forester/ruby/evoruby/lib/evo/io/writer/nexus_writer.rb

   1 #
   2 # = lib/evo/io/writer/nexus_writer.rb - NexusWriter class
   3 #
   4 # Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
   5 # License::    GNU Lesser General Public License (LGPL)
   6 #
   7 # $Id: nexus_writer.rb,v 1.4 2009/11/04 01:50:59 cmzmasek Exp $
   8 #
   9 # last modified: 05/16/2007
  10
  11 require 'lib/evo/io/writer/msa_writer'
  12
  13 module Evoruby
  14
  15     class NexusWriter < MsaWriter
  16
  17         MAX_NAME_LENGTH_DEFAULT = 10
  18
  19         def initialize()
  20             @max_name_length     = MAX_NAME_LENGTH_DEFAULT
  21             @clean               = false
  22             @ex_if_name_too_long = false
  23         end
  24
  25         def set_max_name_length( length = MAX_NAME_LENGTH_DEFAULT )
  26             if length < 1
  27                 length = MAX_NAME_LENGTH_DEFAULT
  28             end
  29             @max_name_length = length
  30         end
  31
  32         def clean( clean = true )
  33             @clean = clean
  34         end
  35
  36         def set_exception_if_name_too_long( exception_if_name_too_long )
  37           @ex_if_name_too_long = exception_if_name_too_long
  38         end
  39
  40         def write( msa, path )
  41             if ( !msa.is_aligned() )
  42                 error_msg = "attempt to write unaligned msa in nexus format"
  43                 raise StandardError, error_msg, caller
  44             end
  45
  46             Util.check_file_for_writability( path )
  47
  48             f = File.open( path, "a" )
  49
  50             f.print( "Begin Data;" )
  51             f.print( Evoruby::Constants::LINE_DELIMITER )
  52             f.print( "   Dimensions NTax=" )
  53             f.print( msa.get_number_of_seqs().to_s() )
  54             f.print( " NChar=" )
  55             f.print( msa.get_length().to_s() )
  56             f.print( ";" )
  57             f.print( Evoruby::Constants::LINE_DELIMITER )
  58             f.print( "   Format DataType=Protein Interleave=No gap=-;" )
  59             f.print( Evoruby::Constants::LINE_DELIMITER )
  60             f.print( "   Matrix" )
  61             f.print( Evoruby::Constants::LINE_DELIMITER )
  62             for i in 0 ... msa.get_number_of_seqs()
  63                 seq_obj = msa.get_sequence( i )
  64                 name = seq_obj.get_name()
  65                 seq  = seq_obj.get_sequence_as_string()
  66                 name = name.gsub( /\s+$/, '')
  67                 name = name.gsub( /\s+/, '_')
  68                 name = Util.normalize_seq_name( name, @max_name_length, @ex_if_name_too_long )
  69                 f.print( "      " )
  70                 f.print( name )
  71                 f.print( " " )
  72                 if ( @clean )
  73                     seq = Util.clean_seq_str( seq )
  74                 end
  75                 f.print( seq )
  76                 f.print( Evoruby::Constants::LINE_DELIMITER )
  77             end
  78             f.print( "   ;" )
  79             f.print( Evoruby::Constants::LINE_DELIMITER )
  80             f.print( "End;" )
  81             f.print( Evoruby::Constants::LINE_DELIMITER )
  82             f.close()
  83         end
  84
  85     end # class NexusWriter
  86
  87 end # module Evoruby