Fix syntax error in inline alignment.py template

adapter.py

@@ -101,15 +101,27 @@ class AbAlignment:
         return numbered_seqs, seqs, number_alignment
     
     def align_encodings(self, encodings, numbered_seqs, seqs, number_alignment):
-        aligned_encodings = np.concatenate([[[create_alignment(res_embed, numbered_seq, seq, number_alignment) for res_embed, numbered_seq, seq in zip(encodings, numbered_seqs, seqs)]], axis=0)
-        return aligned_encodings
+        aligned_encodings = []
+        for res_embed, numbered_seq, seq in zip(encodings, numbered_seqs, seqs):
+            aligned_encodings.append(create_alignment(res_embed, numbered_seq, seq, number_alignment))
+        return np.concatenate([aligned_encodings], axis=0)
         
     def reformat_subsets(self, subset_list, mode='seqcoding', align=False, numbered_seqs=None, seqs=None, number_alignment=None):
         if mode in ['seqcoding', 'restore', 'pseudo_log_likelihood', 'confidence']:
             return np.concatenate(subset_list)
         elif align:
-            subset_list = [self.align_encodings(subset, numbered_seqs[num*len(subset):(num+1)*len(subset)], seqs[num*len(subset):(num+1)*len(subset)], number_alignment) for num, subset in enumerate(subset_list)]
-            subset = np.concatenate(subset_list)
+            aligned_subsets = []
+            for num, subset in enumerate(subset_list):
+                start_idx = num * len(subset)
+                end_idx = (num + 1) * len(subset)
+                aligned_subset = self.align_encodings(
+                    subset, 
+                    numbered_seqs[start_idx:end_idx], 
+                    seqs[start_idx:end_idx], 
+                    number_alignment
+                )
+                aligned_subsets.append(aligned_subset)
+            subset = np.concatenate(aligned_subsets)
             return aligned_results(
                 aligned_seqs=[''.join(alist) for alist in subset[:,:,-1]],
                 aligned_embeds=subset[:,:,:-1].astype(float),