Remove ablang2.pretrained dependency - add local format_seq_input implementation

adapter.py

@@ -116,7 +116,34 @@ class AbLang2PairedHuggingFaceAdapter(AbEncoding, AbRestore, AbAlignment, AbScor
         """
         Use different modes for different usecases, mimicking the original pretrained class.
         """
-        from ablang2.pretrained import format_seq_input
+        # Local implementation of format_seq_input
+        def format_seq_input(seqs, fragmented=False):
+            """Format input sequences for processing."""
+            if fragmented:
+                # For fragmented sequences, assume they're already in the right format
+                return seqs, 'HL'
+            
+            # For paired sequences, format them as VH|VL
+            formatted_seqs = []
+            for seq in seqs:
+                if isinstance(seq, (list, tuple)):
+                    if len(seq) == 2:
+                        # Heavy and light chain
+                        heavy, light = seq[0], seq[1]
+                        if heavy and light:
+                            formatted_seqs.append(f"{heavy}|{light}")
+                        elif heavy:
+                            formatted_seqs.append(heavy)
+                        elif light:
+                            formatted_seqs.append(light)
+                        else:
+                            formatted_seqs.append("")
+                    else:
+                        formatted_seqs.append(seq[0] if seq else "")
+                else:
+                    formatted_seqs.append(seq)
+            
+            return formatted_seqs, 'HL'
 
         valid_modes = [
             'rescoding', 'seqcoding', 'restore', 'likelihood', 'probability',