Updated color legend. Fixes for HTML generation with no image

DDV.py

@@ -124,8 +124,10 @@ def ddv(args):
                                             batch.fastas)
         sys.exit(0)
 
-    if args.layout_type == "NONE":  # DEPRECATED: Shortcut for old visualizations to create dz stack from existing large image
+    if args.layout_type == "NONE":  # Complete webpage generation from existing image
         output_dir = make_output_dir_with_suffix(base_path, '')
+        layout = TileLayout(use_titles=not args.no_titles, sort_contigs=args.sort_contigs)
+        layout.generate_html(base_path, output_dir, args.output_name)
         print("Creating Deep Zoom Structure for Existing Image...")
         create_deepzoom_stack(args.image, os.path.join(output_dir, 'GeneratedImages', "dzc_output.xml"))
         print("Done creating Deep Zoom Structure.")
@@ -209,26 +211,23 @@ def create_parallel_viz_from_fastas(args, n_genomes, output_dir, output_name, fa
     layout = ParallelLayout(n_genomes=n_genomes)
     layout.process_file(output_dir, output_name, fastas)
     layout_final_output_location = layout.final_output_location
+    del layout
     try:
         for extra_fasta in fastas:
             shutil.copy(extra_fasta, os.path.join(output_dir, os.path.basename(extra_fasta)))
     except shutil.SameFileError:
         pass  # not a problem
-    print("Done creating Large Image.")
-    if not args.no_webpage:
-        layout.generate_html(fasta, output_dir, output_name)
-        del layout
-        print("Creating Deep Zoom Structure from Generated Image...")
-        create_deepzoom_stack(os.path.join(output_dir, layout_final_output_location),
-                              os.path.join(output_dir, 'GeneratedImages', "dzc_output.xml"))
-        print("Done creating Deep Zoom Structure.")
-    else:
-        del layout
+    print("Done creating Large Image and HTML.")
+    print("Creating Deep Zoom Structure from Generated Image...")
+    create_deepzoom_stack(os.path.join(output_dir, layout_final_output_location),
+                          os.path.join(output_dir, 'GeneratedImages', "dzc_output.xml"))
+    print("Done creating Deep Zoom Structure.")
 
     if args.run_server:
         run_server(output_dir)
 
 
+
 def create_tile_layout_viz_from_fasta(args, fasta, output_dir, output_name, layout=None):
     print("Creating Large Image from Input Fasta...")
     if layout is None:

TileLayout.py

@@ -146,7 +146,7 @@ def calc_all_padding(self):
         if len(self.contigs) > 10000:
             print("Over 10,000 scaffolds detected!  Titles for entries less than 10,000bp will not be drawn.")
             self.skip_small_titles = True
-            # self.sort_contigs = True  # Important! Skipping isn't valid unless they're sorted
+            self.sort_contigs = True  # Important! Skipping isn't valid unless they're sorted
         if self.sort_contigs:
             print("Scaffolds are being sorted by length.")
             self.contigs.sort(key=lambda fragment: -len(fragment.seq))  # Best to bring the largest contigs to the forefront
@@ -298,7 +298,7 @@ def output_image(self, output_folder, output_file_name):
         print("-- Writing:", output_file_name, "--")
         self.final_output_location = os.path.join(output_folder, output_file_name + ".png")
         self.image.save(self.final_output_location, 'PNG')
-        del self.image
+        # del self.image
 
 
     def max_dimensions(self, image_length):
@@ -329,8 +329,8 @@ def generate_html(self, input_file_path, output_folder, output_file_name):
             copytree(os.path.join(os.getcwd(), 'html template'), output_folder)  # copies the whole template directory
             html_path = os.path.join(output_folder, 'index.html')
             html_content = {"title": output_file_name.replace('_', ' '),
-                            "originalImageWidth": str(self.image.width),
-                            "originalImageHeight": str(self.image.height),
+                            "originalImageWidth": str(self.image.width if self.image else 1),
+                            "originalImageHeight": str(self.image.height if self.image else 1),
                             "image_origin": str(self.origin),
                             "ColumnPadding": str(self.levels[2].padding),
                             "columnWidthInNucleotides": str(self.levels[1].chunk_size),