From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Thu, 24 Jan 2013 21:14:11 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9b2d675e85942aa2824ee825bd6f74ccb07a6975;p=jalview.git

inprogress
---

diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index 3620fc5..1128be6 100644
--- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@ -23,7 +23,8 @@ module Evoruby
   class PhylogeniesDecorator
 
     #DECORATOR_OPTIONS_SEQ_NAMES = '-r=1 -mdn'
-    DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -sn'
+    #DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -sn'
+    DECORATOR_OPTIONS_SEQ_NAMES = '-p -t -c -tc'
     # -mdn is a hidden expert option to rename e.g. "6_ORYLA3" to "6_[3]_ORYLA"
     #DECORATOR_OPTIONS_SEQ_NAMES = '-sn -r=1'
     #DECORATOR_OPTIONS_DOMAINS = '-r=1'
@@ -233,7 +234,7 @@ module Evoruby
               my_infile = phylogeny_file
             end
             cmd = decorator + ' ' +  DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
-             '-f=s ' + my_infile + ' ' +
+             '-f=n ' + my_infile + ' ' +
              ids_mapfile_name + ' ' + outfile
             execute_cmd( cmd, log )
           end