X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fevoruby%2Flib%2Fevo%2Ftool%2Ftaxonomy_processor.rb;h=bf194c7196705280bc89790d2d4a6733a941929c;hb=156517428746b21481eb815bf860ffb6cb0314ef;hp=b0e936ed5fd85f9f4cc6907c7642adfb1e600d60;hpb=8e6765310915a8dd68696a2bde2d88173b60642a;p=jalview.git

diff --git a/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb b/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb
index b0e936e..bf194c7 100644
--- a/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb
@@ -22,9 +22,9 @@ module Evoruby
   class TaxonomyProcessor
 
     PRG_NAME       = "tap"
-    PRG_DATE       = "2013.03.20"
+    PRG_DATE       = "130411"
     PRG_DESC       = "replacement of species names in multiple sequence files"
-    PRG_VERSION    = "2.00"
+    PRG_VERSION    = "2.002"
     COPYRIGHT      = "2013 Christian M Zmasek"
     CONTACT        = "phylosoft@gmail.com"
     WWW            = "https://sites.google.com/site/cmzmasek/home/software/forester"
@@ -167,10 +167,11 @@ module Evoruby
 
     def modify_name( desc, counter, file, extract_taxonomy )
       new_desc = nil
-      if desc =~ /^>?\s*\S{1,10}_([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA|CAP)/
-        new_desc = counter.to_s( 16 ) + "_" + $1
-      elsif extract_taxonomy
-        if desc =~/\s\[([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA|CAP)\]/
+      desc.gsub!( /\s+/, ' ' )
+      #if desc =~ /^>?\s*\S{1,10}_(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA|CAP)/
+      #  new_desc = counter.to_s( 16 ) + "_" + $1
+      if extract_taxonomy
+        if desc =~/\s\[(([A-Z9][A-Z]{2}[A-Z0-9]{2})|RAT|PIG|PEA|CAP)\]/
           new_desc = counter.to_s( 16 ) + "_" + $1
         else
           Util.fatal_error( PRG_NAME, "could not get taxonomy from: " + desc )
@@ -178,7 +179,7 @@ module Evoruby
       else
         new_desc = counter.to_s( 16 )
       end
-      file.print( new_desc + ": " + desc + "\n" )
+      file.print( new_desc + "\t" + desc + "\n" )
       new_desc
     end