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Bio/AlignIO/prodom.pm  view on Meta::CPAN

 Returns : L<Bio::Align::AlignI> object
 Args    : NONE

=cut

sub next_aln {
    my $self = shift;
    my $entry;
    my ($acc, $fake_id, $start, $end, $seq, $add, %names);

    my $aln =  Bio::SimpleAlign->new(-source => 'prodom');

    while( $entry = $self->_readline) {

       if ($entry =~ /^AC\s+(\S+)\s*$/) {         #ps 9/12/00
	   $aln->id( $1 );
       }
       elsif ($entry =~ /^AL\s+(\S+)\|(\S+)\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s*$/){    #ps 9/12/00
	   $acc=$1;
	   $fake_id=$2;  # Accessions have _species appended
	   $start=$3;
	   $end=$4;
	   $seq=$5;

	   $names{'fake_id'} = $fake_id;

	   $add = Bio::LocatableSeq->new('-seq'      => $seq,
					 '-id'       => $acc,
					 '-start'    => $start,
					 '-end'      => $end,
					 '-alphabet' => $self->alphabet,
			       );

	   $aln->add_seq($add);
       }
       elsif ($entry =~ /^CO/) {
	   # the consensus line marks the end of the alignment part of the entry
	   last;
       }
	}
	
   return $aln if $aln->num_sequences;
   return;
}



=head2 write_aln

 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in prodom format  ###Not yet implemented!###
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object


=cut

sub write_aln {
    my ($self,@aln) = @_;
    $self->throw_not_implemented();
}

1;