forester/ruby/evoruby/lib/evo/util/constants.rb

   1 #
   2 # = lib/evo/util/constants.rb - Constants class
   3 #
   4 # Copyright::    Copyright (C) 2017 Christian M. Zmasek
   5 # License::      GNU Lesser General Public License (LGPL)
   6
   7 module Evoruby
   8   class Constants
   9
  10     VERBOSE = true
  11
  12     EVORUBY_VERSION = '1.1'
  13
  14     ID_NORMALIZED_FASTA_FILE_SUFFIX          = "_ni.fasta"
  15     ID_MAP_FILE_SUFFIX                       = ".nim"
  16     DOMAIN_TABLE_SUFFIX                      = "_domain_table"
  17     HMMSCAN                                  = "_hmmscan_"
  18     DOMAINS_TO_FORESTER_OUTFILE_SUFFIX       = ".dff"
  19     DOMAINS_TO_FORESTER_EVALUE_CUTOFF_SUFFIX = "_dtfE"
  20
  21     PFAM_V_FOR_EX                             = "300" # Pfam version for examples
  22
  23     FORESTER_HOME_ENV_VARIABLE = 'FORESTER_HOME'
  24     JAVA_HOME_ENV_VARIABLE     = 'JAVA_HOME'
  25
  26     EVORUBY         = 'evoruby'
  27
  28     LINE_DELIMITER  = "\n"
  29
  30     FILE_SEPARATOR  = File::SEPARATOR
  31
  32     DOMAIN_STRUCTURE_NHX_SEPARATOR = '>'
  33
  34   end # class Constants
  35
  36 end # module Evoruby