improved removal of identical seqs

[jalview.git] / forester / ruby / evoruby / lib / evo / apps / taxonomy_processor.rb

diff --git a/forester/ruby/evoruby/lib/evo/apps/taxonomy_processor.rb b/forester/ruby/evoruby/lib/evo/apps/taxonomy_processor.rb
index d688844..39a48b7 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/apps/taxonomy_processor.rb
+++ b/forester/ruby/evoruby/lib/evo/apps/taxonomy_processor.rb
@@ -29,6 +29,8 @@ module Evoruby
     CONTACT        = "phylosoft@gmail.com"
     WWW            = "www.phylosoft.org"
 
+    SIMPLE = true
+
     EXTRACT_TAXONOMY_OPTION = "t"
 
     def initialize()
@@ -197,8 +199,11 @@ module Evoruby
     def modify_name( desc, counter, file, species_map, extract_taxonomy )
       new_desc = nil
       my_species = nil
-      if desc =~ /^>?\s*\S{1,10}_([0-9A-Z]{3,5})/
+     # if desc =~ /^>?\s*\S{1,10}_([0-9A-Z]{3,5})/
+      if desc =~ /^>?\s*\S{1,10}_([A-Z]{3,5})/
         new_desc = counter.to_s( 16 ) + "_" + $1
+      elsif SIMPLE
+        new_desc = counter.to_s( 16 )
       elsif extract_taxonomy
         if ( desc.count( "[" ) != desc.count( "]" ) )
           Util.fatal_error( PRG_NAME, "illegal bracket count in: " + desc )