Update app.py

app.py

@@ -730,6 +730,7 @@ def run_pipeline(dna_input, similarity_score=95.0, build_ml_tree=False):
             None, None, None, error_msg
         )
 
+# --- Gradio Interface ---
 # --- Gradio Interface ---
 def create_interface():
     """Create the Gradio interface with enhanced layout and features"""
@@ -746,28 +747,6 @@ def create_interface():
         height: 600px !important;
         overflow: auto;
     }
-    .modal {
-        display: none;
-        position: fixed;
-        top: 0;
-        left: 0;
-        width: 100%;
-        height: 100%;
-        background-color: rgba(0,0,0,0.5);
-    }
-    .modal-content {
-        background-color: white;
-        margin: 5% auto;
-        padding: 20px;
-        width: 80%;
-        max-height: 80%;
-        overflow: auto;
-    }
-    .close {
-        float: right;
-        font-size: 24px;
-        cursor: pointer;
-    }
     """
     
     with gr.Blocks(css=custom_css, title="F Gene Analysis Pipeline") as iface:
@@ -887,11 +866,9 @@ def create_interface():
             gr.Markdown("### 🌲 Phylogenetic Tree Visualization")
             tree_html = gr.HTML(
                 label="Interactive Tree",
-                value="<p>Click 'View Tree' to see the phylogenetic tree after running analysis.</p>"
+                value="<p>Click 'Open Tree' to view the phylogenetic tree in your browser after running analysis.</p>"
             )
-            view_tree_btn = gr.Button("👁️ View Tree", variant="secondary")
-            tree_modal = gr.HTML(visible=False, elem_classes=["modal-content"])
-            close_btn = gr.Button("✖️ Close", visible=False, elem_classes=["close"])
+            open_tree_btn = gr.Button("🌳 Open Tree", variant="secondary")
 
             # File downloads
             gr.Markdown("### 📁 Download Results")
@@ -1000,17 +977,14 @@ def create_interface():
         def clear_inputs():
             return "", None, 95.0, False, "Ready to analyze"
         
-        def view_tree(html_file):
+        def open_tree(html_file):
             if html_file and os.path.exists(html_file):
                 try:
-                    with open(html_file, "r", encoding='utf-8') as f:
-                        return f.read(), gr.update(visible=True), gr.update(visible=True)
+                    # Serve the file via Gradio's static file serving (temporary URL)
+                    return gr.File.update(value=html_file, visible=True), gr.update(value=f"<script>window.open('{html_file}', '_blank');</script>")
                 except Exception as e:
-                    return f"<p>Error loading tree: {str(e)}</p>", gr.update(visible=True), gr.update(visible=True)
-            return "<p>No tree file available. Run analysis to generate one.</p>", gr.update(visible=True), gr.update(visible=True)
-        
-        def close_modal():
-            return gr.update(visible=False), gr.update(visible=False)
+                    return gr.File.update(value=None, visible=False), gr.update(value=f"<p>Error opening tree: {str(e)}. Please download and open the file manually.</p>")
+            return gr.File.update(value=None, visible=False), gr.update(value="<p>No tree file available. Run analysis to generate one.</p>")
         
         # Connect events
         run_btn.click(
@@ -1028,15 +1002,10 @@ def create_interface():
             outputs=[dna_input, fasta_file, similarity_score, build_ml_tree, status_display]
         )
         
-        view_tree_btn.click(
-            fn=view_tree,
+        open_tree_btn.click(
+            fn=open_tree,
             inputs=[html_file],
-            outputs=[tree_modal, tree_modal, close_btn]
-        )
-        
-        close_btn.click(
-            fn=close_modal,
-            outputs=[tree_modal, close_btn]
+            outputs=[html_file, tree_html]
         )
         
         # Example data loading