From 610ca99f1de9956bbe4c964acc48ea33b5049e4b Mon Sep 17 00:00:00 2001 From: zma Date: Mon, 6 Feb 2017 23:06:35 -0800 Subject: [PATCH] back from the dead... --- forester/ruby/evoruby/exe/tap.rb | 2 -- forester/ruby/evoruby/lib/evo/io/parser/fasta_parser.rb | 6 ++---- .../ruby/evoruby/lib/evo/io/parser/general_msa_parser.rb | 4 +--- forester/ruby/evoruby/lib/evo/tool/taxonomy_processor.rb | 10 +++++----- forester/ruby/evoruby/lib/evo/util/util.rb | 8 ++++---- 5 files changed, 12 insertions(+), 18 deletions(-) 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 -- 1.7.10.2