forester/ruby/evoruby/lib/evo/sequence/domain_structure.rb

   1 #
   2 # = lib/evo/sequence/domain_structure.rb - DomainStructure class
   3 #
   4 # Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
   5 # License::    GNU Lesser General Public License (LGPL)
   6 #
   7 # $Id: domain_structure.rb,v 1.2 2007/06/12 04:51:33 cmzmasek Exp $
   8 #
   9 # last modified: 05/16/2007
  10
  11 require 'lib/evo/util/constants'
  12
  13 module Evoruby
  14
  15     class DomainStructure
  16
  17         def initialize( total_length )
  18             @domains = Hash.new
  19             @total_length = total_length
  20         end
  21
  22         def add_domain( domain, overwrite_if_same_from_to )
  23             key = domain.get_from
  24             if ( @domains.has_key?( key ) )
  25                 prev_domain = @domains[ key ]
  26                 if ( prev_domain.get_to == domain.get_to )
  27                     puts( "WARNING: more than one domain at the same location [" +
  28                         key.to_s + "-" + domain.get_to.to_s + "]: " + prev_domain.get_name + " and " + domain.get_name)
  29                     if ( overwrite_if_same_from_to )
  30                         puts( "         ignored the one with higher E-value [" +
  31                         prev_domain.get_confidence().to_s + " vs " + domain.get_confidence().to_s + "]" )
  32                         if prev_domain.get_confidence() < domain.get_confidence()
  33                             return # keep previous one
  34                         else
  35                             @domains[ key ] = domain
  36                             return
  37                         end
  38                     end
  39                 end
  40
  41                 while ( @domains.has_key?( key ) )
  42                     key = key + 0.0001
  43                 end
  44
  45             end
  46             @domains[ key ] = domain
  47         end
  48
  49         def to_NHX
  50             str = String.new
  51             str << get_total_length.to_s
  52             a = @domains.sort
  53             for d in a
  54                 domain = d[ 1 ]
  55                 str << Evoruby::Constants::DOMAIN_STRUCTURE_NHX_SEPARATOR
  56                 str << domain.get_from.to_s
  57                 str << Evoruby::Constants::DOMAIN_STRUCTURE_NHX_SEPARATOR
  58                 str << domain.get_to.to_s
  59                 str << Evoruby::Constants::DOMAIN_STRUCTURE_NHX_SEPARATOR
  60                 str << domain.get_confidence.to_s
  61                 str << Evoruby::Constants::DOMAIN_STRUCTURE_NHX_SEPARATOR
  62                 str << domain.get_name
  63             end
  64             return str
  65         end
  66
  67         def get_total_length
  68             return @total_length
  69         end
  70
  71     end # class DomainStructure
  72
  73 end # module Evoruby