From: zma <zma@localhost>
Date: Tue, 7 Feb 2017 07:06:35 +0000 (-0800)
Subject: back from the dead...
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=610ca99f1de9956bbe4c964acc48ea33b5049e4b;p=jalview.git

back from the dead...
---

diff --git a/forester/ruby/evoruby/exe/tap.rb b/forester/ruby/evoruby/exe/tap.rb
index 33c66e0..6a69f79 100755
--- a/forester/ruby/evoruby/exe/tap.rb
+++ b/forester/ruby/evoruby/exe/tap.rb
@@ -5,8 +5,6 @@
 # Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
 # License::    GNU Lesser General Public License (LGPL)
 #
-# $Id: tap.rb,v 1.3 2008/08/28 17:09:06 cmzmasek Exp $
-#
 # last modified: 05/18/2007
 
 require 'lib/evo/tool/taxonomy_processor'
diff --git a/forester/ruby/evoruby/lib/evo/io/parser/fasta_parser.rb b/forester/ruby/evoruby/lib/evo/io/parser/fasta_parser.rb
index e4c35d9..94c2193 100644
--- a/forester/ruby/evoruby/lib/evo/io/parser/fasta_parser.rb
+++ b/forester/ruby/evoruby/lib/evo/io/parser/fasta_parser.rb
@@ -1,17 +1,15 @@
 #
 # = lib/evo/io/parser/fasta_parser - FastaParser class
 #
-# Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
+# Copyright::  Copyright (C) 20017 Christian M. Zmasek
 # License::    GNU Lesser General Public License (LGPL)
 #
-# $Id: fasta_parser.rb,v 1.11 2010/10/08 22:04:17 cmzmasek Exp $
-#
 # last modified: 05/17/2007
 
 require 'lib/evo/io/parser/msa_parser'
 require 'lib/evo/msa/msa'
 
-require 'iconv'
+#require 'iconv'
 
 module Evoruby
 
diff --git a/forester/ruby/evoruby/lib/evo/io/parser/general_msa_parser.rb b/forester/ruby/evoruby/lib/evo/io/parser/general_msa_parser.rb
index 6a170e3..dbab203 100644
--- a/forester/ruby/evoruby/lib/evo/io/parser/general_msa_parser.rb
+++ b/forester/ruby/evoruby/lib/evo/io/parser/general_msa_parser.rb
@@ -4,14 +4,12 @@
 # Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
 # License::    GNU Lesser General Public License (LGPL)
 #
-# $Id: general_msa_parser.rb,v 1.8 2009/10/08 22:44:54 cmzmasek Exp $
-#
 # last modified: 2009/10/08
 
 require 'lib/evo/io/parser/msa_parser'
 require 'lib/evo/msa/msa'
 
-require 'iconv'
+#require 'iconv'
 
 module Evoruby
 
diff --git a/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb b/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb
index bf194c7..862a91a 100644
--- a/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb
+++ b/forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb
@@ -1,10 +1,10 @@
 #
 # = lib/evo/apps/taxonomy_processor - TaxonomyProcessor class
 #
-# Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
+# Copyright::  Copyright (C) 20017 Christian M. Zmasek
 # License::    GNU Lesser General Public License (LGPL)
 #
-# $Id: taxonomy_processor.rb,v 1.26 2010/12/13 19:00:11 cmzmasek Exp $
+
 
 
 require 'lib/evo/util/util'
@@ -22,12 +22,12 @@ module Evoruby
   class TaxonomyProcessor
 
     PRG_NAME       = "tap"
-    PRG_DATE       = "130411"
+    PRG_DATE       = "170206"
     PRG_DESC       = "replacement of species names in multiple sequence files"
     PRG_VERSION    = "2.002"
-    COPYRIGHT      = "2013 Christian M Zmasek"
+    COPYRIGHT      = "2017 Christian M Zmasek"
     CONTACT        = "phylosoft@gmail.com"
-    WWW            = "https://sites.google.com/site/cmzmasek/home/software/forester"
+    WWW            = ""
 
     EXTRACT_TAXONOMY_OPTION = "t"
 
diff --git a/forester/ruby/evoruby/lib/evo/util/util.rb b/forester/ruby/evoruby/lib/evo/util/util.rb
index e4173d3..27bdb5e 100644
--- a/forester/ruby/evoruby/lib/evo/util/util.rb
+++ b/forester/ruby/evoruby/lib/evo/util/util.rb
@@ -138,10 +138,10 @@ module Evoruby
         www,
         io = STDOUT )
 
-      if RUBY_VERSION !~ /1.9/
-        puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
-        exit( -1 )
-      end
+    #  if RUBY_VERSION !~ /1.9/
+    #    puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+    #    exit( -1 )
+    #  end
 
       ruby_version = RUBY_VERSION
       l = prg_name.length + prg_version.length + date.length + ruby_version.length + 12