Update app.py

app.py

@@ -523,7 +523,43 @@ def analyze_sequence_for_tree(sequence: str, matching_percentage: float) -> tupl
         import traceback
         logging.error(f"Full traceback: {traceback.format_exc()}")
         return error_msg, None
-
+def get_tree_display_content(html_path):
+    """Extract Plotly JSON from HTML and create embeddable content"""
+    try:
+        if not html_path or not os.path.exists(html_path):
+            return None
+            
+        with open(html_path, 'r', encoding='utf-8') as f:
+            html_content = f.read()
+        
+        # Extract the Plotly JSON data
+        import re
+        json_match = re.search(r'Plotly\.newPlot\([^,]+,\s*(\{.*?\}),', html_content, re.DOTALL)
+        if json_match:
+            plotly_json = json_match.group(1)
+            
+            # Create a minimal HTML with just the essential Plotly code
+            minimal_html = f"""
+            <div id="plotly-div" style="width:100%;height:600px;"></div>
+            <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
+            <script>
+                var plotlyData = {plotly_json};
+                var layout = {{
+                    title: 'Phylogenetic Tree',
+                    xaxis: {{title: 'Distance'}},
+                    yaxis: {{title: 'Taxa'}},
+                    width: 800,
+                    height: 600
+                }};
+                Plotly.newPlot('plotly-div', plotlyData.data, layout, {{responsive: true}});
+            </script>
+            """
+            return minimal_html
+        
+        return None
+    except Exception as e:
+        logging.error(f"Failed to extract Plotly content: {e}")
+        return None
 # --- Keras Prediction ---
 def predict_with_keras(sequence):
     try:
@@ -655,9 +691,6 @@ 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"
@@ -685,17 +718,9 @@ 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
                     
-                    # 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>
-                    """
+                    # Read HTML content for display
+                    with open(html_path, 'r', encoding='utf-8') as f:
+                        tree_html_content = f.read()
                     
                     simplified_ml_output = tree_result
                     logging.info(f"Tree analysis completed successfully: {html_filename}")
@@ -708,12 +733,12 @@ 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; padding: 20px; background: #fef2f2; border: 2px solid #ef4444; border-radius: 10px;'>{tree_result}</div>"
+                    tree_html_content = f"<div style='color: red;'>{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; padding: 20px; background: #fef2f2; border: 2px solid #ef4444; border-radius: 10px;'>{error_msg}</div>"
+                tree_html_content = f"<div style='color: red;'>{error_msg}</div>"
                 logging.error(f"Tree analysis failed: {e}")
         else:
             if not analyzer:
@@ -723,7 +748,7 @@ 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; padding: 20px; background: #fffbeb; border: 2px solid #f59e0b; border-radius: 10px;'>{simplified_ml_output}</div>"
+            tree_html_content = f"<div style='color: orange;'>{simplified_ml_output}</div>"
 
         # Final summary
         summary_output = f"""