feat: improve option of coordinates vs input sequence

app.py

@@ -391,7 +391,7 @@ def predict(
     chrom: str,
     start: int,
     end: int,
-    use_coords: bool,
+    input_type: str,
     bigwig_selected: list[str],
     bed_elements: list[str],
 ):
@@ -402,6 +402,9 @@ def predict(
     # Extract track IDs from display format if needed
     bigwig_selected = [_extract_track_id(tid) for tid in bigwig_selected]
     
+    # Determine if using coordinates based on input_type radio button
+    use_coords = input_type == "Use genomic coordinates"
+    
     if use_coords:
         # Check if this species supports coordinate-based fetching
         if species not in SPECIES_WITH_COORDINATE_SUPPORT:
@@ -699,6 +702,61 @@ CSS = """
     font-size: 2.0rem !important;
   }
 }
+
+/* Remove borders/lines from input sections */
+.gr-group {
+  border: none !important;
+  box-shadow: none !important;
+  margin-bottom: 0 !important;
+  padding-bottom: 0 !important;
+}
+
+/* Remove any borders or separators from textbox components in input sections */
+.gr-textbox {
+  border-top: none !important;
+  margin-top: 0 !important;
+}
+
+/* Remove borders from form sections */
+.form {
+  border: none !important;
+}
+
+/* Remove any hr or separator lines */
+hr {
+  display: none !important;
+}
+
+/* Remove line above DNA sequence input */
+#dna_sequence_input {
+  border-top: none !important;
+  margin-top: 0 !important;
+  padding-top: 0 !important;
+}
+
+/* Remove any border or separator before the DNA sequence input */
+#dna_sequence_input::before,
+#dna_sequence_input .wrap::before {
+  display: none !important;
+  content: none !important;
+}
+
+/* Ensure coordinates group doesn't leave a border when hidden */
+#coords_group[style*="display: none"],
+#coords_group:not(:visible) {
+  display: none !important;
+  border: none !important;
+  margin: 0 !important;
+  padding: 0 !important;
+}
+
+/* Remove any separator between input sections */
+#coords_group + *,
+#coords_group ~ #dna_sequence_input {
+  border-top: none !important;
+  margin-top: 0 !important;
+  padding-top: 0 !important;
+}
 """
 
 JS = """
@@ -825,7 +883,7 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
 
 <div class="intro-tip">
   <span class="intro-tip-icon">💡</span>
-  <span><strong>Tip:</strong> The demo includes default settings that you can use to get started, taking ~ 1 minute to run.</span>
+  <span><strong>Tip:</strong> The demo includes default settings that you can use to get started, taking ~ 10 seconds to run.</span>
 </div>
 
 <div style="margin-top: 16px; padding: 12px; background: rgba(0,0,0,0.03); border-radius: 12px; font-size: 0.95rem;">
@@ -862,31 +920,44 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
     
     model_status = gr.Markdown("", visible=False)
     
-    gr.Markdown("## Input sequence (Genomic coordinate or DNA sequence)\n"
-    "Supported species for coordinate-based sequence fetching: " + ", ".join(sorted(SPECIES_WITH_COORDINATE_SUPPORT)) + "\n"
-    )
+    gr.Markdown("## Input DNA sequence")
     
     # Get all available species from the pipeline
     all_species = sorted(ASSEMBLY_TO_SPECIES.values())
 
-    with gr.Row():
-        species = gr.Dropdown(
-            choices=all_species,
-            value=DEFAULT_SPECIES,
-            label="Species",
-        )
-        use_coords = gr.Checkbox(
-            True, 
-            label="Use genome coordinate (only for supported species)",
-            visible=DEFAULT_SPECIES in SPECIES_WITH_COORDINATE_SUPPORT
-        )
-
-    with gr.Row(visible=True) as coords_row:
-        chrom = gr.Textbox(label="Chromosome", value=_default_coords["chrom"])
-        start = gr.Number(label="Start", value=_default_coords["start"], precision=0)
-        end = gr.Number(label="End", value=_default_coords["end"], precision=0)
-
-    seq = gr.Textbox(lines=4, label="Input DNA sequence", placeholder="ACGT...")
+    species = gr.Dropdown(
+        choices=all_species,
+        value=DEFAULT_SPECIES,
+        label="Species",
+    )
+    
+    # Radio buttons for input type selection
+    is_supported_default = DEFAULT_SPECIES in SPECIES_WITH_COORDINATE_SUPPORT
+    initial_input_type = "Use genomic coordinates" if is_supported_default else "Enter DNA sequence"
+    input_type = gr.Radio(
+        choices=["Use genomic coordinates", "Enter DNA sequence"],
+        value=initial_input_type,
+        label="Input method",
+        visible=is_supported_default,  # Only show if species supports coordinates
+    )
+    
+    # Coordinates section - visible only when "Use genomic coordinates" is selected
+    with gr.Group(visible=is_supported_default and initial_input_type == "Use genomic coordinates", elem_id="coords_group") as coords_group:
+        gr.Markdown("**Genomic coordinates** (supported species: " + ", ".join(sorted(SPECIES_WITH_COORDINATE_SUPPORT)) + ")")
+        with gr.Row():
+            chrom = gr.Textbox(label="Chromosome", value=_default_coords["chrom"])
+            start = gr.Number(label="Start", value=_default_coords["start"], precision=0)
+            end = gr.Number(label="End", value=_default_coords["end"], precision=0)
+    
+    # DNA sequence section - visible only when "Enter DNA sequence" is selected
+    # Using Textbox directly (not wrapped in Group) to avoid visual border/line
+    seq = gr.Textbox(
+        lines=4, 
+        label="Input DNA sequence", 
+        placeholder="ACGT...",
+        visible=initial_input_type == "Enter DNA sequence",
+        elem_id="dna_sequence_input"
+    )
     
     def change_model(display_name: str, species: str):
         """Reload pipeline with new model."""
@@ -967,8 +1038,8 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
     )
 
     with gr.Row(visible=True) as bigwig_buttons_row:
-        bigwig_clear_btn = gr.Button("Clear results")
-        bigwig_remove_btn = gr.Button("Remove checked from Selected")
+        bigwig_clear_btn = gr.Button("Clear search results")
+        bigwig_remove_btn = gr.Button("Remove all selected")
 
     gr.Markdown("## Select genome annotation elements")
     
@@ -982,6 +1053,7 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
     btn = gr.Button("Predict", elem_id="predict_btn")
 
     gr.Markdown("## NTv3 predictions for selected tracks and elements")
+    gr.Markdown("Note: NTv3 predictions are for the 37.5% center of the input sequence.")
     
     plot = gr.Plot(label="", elem_id="tracks_plot")
     export_png = gr.File(elem_id="export_png_hidden", interactive=False)
@@ -1152,13 +1224,15 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
     )
     
     # Update coordinates visibility and values when species changes
-    def update_on_species_change(species: str, use_coords_val: bool):
+    def update_on_species_change(species: str, input_type_val: str):
         """Update coordinates visibility and values when species changes."""
         is_supported = species in SPECIES_WITH_COORDINATE_SUPPORT
         has_bigwigs = _has_bigwigs(species)
         coords = DEFAULT_COORDS.get(species, DEFAULT_COORDS["human"])
-        # Show coordinates only if species is supported AND use_coords is True
-        show_coords = is_supported and use_coords_val
+        # Show coordinates only if species is supported AND input type is coordinates
+        use_coords = input_type_val == "Use genomic coordinates"
+        show_coords = is_supported and use_coords
+        show_seq = not show_coords
         
         # Format available tracks for display if species has bigwigs
         if has_bigwigs:
@@ -1183,8 +1257,9 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
             gr.update(visible=show_coords, value=coords["chrom"]),
             gr.update(visible=show_coords, value=coords["start"]),
             gr.update(visible=show_coords, value=coords["end"]),
-            gr.update(value=is_supported, visible=is_supported),  # Show/hide and enable use_coords only if supported
-            gr.update(visible=show_coords),  # Show/hide the row
+            gr.update(visible=is_supported, value="Use genomic coordinates" if is_supported else "Enter DNA sequence"),  # Update input_type radio
+            gr.update(visible=show_coords),  # Show/hide coords_group
+            gr.update(visible=show_seq),     # Show/hide seq
             gr.update(visible=not has_bigwigs),  # Show "no tracks" message if no bigwigs
             gr.update(visible=show_selected_tracks, choices=formatted_tracks, value=default_formatted),  # Show bigwig selection with defaults if available
             gr.update(visible=has_bigwigs),  # Show bigwig query if available
@@ -1192,36 +1267,62 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
             gr.update(visible=has_bigwigs),  # Show bigwig buttons if available
         )
     
-    # Update coordinates visibility when checkbox changes
-    def update_coords_visibility(use_coords_val: bool, species: str):
-        """Update coordinates visibility when checkbox changes."""
+    # Update input type radio visibility and value when species changes
+    def update_input_type_on_species_change(species: str):
+        """Update input type radio when species changes."""
         is_supported = species in SPECIES_WITH_COORDINATE_SUPPORT
-        show_coords = is_supported and use_coords_val
-        return (
-            gr.update(visible=show_coords),
-            gr.update(visible=show_coords),
-            gr.update(visible=show_coords),
-            gr.update(visible=show_coords),  # Show/hide the row
-        )
+        # If species doesn't support coordinates, default to sequence input
+        default_value = "Use genomic coordinates" if is_supported else "Enter DNA sequence"
+        return gr.update(visible=is_supported, value=default_value)
+    
+    # Update input visibility when radio button changes
+    def update_input_visibility(input_type_val: str, species: str):
+        """Update input visibility when radio button changes."""
+        # Explicitly check the input type value
+        if input_type_val == "Enter DNA sequence":
+            # Hide coordinates, show sequence
+            return (
+                gr.update(visible=False),  # coords_group - always hide when sequence is selected
+                gr.update(visible=True),   # seq - always show when sequence is selected
+            )
+        elif input_type_val == "Use genomic coordinates":
+            # Show coordinates only if species supports it
+            is_supported = species in SPECIES_WITH_COORDINATE_SUPPORT
+            return (
+                gr.update(visible=is_supported),  # coords_group - show only if supported
+                gr.update(visible=not is_supported),  # seq - hide when coordinates are shown
+            )
+        else:
+            # Fallback: hide both (shouldn't happen)
+            return (
+                gr.update(visible=False),
+                gr.update(visible=False),
+            )
+    
+    species.change(
+        fn=update_input_type_on_species_change,
+        inputs=[species],
+        outputs=[input_type],
+    )
     
     species.change(
         fn=update_on_species_change,
-        inputs=[species, use_coords],
+        inputs=[species, input_type],
         outputs=[
-            chrom, start, end, use_coords, coords_row,
+            chrom, start, end, input_type, coords_group, seq,
             bigwig_no_tracks_msg, bigwig_selected, bigwig_query, bigwig_results, bigwig_buttons_row
         ],
     )
     
-    use_coords.change(
-        fn=update_coords_visibility,
-        inputs=[use_coords, species],
-        outputs=[chrom, start, end, coords_row],
+    input_type.change(
+        fn=update_input_visibility,
+        inputs=[input_type, species],
+        outputs=[coords_group, seq],
     )
 
     btn.click(
         fn=predict,
-        inputs=[seq, species, chrom, start, end, use_coords, bigwig_selected, bed_elements],
+        inputs=[seq, species, chrom, start, end, input_type, bigwig_selected, bed_elements],
         outputs=[plot, export_png, meta, prediction_state, bigwig_selected_state, bed_elements_state],
         api_name="predict",
     )
@@ -1252,3 +1353,4 @@ if __name__ == "__main__":
         css=CSS,
         js=JS,
     )
+