#
# BioPerl module for FAST::Bio::AlignIO::mase
# based on the FAST::Bio::SeqIO::mase module
# by Ewan Birney <birney@ebi.ac.uk>
# and Lincoln Stein <lstein@cshl.org>
#
# and the SimpleAlign.pm module of Ewan Birney
#
# Copyright Peter Schattner
#
# You may distribute this module under the same terms as perl itself
# _history
# September 5, 2000
# POD documentation - main docs before the code
=head1 NAME
FAST::Bio::AlignIO::mase - mase sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the L<FAST::Bio::AlignIO> class.
=head1 DESCRIPTION
This object can transform L<FAST::Bio::Align::AlignI> objects to and from mase flat
file databases.
=head1 FEEDBACK
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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:
=head1 AUTHORS - Peter Schattner
Email: schattner@alum.mit.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...
use strict;
=head2 next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
Returns : L<FAST::Bio::Align::AlignI> object
Args : NONE
=cut
sub next_aln {
my $self = shift;
my $entry;
my $name;
my $start;
my $end;
my $seq;
my $add;
my $count = 0;
my $seq_residues;
my $aln = FAST::Bio::SimpleAlign->new(-source => 'mase');
while( $entry = $self->_readline) {
$entry =~ /^;/ && next;
if( $entry =~ /^(\S+)\/(\d+)-(\d+)/ ) {
$name = $1;
$start = $2;
$end = $3;
} else {
$entry =~ s/\s//g;
$name = $entry;
$end = -1;
}
$seq = "";
while( $entry = $self->_readline) {
$entry =~ /^;/ && last;
$entry =~ s/[^A-Za-z\.\-]//g;
$seq .= $entry;
}
if( $end == -1) {
$start = 1;
$seq_residues = $seq;
$seq_residues =~ s/\W//g;
$end = length($seq_residues);
}
$add = FAST::Bio::LocatableSeq->new('-seq' => $seq,
'-display_id' => $name,
'-start' => $start,
'-end' => $end,
'-alphabet' => $self->alphabet,
);
$aln->add_seq($add);
# If $end <= 0, we have either reached the end of
# file in <> or we have encountered some other error
#
if ($end <= 0) { undef $aln;}
}
return $aln if $aln->num_sequences;
return;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in mase format ###Not yet implemented!###
Returns : 1 for success and 0 for error
Args : L<FAST::Bio::Align::AlignI> object
=cut
sub write_aln {
my ($self,@aln) = @_;
$self->throw_not_implemented();
}
1;