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# $Id: maf.pm,v 1.10.4.1 2006/10/02 23:10:12 sendu Exp $
#
# BioPerl module for Bio::AlignIO::maf
#
# Copyright Allen Day
#
HideShow 62 lines of Pod
=head1 NAME
Bio::AlignIO::maf - Multipla Alignment Format sequence input stream
=head1 SYNOPSIS
 Do not use this module directly.  Use it via the Bio::AlignIO class.
 use Bio::AlignIO;
 my $alignio = Bio::AlignIO->new(-fh => \*STDIN, -format => 'maf');
 while(my $aln = $alignio->next_aln()){
   my $match_line = $aln->match_line;
   print $aln, "\n";
   print $aln->length, "\n";
   print $aln->no_residues, "\n";
   print $aln->is_flush, "\n";
   print $aln->no_sequences, "\n";
   $aln->splice_by_seq_pos(1);
   print $aln->consensus_string(60), "\n";
   print $aln->get_seq_by_pos(1)->seq, "\n";
   print $aln->match_line(), "\n";
   print "\n";
 }
=head1 DESCRIPTION
This class constructs Bio::SimpleAlign objects from an MAF-format
multiple alignment file.
Writing in MAF format is currently unimplemented.
Spec of MAF format is here:
  http://hgwdev-sugnet.cse.ucsc.edu/cgi-bin/hgGateway?org=human
=head1 FEEDBACK
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:
  http://bugzilla.open-bio.org/
=head1 AUTHORS - Allen Day
Email: allenday@ucla.edu
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::AlignIO::maf;
use vars qw($seen_header);
use strict;
use Bio::SimpleAlign;
$seen_header = 0;
use base qw(Bio::AlignIO);
HideShow 13 lines of Pod
=head2 new
 Title   : new
 Usage   : my $alignio = new Bio::AlignIO(-format => 'maf'
                                          -file   => '>file',
                                          -idlength => 10,
                                          -idlinebreak => 1);
 Function: Initialize a new L<Bio::AlignIO::maf> reader
 Returns : L<Bio::AlignIO> object
 Args    :
=cut
sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);
  1;
}
HideShow 12 lines of Pod
=head2 next_aln
 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
           Throws an exception if trying to read in PHYLIP
           sequential format.
 Returns : L<Bio::SimpleAlign> object
 Args    : 
=cut
sub next_aln {
    my $self = shift;
    if(!$seen_header){
        my $line = $self->_readline;
        $self->throw("This doesn't look like a MAF file.  First line should start with ##maf, but it was: ".$line)
            unless $line =~ /^##maf/;
        $seen_header = 1;
    }
    my $aln =  Bio::SimpleAlign->new(-source => 'maf');
    my($aline, @slines);
    while(my $line = $self->_readline()){
        $aline = $line if $line =~ /^a/;
        push @slines, $line if $line =~ /^s /;
        last if $line !~ /\S/;
    }
    return unless $aline;
    my($kvs) = $aline =~ /^a\s+(.+)$/;
    my @kvs  = split /\s+/, $kvs if $kvs;
    my %kv;
    foreach my $kv (@kvs){
        my($k,$v) = $kv =~ /(.+)=(.+)/;
        $kv{$k} = $v;
    }
    $aln->score($kv{score});
    foreach my $sline (@slines){
        my($s,$src,$start,$size,$strand,$srcsize,$text) =
            split /\s+/, $sline;
        # adjust coordinates to be one-based inclusive
        $start = $start + 1;
        my $seq = new Bio::LocatableSeq('-seq'    => $text,
                                        '-id'     => $src,
                                        '-start'  => $start,
                                        '-end'    => $start + $size - 1,
                                        '-strand' => $strand,
                                        );
        $aln->add_seq($seq);
    }
    return $aln;
}
sub write_aln {
  shift->throw_not_implemented
}
1;