Update app.py

app.py

@@ -292,19 +292,31 @@ def extract_window_coords(residues, window_indices):
 
 
 
-def generate_windows_from_selection(selected_indices, win_size, win_type):
-    """Generate windows from selected indices"""
-    if len(selected_indices) < win_size:
+def generate_windows_from_selection(selected_indices, window_size, window_type):
+    """Generate windows from selected residue indices"""
+    if len(selected_indices) < window_size:
         return []
     
-    if win_type == "contiguous":
-        windows = []
-        for i in range(len(selected_indices) - win_size + 1):
-            windows.append(selected_indices[i:i + win_size])
-        return windows
+    windows = []
+    if window_type == "contiguous":
+        # Only sliding windows
+        for i in range(len(selected_indices) - window_size + 1):
+            windows.append(selected_indices[i:i+window_size])
     else:  # non-contiguous
-        return [list(combo) for combo in combinations(selected_indices, win_size)]
-
+        from itertools import combinations
+        all_combos = list(combinations(selected_indices, window_size))
+        
+        # Get the contiguous windows (to exclude them)
+        contiguous_windows = []
+        for i in range(len(selected_indices) - window_size + 1):
+            contiguous_windows.append(tuple(selected_indices[i:i+window_size]))
+        
+        # Filter: keep only combinations that are NOT in contiguous_windows
+        for combo in all_combos:
+            if combo not in contiguous_windows:
+                windows.append(list(combo))
+    
+    return windows
 
 def main():
     st.markdown('<h1 class="main-header">🧬 RNA Motif Multi-Structure Comparison</h1>', unsafe_allow_html=True)