inprogress

[jalview.git] / forester / ruby / evoruby / lib / evo / tool / phylogenies_decorator.rb

diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index 3620fc5..4e26acb 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
@@ -10,7 +10,7 @@
 # $Id: phylogenies_decorator.rb,v 1.34 2010/12/13 19:00:11 cmzmasek Exp $
 #
 # Environment variable FORESTER_HOME needs to point to the appropriate
-# directory (e.g. setenv FORESTER_HOME $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/)
+# directory (e.g. setenv FORESTER_HOME $HOME/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester/)
 
 require 'lib/evo/util/constants'
 require 'lib/evo/util/util'
@@ -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'
@@ -43,7 +44,7 @@ module Evoruby
     PRG_VERSION    = "1.02"
     COPYRIGHT      = "2012 Christian M Zmasek"
     CONTACT        = "phylosoft@gmail.com"
-    WWW            = "www.phylosoft.org"
+    WWW            = "https://sites.google.com/site/cmzmasek/home/software/forester"
 
     IDS_ONLY_OPTION     = "n"
     DOMAINS_ONLY_OPTION = "d"
@@ -223,6 +224,7 @@ module Evoruby
             cmd = decorator + ' ' + DECORATOR_OPTIONS_DOMAINS + ' ' +
              '-f=d ' + phylogeny_file + ' ' +
              domains_mapfile_name + ' ' + my_outfile
+            puts cmd
             execute_cmd( cmd, log )
           end
 
@@ -233,8 +235,9 @@ 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
+            puts cmd
             execute_cmd( cmd, log )
           end