#
# = lib/evo/io/parser/fasta_parser - FastaParser class
#
# Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
# License::    GNU Lesser General Public License (LGPL)
#
# $Id: fasta_parser.rb,v 1.11 2010/10/08 22:04:17 cmzmasek Exp $
#
# last modified: 05/17/2007

require 'lib/evo/io/parser/msa_parser'
require 'lib/evo/msa/msa'

require 'iconv'

module Evoruby

    class FastaParser < MsaParser

        def initialize
        end

        def parse( path )
            Util.check_file_for_readability( path )
            msa = Msa.new
            current_seq = String.new()
            name        = String.new()
            saw_first_seq = false
            ic = Iconv.new( 'UTF-8//IGNORE', 'UTF-8' )
            File.open( path ) do | file |
                while line = file.gets
                    line = ic.iconv( line )
                    if can_ignore?( line, saw_first_seq )

                    elsif line =~ /^\s*>\s*(.+)/
                        saw_first_seq = true
                        add_seq( name, current_seq, msa )
                        name = $1
                        current_seq = String.new()
                    elsif line =~ /^\s*(.+)/
                        if name.length < 1
                            error_msg = "format error at: " + line
                            raise IOError, error_msg
                        end
                        # was: seq = $1.rstrip
                        seq =  $1.gsub(/\s+/, '')
                        current_seq = current_seq + seq
                    else
                        error_msg = "Unexpected line: " + line
                        raise IOError, error_msg
                    end
                end
            end
            add_seq( name, current_seq, msa )
            return msa
        end

        private

        def add_seq( name, seq, msa )
            if name.length > 0 && seq.length > 0
                msa.add( name, seq )
            end
        end

        def can_ignore?( line, saw_first_seq )
            return ( line !~ /\S/  ||
                 line =~ /^\s*#/ ||
                 line =~ /^\s*%/ ||
                 line =~ /^\s*\/\// ||
                 line =~ /^\s*!!/ ||
                 ( !saw_first_seq && line =~/^\s*[^>]/ ) )
        end

    end # class FastaParser

end # module Evoruby