Update app.py

app.py

@@ -464,6 +464,8 @@ def build_maximum_likelihood_tree(f_gene_sequence):
         return False, f"ML tree construction failed: {str(e)}", None, None
 
 # --- NEW Tree Analysis Function (Using the new analyzer API) ---
+# Replace this part in your analyze_sequence_for_tree function:
+
 def analyze_sequence_for_tree(sequence: str, matching_percentage: float) -> tuple:
     """
     Analyze sequence and create phylogenetic tree and detailed report using the new analyzer API
@@ -514,8 +516,8 @@ def analyze_sequence_for_tree(sequence: str, matching_percentage: float) -> tupl
         tree_html_path = os.path.join(temp_dir, f'phylogenetic_tree_interactive_{query_id}.html')
         fig.write_html(tree_html_path)
         
-        # Generate detailed report
-        report_success = analyzer.generate_detailed_report(matched_ids, actual_percentage)
+        # Generate detailed report - FIXED: Pass the user's input threshold
+        report_success = analyzer.generate_detailed_report(matched_ids, actual_percentage, matching_percentage)
         report_html_path = None
         if report_success:
             report_filename = f"detailed_report_{query_id.replace('/', '_')}.html"