Update app.py

app.py

@@ -863,9 +863,11 @@ def create_interface():
             gr.Markdown("### 🌲 Phylogenetic Tree Visualization (ML Simplified Tree)")
             tree_html = gr.HTML(
                 label="Interactive Tree",
-                value="<p>Click 'Open Tree' to view the ML Simplified Tree in your browser after running analysis.</p>"
+                value="<p>Click 'Show Tree' to view the ML Simplified Tree in a new tab or 'Download Tree' to save it.</p>"
             )
-            open_tree_btn = gr.Button("🌳 Open Tree", variant="secondary")
+            with gr.Row():
+                show_tree_btn = gr.Button("👁️ Show Tree", variant="secondary")
+                download_tree_btn = gr.Button("⬇️ Download Tree", variant="secondary")
 
             # File downloads
             gr.Markdown("### 📁 Download Results")
@@ -885,78 +887,7 @@ def create_interface():
                     interactive=False
                 )
         
-        with gr.Tab("ℹ️ Help & Info"):
-            gr.Markdown("""
-            ## About This Tool
-            
-            ### F Gene Analysis Pipeline
-            This comprehensive pipeline analyzes F genes through multiple computational approaches:
-            
-            #### 🎯 Gene Boundary Detection
-            - Uses deep learning to identify and extract F gene sequences from larger genomic sequences
-            - Provides confidence scores for detected boundaries
-            - Automatically trims sequences to focus on the F gene region
-            
-            #### 🔍 Gene Validation
-            - Employs k-mer based machine learning models to validate extracted sequences
-            - Provides probability scores indicating likelihood of being a genuine F gene
-            - Uses 6-mer frequency patterns for classification
-            
-            #### 🌳 Phylogenetic Analysis
-            
-            **Maximum Likelihood Trees:**
-            - Requires MAFFT (sequence alignment) and IQ-TREE (phylogenetic reconstruction)
-            - Performs model selection and bootstrap analysis
-            - Generates publication-quality phylogenetic trees
-            - Provides detailed evolutionary analysis
-            
-            **Simplified Trees:**
-            - Uses built-in algorithms for quick phylogenetic analysis
-            - Interactive visualization with similarity-based clustering
-            - Faster alternative when external tools are not available
-            
-            ### Input Requirements
-            - **DNA Sequences**: ATCG format, minimum 50 bp for meaningful analysis
-            - **FASTA Files**: Standard FASTA format with single or multiple sequences
-            - **Similarity Threshold**: 1-99% for controlling phylogenetic analysis sensitivity
-            
-            ### Dependencies
-            
-            **Required for ML Trees:**
-            ```bash
-            # Ubuntu/Debian
-            sudo apt-get install mafft iqtree
-            
-            # macOS
-            brew install mafft iqtree
-            
-            # Conda
-            conda install -c bioconda mafft iqtree
-            ```
-            
-            ### Output Files
-            - **Aligned FASTA**: Multiple sequence alignment in FASTA format
-            - **Tree File**: Newick format phylogenetic tree
-            - **HTML Tree**: Interactive visualization for web browsers (ML Simplified Tree)
-            
-            ### Troubleshooting
-            
-            **Common Issues:**
-            - *"No similar sequences found"*: Lower the similarity threshold
-            - *"Sequence too short"*: Provide sequences longer than 50 bp
-            - *"MAFFT/IQ-TREE not found"*: Install required dependencies
-            - *"Model not available"*: Check model files are properly downloaded
-            
-            **Performance Tips:**
-            - Use sequences between 100-2000 bp for optimal performance  
-            - Limit to <50 sequences for faster tree construction
-            - Lower similarity thresholds find more distant relatives
-            - Higher thresholds focus on closely related sequences
-            
-            ### Citation
-            If you use this tool in your research, please cite the appropriate methods and tools used.
-            """)
-        
+          
         # Event handlers
         def run_analysis_text(dna_seq, sim_score, build_tree):
             return run_pipeline(dna_seq, sim_score, build_tree)
@@ -974,16 +905,21 @@ def create_interface():
         def clear_inputs():
             return "", None, 95.0, False, "Ready to analyze"
         
-        def open_tree(html_file):
+        def show_tree(html_file):
             if html_file and os.path.exists(html_file):
                 try:
-               # Use Gradio's file serving by providing the file path directly
+                    # Serve the file directly using Gradio's file endpoint
                     file_url = f"/file={html_file}"
                     return gr.update(value=f"<script>window.open('{file_url}', '_blank');</script>")
                 except Exception as e:
-                    return gr.update(value=f"<p>Error opening tree: {str(e)}. Please download the file and open it manually: <a href='/file={html_file}' download>Download</a></p>")
+                    return gr.update(value=f"<p>Error showing tree: {str(e)}. Please use the 'Download Tree' button and open manually.</p>")
             return gr.update(value="<p>No tree file available. Run analysis to generate one.</p>")
         
+        def download_tree(html_file):
+            if html_file and os.path.exists(html_file):
+                return gr.File.update(value=html_file, visible=True)
+            return gr.File.update(value=None, visible=False)
+        
         # Connect events
         run_btn.click(
             fn=run_analysis_combined,
@@ -1000,12 +936,18 @@ def create_interface():
             outputs=[dna_input, fasta_file, similarity_score, build_ml_tree, status_display]
         )
         
-        open_tree_btn.click(
-            fn=open_tree,
+        show_tree_btn.click(
+            fn=show_tree,
             inputs=[html_file],
             outputs=[tree_html]
         )
         
+        download_tree_btn.click(
+            fn=download_tree,
+            inputs=[html_file],
+            outputs=[html_file]
+        )
+        
         # Example data loading
         gr.Markdown("### 🧪 Example Data")
         example_btn = gr.Button("Load Example F Gene Sequence", variant="secondary")
@@ -1020,7 +962,7 @@ def create_interface():
         )
     
     return iface
-
+    
 # --- Main Execution ---
 if __name__ == "__main__":
     # Initialize and launch interface