From 72d359e5c3d18227f986eee73db8d04d4f9da336 Mon Sep 17 00:00:00 2001
From: Josiah Seaman <josiah@newline.us>
Date: Mon, 4 Dec 2017 14:00:40 +0000
Subject: [PATCH] Bug fixes for webpage generation

---
 DDV.py        | 10 ++++++++--
 TileLayout.py |  2 +-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/DDV.py b/DDV.py
index a5f22e9..cb95d69 100644
--- a/DDV.py
+++ b/DDV.py
@@ -209,7 +209,6 @@ 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)))
@@ -217,10 +216,15 @@ def create_parallel_viz_from_fastas(args, n_genomes, output_dir, output_name, fa
         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
+
     if args.run_server:
         run_server(output_dir)
 
@@ -231,7 +235,6 @@ def create_tile_layout_viz_from_fasta(args, fasta, output_dir, output_name, layo
         layout = TileLayout(use_titles=not args.no_titles, sort_contigs=args.sort_contigs)
     layout.process_file(fasta, output_dir, output_name)
     layout_final_output_location = layout.final_output_location
-    del layout
     # try:
     #     shutil.copy(fasta, os.path.join(output_dir, os.path.basename(fasta)))
     # except shutil.SameFileError:
@@ -239,9 +242,12 @@ def create_tile_layout_viz_from_fasta(args, fasta, output_dir, output_name, layo
     print("Done creating Large Image at ", layout_final_output_location)
     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
 
 
 if __name__ == "__main__":
diff --git a/TileLayout.py b/TileLayout.py
index d1a6173..f8e6ca6 100644
--- a/TileLayout.py
+++ b/TileLayout.py
@@ -12,7 +12,7 @@
 
 
 small_title_bp = 10000
-title_skip_padding = self.levels[0].modulo
+title_skip_padding = 100
 
 
 def hex_to_rgb(h):