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

   1 #
   2 # = lib/evo/io/writer/phylip_sequential_writer.rb - PhylipSequentialWriter class
   3 #
   4 # Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
   5 # License::    GNU Lesser General Public License (LGPL)
   6 #
   7 # $Id: phylip_sequential_writer.rb,v 1.4 2008/09/03 00:31:38 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 PhylipSequentialWriter < MsaWriter
  16
  17         MAX_NAME_LENGTH_DEFAULT = 10
  18
  19         def initialize()
  20             @max_name_length = MAX_NAME_LENGTH_DEFAULT
  21             @clean           = false
  22         end
  23
  24         def set_max_name_length( length = MAX_NAME_LENGTH_DEFAULT )
  25             if length < 1
  26                 length = MAX_NAME_LENGTH_DEFAULT
  27             end
  28             @max_name_length = length
  29         end
  30
  31         def clean( clean = true )
  32             @clean = clean
  33         end
  34
  35         def write( msa, path )
  36             if ( !msa.is_aligned() )
  37                 error_msg = "attempt to write unaligned msa in phylip sequential format"
  38                 raise StandardError, error_msg, caller
  39             end
  40
  41
  42             Util.check_file_for_writability( path )
  43
  44             f = File.open( path, "a" )
  45
  46             f.print( msa.get_number_of_seqs().to_s() )
  47             f.print( " " )
  48             f.print( msa.get_length().to_s() )
  49             f.print( Evoruby::Constants::LINE_DELIMITER )
  50             for i in 0 ... msa.get_number_of_seqs()
  51                 seq_obj = msa.get_sequence( i )
  52                 name = seq_obj.get_name()
  53                 seq  = seq_obj.get_sequence_as_string()
  54                 name = name.gsub( /\s+$/, '')
  55                 name = name.gsub( /\s+/, '_')
  56                 name = Util.normalize_seq_name( name, @max_name_length )
  57                 f.print( name )
  58                 f.print( " " )
  59                 if ( @clean )
  60                     seq = Util.clean_seq_str( seq )
  61                 end
  62                 f.print( seq )
  63                 f.print( Evoruby::Constants::LINE_DELIMITER )
  64             end
  65             f.close()
  66         end
  67
  68     end # class PhylipSequentialWriter
  69
  70 end # module Evoruby