refactored

diff --git a/forester/ruby/evoruby/exe/d2f.rb b/forester/ruby/evoruby/exe/d2f.rb
index cb48db9..132ed3a 100755 (executable)
--- 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 (executable)
--- 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 (executable)
--- 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 (executable)
--- 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 (executable)
--- 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 (executable)
--- 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 (executable)
--- 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 (executable)
--- 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 (executable)
--- 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 (file)
--- 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 (executable)
--- 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 (executable)
--- 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 (executable)
--- 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