# $Id: stockholm.pm,v 1.11 2003/03/14 09:38:26 heikki Exp $
#
# BioPerl module for Bio::AlignIO::stockholm

#	based on the Bio::SeqIO::stockholm module
#       by Ewan Birney <birney@sanger.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::stockholm - stockholm 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
stockholm 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 email
or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

=head1 AUTHORS - Peter Schattner

Email: schattner@alum.mit.edu

=head1 CONTRIBUTORS

Andreas Kahari, ak@ebi.ac.uk

=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::stockholm;
use vars qw(@ISA);
use strict;

use Bio::AlignIO;

@ISA = 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 ($start,$end,%align,$name,$seqname,$seq,$count,
	%hash,%c2name, %accession, $no);

    # in stockholm format, every non-blank line that does not start
    # with '#=' is an alignment segment; the '#=' lines are mark up lines.
    # Of particular interest are the '#=GF <name/st-ed> AC <accession>'
    # lines, which give accession numbers for each segment

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

    while( defined($entry = $self->_readline) ) {
        $entry !~ /\w+/ && next;

	if ($entry =~ /^#\s*STOCKHOLM\s+/) {
	    last;
	}
	else {
	    $self->throw("Not Stockholm format: Expecting \"# STOCKHOLM 1.0\"; Found \"$_\"");
	}
    }
#
#    Next section is same as for selex format
#
    while( defined($entry = $self->_readline) ) {
	# Double slash (//) signals end of file.  The flat Pfam-A data from
	# ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Pfam-A.full.gz consists
	# of several concatenated Stockholm-formatted files.  The following
	# line makes it possible to parse it without this module trying to
	# read the whole file into memory.  Andreas Kähäri 10/3/2003.
	last if $entry =~ /^\/\//;

	# Extra bonus:  Get the name of the alignment.
	# Andreas Kähäri 10/3/2003.
	if ($entry =~ /^#=GF\s+AC\s+(\S+)/) {
	    $aln->id($1);
	    next;
	}

	$entry =~ /^#=GS\s+(\S+)\s+AC\s+(\S+)/ && do {
	    $accession{ $1 } = $2;
	    next;
	};
	$entry =~ /^([A-Za-z.-]+)$/ && ( $align{$name} .= $1 ) && next; 
	$entry !~ /^([^#]\S+)\s+([A-Za-z.-]+)\s*/ && next;

	
	$name = $1;
	$seq = $2;

	if( ! defined $align{$name}  ) {
	    $count++;
	    $c2name{$count} = $name;
	}
	$align{$name} .= $seq;
    }

    # ok... now we can make the sequences

     foreach $no ( sort { $a <=> $b } keys %c2name ) {
	$name = $c2name{$no};

	if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) {
	    $seqname = $1;
	    $start = $2;
	    $end = $3;
	} else {
	    $seqname=$name;
	    $start = 1;
	    $end = length($align{$name});
	}
	$seq = new Bio::LocatableSeq('-seq'=>$align{$name},
			    '-id'=>$seqname,
			    '-start'=>$start,
			    '-end'=>$end,
			    '-type'=>'aligned',
				     '-accession_number' => $accession{$name},

			    );

       $aln->add_seq($seq);

   }

#  If $end <= 0, we have either reached the end of
#  file in <fh> or we have encountered some other error
#
   if ($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 stockholm 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("Sorry: stockholm-format output, not yet implemented! /n");
}

1;
