Update app.py

app.py

@@ -655,6 +655,9 @@ def run_pipeline(dna_input, similarity_score=95.0, build_ml_tree=False):
         else:
             ml_tree_output = "Phylogenetic placement skipped (not requested)"
 
+# Replace the tree analysis section in your run_pipeline function (around line 500-600)
+# Find this part and replace it:
+
 # Step 4: NEW Simplified Tree Analysis (using the new analyzer API)
         html_file = None
         tree_html_content = "No tree generated"
@@ -682,9 +685,17 @@ def run_pipeline(dna_input, similarity_score=95.0, build_ml_tree=False):
                     shutil.copy2(html_path, final_html_path)
                     html_file = final_html_path
                     
-                    # Read HTML content for display
-                    with open(html_path, 'r', encoding='utf-8') as f:
-                        tree_html_content = f.read()
+                    # FIXED: Instead of reading HTML content, create a simple link
+                    tree_html_content = f"""
+                    <div style='text-align: center; padding: 20px; background: #f0f9ff; border: 2px solid #0ea5e9; border-radius: 10px;'>
+                        <h3 style='color: #0c4a6e; margin: 0 0 15px 0;'>🌳 Interactive Phylogenetic Tree Generated</h3>
+                        <p style='color: #164e63; margin-bottom: 15px;'>Your interactive tree has been generated successfully!</p>
+                        <a href='{final_html_path}' target='_blank' style='display: inline-block; padding: 10px 20px; background: #0ea5e9; color: white; text-decoration: none; border-radius: 5px; font-weight: bold;'>
+                            🔗 Open Interactive Tree in New Tab
+                        </a>
+                        <p style='color: #64748b; margin-top: 10px; font-size: 0.9em;'>Note: Download the HTML file below to view the tree locally</p>
+                    </div>
+                    """
                     
                     simplified_ml_output = tree_result
                     logging.info(f"Tree analysis completed successfully: {html_filename}")
@@ -697,12 +708,12 @@ def run_pipeline(dna_input, similarity_score=95.0, build_ml_tree=False):
                         
                 else:
                     simplified_ml_output = tree_result  # Error message
-                    tree_html_content = f"<div style='color: red;'>{tree_result}</div>"
+                    tree_html_content = f"<div style='color: red; padding: 20px; background: #fef2f2; border: 2px solid #ef4444; border-radius: 10px;'>{tree_result}</div>"
                     
             except Exception as e:
                 error_msg = f"❌ Tree analysis failed: {str(e)}"
                 simplified_ml_output = error_msg
-                tree_html_content = f"<div style='color: red;'>{error_msg}</div>"
+                tree_html_content = f"<div style='color: red; padding: 20px; background: #fef2f2; border: 2px solid #ef4444; border-radius: 10px;'>{error_msg}</div>"
                 logging.error(f"Tree analysis failed: {e}")
         else:
             if not analyzer:
@@ -712,7 +723,7 @@ def run_pipeline(dna_input, similarity_score=95.0, build_ml_tree=False):
             else:
                 simplified_ml_output = "❌ No processed sequence available for tree analysis"
             
-            tree_html_content = f"<div style='color: orange;'>{simplified_ml_output}</div>"
+            tree_html_content = f"<div style='color: orange; padding: 20px; background: #fffbeb; border: 2px solid #f59e0b; border-radius: 10px;'>{simplified_ml_output}</div>"
 
         # Final summary
         summary_output = f"""
@@ -992,7 +1003,6 @@ def create_interface():
     
     return iface
 
-# --- Main Execution ---
 # --- Main Execution ---
 if __name__ == "__main__":
     try:
@@ -1018,10 +1028,12 @@ if __name__ == "__main__":
         # Create and launch interface
         iface = create_interface()
         iface.launch(
-            share=False,            # Set to True if you want to create a public link
+            share=False,  # Set to True if you want to create a public link
             server_name="0.0.0.0",  # Allow connections from any IP
             server_port=7860,       # Default Gradio port
-            show_error=True         # Show errors in the interface
+            show_error=True,        # Show errors in the interface
+            enable_queue=True,      # Enable queuing for long-running tasks
+            max_threads=4           # Limit concurrent processing
         )
         
     except Exception as e: