Remove problematic alignment from restore method - return sequences as-is

adapter.py

@@ -600,26 +600,9 @@ class HFAbRestore(AbRestore):
                 restored_seq = restored_seq.replace(' ', '')
                 restored_seqs.append(restored_seq)
         
-        # Handle alignment if requested
-        if align:
-            # Simple alignment: ensure all sequences have the same length by padding
-            if len(restored_seqs) > 1:
-                # Find the maximum length
-                max_len = max(len(seq) for seq in restored_seqs)
-                # Pad shorter sequences with the last character
-                aligned_seqs = []
-                for seq in restored_seqs:
-                    if len(seq) < max_len:
-                        # Pad with the last character of the sequence
-                        padded_seq = seq + seq[-1] * (max_len - len(seq))
-                        aligned_seqs.append(padded_seq)
-                    else:
-                        aligned_seqs.append(seq)
-                return np.array(aligned_seqs)
-            else:
-                return restored_seqs[0]
-        else:
-            return np.array(restored_seqs) if len(restored_seqs) > 1 else restored_seqs[0]
+        # For now, return restored sequences without alignment
+        # Proper ANARCI-based alignment requires full implementation of alignment functions
+        return np.array(restored_seqs) if len(restored_seqs) > 1 else restored_seqs[0]
 
 def add_angle_brackets(seq):
     # Assumes input is 'VH|VL' or 'VH|' or '|VL'