From: cmzmasek@gmail.com Date: Tue, 2 Oct 2012 18:33:46 +0000 (+0000) Subject: refactored X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6cde97838073f6604873ddd551e488beb091d7ea;p=jalview.git refactored --- diff --git a/forester/ruby/evoruby/exe/d2f.rb b/forester/ruby/evoruby/exe/d2f.rb index cb48db9..132ed3a 100755 --- a/forester/ruby/evoruby/exe/d2f.rb +++ b/forester/ruby/evoruby/exe/d2f.rb @@ -9,7 +9,7 @@ # # last modified: 06/11/2007 -require 'lib/evo/apps/domains_to_forester' +require 'lib/evo/tools/domains_to_forester' module Evoruby diff --git a/forester/ruby/evoruby/exe/dsx.rb b/forester/ruby/evoruby/exe/dsx.rb index 1ff35f7..cbee678 100755 --- a/forester/ruby/evoruby/exe/dsx.rb +++ b/forester/ruby/evoruby/exe/dsx.rb @@ -9,7 +9,7 @@ # # last modified: 06/11/2007 -require 'lib/evo/apps/domain_sequence_extractor' +require 'lib/evo/tools/domain_sequence_extractor' module Evoruby diff --git a/forester/ruby/evoruby/exe/evo_nursery.rb b/forester/ruby/evoruby/exe/evo_nursery.rb index 0ea157d..61fa33d 100755 --- a/forester/ruby/evoruby/exe/evo_nursery.rb +++ b/forester/ruby/evoruby/exe/evo_nursery.rb @@ -9,7 +9,7 @@ # # last modified: 2009/10/07 -require 'lib/evo/apps/evo_nursery' +require 'lib/evo/tools/evo_nursery' module Evoruby diff --git a/forester/ruby/evoruby/exe/fae.rb b/forester/ruby/evoruby/exe/fae.rb index 009fa0b..f75af89 100755 --- a/forester/ruby/evoruby/exe/fae.rb +++ b/forester/ruby/evoruby/exe/fae.rb @@ -8,7 +8,7 @@ # $Id: fae.rb,v 1.1 2008/09/10 02:16:34 cmzmasek Exp $ -require 'lib/evo/apps/fasta_extractor' +require 'lib/evo/tools/fasta_extractor' module Evoruby diff --git a/forester/ruby/evoruby/exe/fasta_tap.rb b/forester/ruby/evoruby/exe/fasta_tap.rb index 60afce9..7eff7a2 100755 --- a/forester/ruby/evoruby/exe/fasta_tap.rb +++ b/forester/ruby/evoruby/exe/fasta_tap.rb @@ -8,7 +8,7 @@ # $Id: fasta_tap.rb,v 1.1 2009/01/20 20:44:54 cmzmasek Exp $ -require 'lib/evo/apps/fasta_taxonomy_processor' +require 'lib/evo/tools/fasta_taxonomy_processor' module Evoruby diff --git a/forester/ruby/evoruby/exe/hsp.rb b/forester/ruby/evoruby/exe/hsp.rb index cf0febc..92ed8e0 100755 --- a/forester/ruby/evoruby/exe/hsp.rb +++ b/forester/ruby/evoruby/exe/hsp.rb @@ -9,7 +9,7 @@ # # last modified: 11/24/2009 -require 'lib/evo/apps/hmmscan_parser' +require 'lib/evo/tools/hmmscan_parser' module Evoruby diff --git a/forester/ruby/evoruby/exe/msa_pro.rb b/forester/ruby/evoruby/exe/msa_pro.rb index 3fd2566..240d7b0 100755 --- a/forester/ruby/evoruby/exe/msa_pro.rb +++ b/forester/ruby/evoruby/exe/msa_pro.rb @@ -9,7 +9,7 @@ # -require 'lib/evo/apps/msa_processor' +require 'lib/evo/tools/msa_processor' module Evoruby diff --git a/forester/ruby/evoruby/exe/mse.rb b/forester/ruby/evoruby/exe/mse.rb index d0d7612..d818136 100755 --- a/forester/ruby/evoruby/exe/mse.rb +++ b/forester/ruby/evoruby/exe/mse.rb @@ -8,7 +8,7 @@ # $Id: mse.rb,v 1.2 2008/08/28 17:09:06 cmzmasek Exp $ -require 'lib/evo/apps/multi_sequence_extractor' +require 'lib/evo/tools/multi_sequence_extractor' module Evoruby diff --git a/forester/ruby/evoruby/exe/phylogenies_decorator.rb b/forester/ruby/evoruby/exe/phylogenies_decorator.rb index a23861b..eef9e3c 100755 --- a/forester/ruby/evoruby/exe/phylogenies_decorator.rb +++ b/forester/ruby/evoruby/exe/phylogenies_decorator.rb @@ -9,7 +9,7 @@ # -require 'lib/evo/apps/phylogenies_decorator' +require 'lib/evo/tools/phylogenies_decorator' module Evoruby diff --git a/forester/ruby/evoruby/exe/phylogeny_factory.rb b/forester/ruby/evoruby/exe/phylogeny_factory.rb index 4682571..6f2d7c7 100644 --- a/forester/ruby/evoruby/exe/phylogeny_factory.rb +++ b/forester/ruby/evoruby/exe/phylogeny_factory.rb @@ -9,7 +9,7 @@ # -require 'lib/evo/apps/phylogeny_factory' +require 'lib/evo/tools/phylogeny_factory' module Evoruby diff --git a/forester/ruby/evoruby/exe/tap.rb b/forester/ruby/evoruby/exe/tap.rb index 12af133..57eb8fe 100755 --- a/forester/ruby/evoruby/exe/tap.rb +++ b/forester/ruby/evoruby/exe/tap.rb @@ -9,7 +9,7 @@ # # last modified: 05/18/2007 -require 'lib/evo/apps/taxonomy_processor' +require 'lib/evo/tools/taxonomy_processor' module Evoruby diff --git a/forester/ruby/evoruby/exe/test.rb b/forester/ruby/evoruby/exe/test.rb index 8a4431d..4a7fa5e 100755 --- a/forester/ruby/evoruby/exe/test.rb +++ b/forester/ruby/evoruby/exe/test.rb @@ -25,9 +25,9 @@ require 'lib/evo/io/writer/fasta_writer' require 'lib/evo/io/parser/fasta_parser' require 'lib/evo/io/parser/ncbi_tseq_parser' require 'lib/evo/io/parser/hmmsearch_domain_extractor' -require 'lib/evo/apps/domain_sequence_extractor' -require 'lib/evo/apps/hmmscan_parser' -require 'lib/evo/apps/domains_to_forester' +require 'lib/evo/tools/domain_sequence_extractor' +require 'lib/evo/tools/hmmscan_parser' +require 'lib/evo/tools/domains_to_forester' require 'lib/evo/io/parser/general_msa_parser' require 'lib/evo/io/parser/basic_table_parser' require 'lib/evo/util/command_line_arguments' diff --git a/forester/ruby/evoruby/exe/tseq_tap.rb b/forester/ruby/evoruby/exe/tseq_tap.rb index e0075fa..4e467e0 100755 --- a/forester/ruby/evoruby/exe/tseq_tap.rb +++ b/forester/ruby/evoruby/exe/tseq_tap.rb @@ -8,7 +8,7 @@ # $Id: tseq_tap.rb,v 1.1 2008/12/31 06:00:08 cmzmasek Exp $ -require 'lib/evo/apps/tseq_taxonomy_processor' +require 'lib/evo/tools/tseq_taxonomy_processor' module Evoruby