Add missing likelihood method implementation to adapter class

adapter.py

@@ -798,6 +798,25 @@ class AbLang2PairedHuggingFaceAdapter(AbEncoding, AbRestore, AbAlignment, AbScor
         else:
             return embeddings.cpu().numpy()
 
+    def likelihood(self, seqs, align=False, stepwise_masking=False, **kwargs):
+        """Likelihood of mutations - returns logits for each amino acid at each position."""
+        # Format input: join VH and VL with '|'
+        formatted_seqs = []
+        for s in seqs:
+            if isinstance(s, (list, tuple)):
+                formatted_seqs.append('|'.join(s))
+            else:
+                formatted_seqs.append(s)
+
+        # Get logits
+        if stepwise_masking:
+            logits = self._predict_logits_with_step_masking(formatted_seqs)
+        else:
+            logits = self._predict_logits(formatted_seqs)
+        
+        # Return logits as numpy array
+        return logits.cpu().numpy()
+
     def confidence(self, seqs, **kwargs):
         """Confidence calculation - match original ablang2 implementation by excluding all special tokens from loss."""
         # Format input: join VH and VL with '|'