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[jalview.git] / forester / ruby / evoruby / lib / evo / util / constants.rb

diff --git a/forester/ruby/evoruby/lib/evo/util/constants.rb b/forester/ruby/evoruby/lib/evo/util/constants.rb
index 6546478..c9e15f9 100644 (file)
--- a/forester/ruby/evoruby/lib/evo/util/constants.rb
+++ b/forester/ruby/evoruby/lib/evo/util/constants.rb
@@ -1,33 +1,36 @@
 #
 # = lib/evo/util/constants.rb - Constants class
 #
-# Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
-# License::    GNU Lesser General Public License (LGPL)
-#
-# $Id: constants.rb,v 1.3 2007/12/21 04:13:33 cmzmasek Exp $
-#
-# last modified: 05/11/2007
+# Copyright::    Copyright (C) 2017 Christian M. Zmasek
+# License::      GNU Lesser General Public License (LGPL)
 
 module Evoruby
+  class Constants
 
-    class Constants
-
-        VERBOSE = true
+    VERBOSE = true
 
-        EVORUBY_VERSION = '1.0'
+    EVORUBY_VERSION = '1.1'
 
-        FORESTER_HOME_ENV_VARIABLE = 'FORESTER_HOME'
-        JAVA_HOME_ENV_VARIABLE     = 'JAVA_HOME'
+    ID_NORMALIZED_FASTA_FILE_SUFFIX          = "_ni.fasta"
+    ID_MAP_FILE_SUFFIX                       = ".nim"
+    DOMAIN_TABLE_SUFFIX                      = "_domain_table"
+    HMMSCAN                                  = "_hmmscan_"
+    DOMAINS_TO_FORESTER_OUTFILE_SUFFIX       = ".dff"
+    DOMAINS_TO_FORESTER_EVALUE_CUTOFF_SUFFIX = "_dtfE"
+    
+    PFAM_V_FOR_EX                             = "300" # Pfam version for examples
 
-        EVORUBY         = 'evoruby'
+    FORESTER_HOME_ENV_VARIABLE = 'FORESTER_HOME'
+    JAVA_HOME_ENV_VARIABLE     = 'JAVA_HOME'
 
-        LINE_DELIMITER  = "\n"
+    EVORUBY         = 'evoruby'
 
-        FILE_SEPARATOR  = File::SEPARATOR
+    LINE_DELIMITER  = "\n"
 
-        DOMAIN_STRUCTURE_NHX_SEPARATOR = '>'
+    FILE_SEPARATOR  = File::SEPARATOR
 
+    DOMAIN_STRUCTURE_NHX_SEPARATOR = '>'
 
-    end # class Constants
+  end # class Constants
 
 end # module Evoruby