding for reused parts based on their amino acid sequence.
- Introduced `ScramblerSettings` component for advanced configuration of the scrambling process.
- Created `PartAssembler` component to manage the assembly of parts and linkers, including a drag-and-drop interface.
- Updated `ResultsView` to handle part locking and integrate scrambler settings.
- Enhanced `SequenceAnnotator` and `SequenceInput` components to display part names consistently.
- Added persistence for part DNA encoding using local storage.
- Introduced default scrambler configuration and validation for user-defined constraints.

Author: cborac

frontend/src/App.tsx

@@ -6,15 +6,18 @@ import ResultsView from './components/ResultsView';
 import PartSwapper from './components/PartSwapper';
 import type { Region, ScrambleResult, WorkSession } from './types';
 import { readRepeatMotif, writeRepeatMotif } from './repeat';
+import { clearAutosavedSession, readAutosavedSession } from './sessionStore';
 
 const FAST_MODE_ENABLED = false
 
 export default function App() {
-  const [active, setActive] = useState(0);
-  const [sequence, setSequence] = useState('');
-  const [regions, setRegions] = useState<Region[]>([]);
-  const [result, setResult] = useState<ScrambleResult | null>(null);
-  const [loadedSession, setLoadedSession] = useState<WorkSession | null>(null);
+  const [autosaved] = useState(() => readAutosavedSession());
+  const [active, setActive] = useState(autosaved ? 3 : 0);
+  const [sequence, setSequence] = useState(autosaved?.sequence ?? '');
+  const [regions, setRegions] = useState<Region[]>(autosaved?.regions ?? []);
+  const [result, setResult] = useState<ScrambleResult | null>(autosaved?.result ?? null);
+  const [assembled, setAssembled] = useState(false);
+  const [loadedSession, setLoadedSession] = useState<WorkSession | null>(autosaved);
   const [fastMode, setFastMode] = useState(false);
   const [repeatMotif, setRepeatMotif] = useState<string>(() => readRepeatMotif());
 
@@ -29,19 +32,22 @@ export default function App() {
     // Clear downstream state when sequence changes
     setRegions([]);
     setResult(null);
+    setAssembled(false);
     setActive(1);
   };
 
   const handleAnnotateNext = (r: Region[]) => {
     setRegions(r);
     setResult(null);
+    setAssembled(false);
     setActive(2);
   };
 
   const handleAssembleNext = (seq: string, r: Region[]) => {
     setSequence(seq);
     setRegions(r);
     setResult(null);
+    setAssembled(true);
     setActive(2);
   };
 
@@ -114,6 +120,7 @@ export default function App() {
             onBack={() => setActive(1)}
             onNext={() => setActive(3)}
             fastMode={fastMode}
+            lockPartDna={assembled}
           />
         )}
         {active === 3 && (
@@ -122,7 +129,7 @@ export default function App() {
             regions={regions}
             result={result}
             onResultChange={setResult}
-            onRestart={() => { setSequence(''); setRegions([]); setResult(null); setLoadedSession(null); setActive(0); }}
+            onRestart={() => { clearAutosavedSession(); setSequence(''); setRegions([]); setResult(null); setLoadedSession(null); setActive(0); }}
             initialSession={loadedSession}
             fastMode={fastMode}
           />

frontend/src/api.ts

@@ -1,11 +1,11 @@
-import type { Region, ScrambleResult } from './types';
+import type { Region, ScrambleResult, ScramblerConfig } from './types';
 import { wasmScrambleConstruct, wasmSwapPart } from './wasm-api';
 
 export function scrambleConstruct(
   sequence: string,
   regions: Region[],
   fast = false,
-  config?: Record<string, unknown>
+  config?: ScramblerConfig
 ): Promise<ScrambleResult> {
   const req = JSON.stringify({ sequence, regions, config, fast });
   return Promise.resolve(JSON.parse(wasmScrambleConstruct(req)) as ScrambleResult);
@@ -17,12 +17,14 @@ export function swapPart(
   regions: Region[],
   regionDnas: Record<string, string>,
   fast = false,
+  config?: ScramblerConfig,
 ): Promise<{ dna: string; swapped_dna: string }> {
   const req = JSON.stringify({
     new_aa: newAa,
     part_name: partName,
     regions,
     region_dnas: regionDnas,
+    config,
     fast,
   });
   return Promise.resolve(JSON.parse(wasmSwapPart(req)) as { dna: string; swapped_dna: string });