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SENDU / bioperl-1.5.2_004-RCf / Bio / AlignIO / prodom.pm 

            

              
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# $Id: prodom.pm,v 1.10.4.3 2006/10/02 23:10:12 sendu Exp $
#
# BioPerl module for Bio::AlignIO::prodom
#   based on the Bio::SeqIO::prodom 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
Bio::AlignIO::prodom - prodom sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly.  Use it via the L<Bio::AlignIO> class.
=head1 DESCRIPTION
This object can transform L<Bio::Align::AlignI> objects to and from prodom flat
file databases.
=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 - 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...
package Bio::AlignIO::prodom;
use strict;
use base qw(Bio::AlignIO);
=head2 next_aln
 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream.
 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;
           $add = new Bio::LocatableSeq('-seq'=>$seq,
                               '-id'=>$acc,
                               '-start'=>$start,
                               '-end'=>$end,
                               );
           $aln->add_seq($add);
       }
       elsif ($entry =~ /^CO/) {
           # the consensus line marks the end of the alignment part of the entry
           last;
       }
   }
#  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;
}
=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;