From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Fri, 22 Mar 2013 22:54:15 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fd508ee418219eda297f3a4da5f4d3be7f8a6db8;p=jalview.git

inprogress
---

diff --git a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
index b499c72..5695cd4 100644
--- a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb
@@ -25,10 +25,10 @@ module Evoruby
     PRG_NAME                           = "mse"
     PRG_VERSION                        = "1.02"
     PRG_DESC                           = "extraction of sequences by name from multiple multi-sequence ('fasta') files"
-    PRG_DATE                           = "2012.07.20"
-    COPYRIGHT                          = "2008-2012 Christian M Zmasek"
+    PRG_DATE                           = "130322"
+    COPYRIGHT                          = "2008-2013 Christian M Zmasek"
     CONTACT                            = "phylosoft@gmail.com"
-    WWW                                = "www.phylosoft.org"
+    WWW                                = "https://sites.google.com/site/cmzmasek/home/software/forester"
     HELP_OPTION_1                      = 'help'
     HELP_OPTION_2                      = 'h'
 
@@ -314,7 +314,7 @@ module Evoruby
 
             per_species_counter.to_i
 
-            ids_map_writer.write( normalized_id + ": " + seq.get_name + Constants::LINE_DELIMITER )
+            ids_map_writer.write( normalized_id + "\t" + seq.get_name + Constants::LINE_DELIMITER )
 
             orig_name = nil
             if seq != nil
diff --git a/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb b/forester/ruby/evoruby/lib/evo/tool/phylogenies_decorator.rb
index 1128be6..4e26acb 100644
--- 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'
@@ -44,7 +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"
@@ -224,6 +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
 
@@ -236,6 +237,7 @@ module Evoruby
             cmd = decorator + ' ' +  DECORATOR_OPTIONS_SEQ_NAMES + ' ' +
              '-f=n ' + my_infile + ' ' +
              ids_mapfile_name + ' ' + outfile
+            puts cmd
             execute_cmd( cmd, log )
           end
 
diff --git a/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb b/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb
index 8496d36..9a77601 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       = "2013.03.22"
     PRG_DESC       = "replacement of species names in multiple sequence files"
-    PRG_VERSION    = "2.00"
+    PRG_VERSION    = "2.001"
     COPYRIGHT      = "2013 Christian M Zmasek"
     CONTACT        = "phylosoft@gmail.com"
     WWW            = "https://sites.google.com/site/cmzmasek/home/software/forester"
@@ -167,6 +167,7 @@ module Evoruby
 
     def modify_name( desc, counter, file, extract_taxonomy )
       new_desc = nil
+      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
       elsif extract_taxonomy
@@ -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