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       @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 phylip sequential format"
  43         raise StandardError, error_msg, caller
  44       end
  45
  46
  47       Util.check_file_for_writability( path )
  48
  49       f = File.open( path, "a" )
  50
  51       f.print( msa.get_number_of_seqs().to_s() )
  52       f.print( " " )
  53       f.print( msa.get_length().to_s() )
  54       f.print( Evoruby::Constants::LINE_DELIMITER )
  55       for i in 0 ... msa.get_number_of_seqs()
  56         seq_obj = msa.get_sequence( i )
  57         name = seq_obj.get_name()
  58         seq  = seq_obj.get_sequence_as_string()
  59         name = name.gsub( /\s+$/, '')
  60         name = name.gsub( /\s+/, '_')
  61         name = Util.normalize_seq_name( name, @max_name_length, @ex_if_name_too_long )
  62         f.print( name )
  63         f.print( " " )
  64         if ( @clean )
  65           seq = Util.clean_seq_str( seq )
  66         end
  67         f.print( seq )
  68         f.print( Evoruby::Constants::LINE_DELIMITER )
  69       end
  70       f.close()
  71     end
  72
  73   end # class PhylipSequentialWriter
  74
  75 end # module Evoruby