#
# BioPerl module for Bio::AlignIO::largemultifasta

#	based on the Bio::SeqIO::largefasta module
#       by Ewan Birney <birney@sanger.ac.uk>
#       and Lincoln Stein  <lstein@cshl.org>
#
#       and the SimpleAlign.pm module of Ewan Birney
#
# Copyright Albert Vilella
#
# You may distribute this module under the same terms as perl itself
# _history
# January 20, 2004
# POD documentation - main docs before the code

=head1 NAME

Bio::AlignIO::largemultifasta - Largemultifasta MSA 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::SimpleAlign> objects to and from
largemultifasta flat file databases.  This is for the fasta sequence
format NOT FastA analysis program.  To process the pairwise alignments
from a FastA (FastX, FastN, FastP, tFastA, etc) use the Bio::SearchIO
module.

Reimplementation of Bio::AlignIO::fasta modules so that creates
temporary files instead of keeping the whole sequences in memory.

=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 - Albert Vilella, Heikki Lehvaslaiho

Email: avilella@ebi.ac.uk, heikki@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::largemultifasta;
use vars qw(@ISA);
use strict;

use Bio::AlignIO;
use Bio::SeqIO;
use Bio::SimpleAlign;
use Bio::Seq::LargeLocatableSeq;
use Bio::Seq::SeqFactory;

@ISA = qw(Bio::AlignIO Bio::SeqIO Bio::SimpleAlign);


sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(new Bio::Seq::SeqFactory
			      (-verbose => $self->verbose(), 
			       -type => 'Bio::Seq::LargeLocatableSeq'));
  }
}

=head2 next_seq

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream while taking care
           of the length
 Returns : Bio::Seq object
 Args    : NONE

=cut

sub next_seq {
    my ($self) = @_;
    my $largeseq = $self->sequence_factory->create();
    my ($id,$fulldesc,$entry);
    my $count = 0;
    my $seen = 0;
    while( defined ($entry = $self->_readline) ) {
	if( $seen == 1 && $entry =~ /^\s*>/ ) {
	    $self->_pushback($entry);
	    return $largeseq;
	}
	if ( ($entry eq '>')  ) { $seen = 1; next; }
	elsif( $entry =~ /\s*>(.+?)$/ ) {
	    $seen = 1;
	    ($id,$fulldesc) = ($1 =~ /^\s*(\S+)\s*(.*)$/)
		or $self->warn("Can't parse fasta header");
	    $largeseq->display_id($id);
	    $largeseq->primary_id($id);
	    $largeseq->desc($fulldesc);
	} else {
	    $entry =~ s/\s+//g;
	    $largeseq->add_sequence_as_string($entry);
	}
	(++$count % 1000 == 0 && $self->verbose() > 0) && print "line $count\n";
    }
    if( ! $seen ) { return undef; }
    return $largeseq;
}


=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 - returns 0 on end of file
	    or on error
 Args    : NONE

=cut

sub next_aln {
    my $self = shift;
    my $largeseq;
    my $aln =  Bio::SimpleAlign->new();
    while (defined ($largeseq = $self->next_seq) ) {
        $aln->add_seq($largeseq);
        $self->debug("sequence readed\n");
    }

    my $alnlen = $aln->length;
    foreach my $largeseq ( $aln->each_seq ) {
	if( $largeseq->length < $alnlen ) {
	    my ($diff) = ($alnlen - $largeseq->length);
	    $largeseq->seq("-" x $diff);
	}
    }

    return $aln;

}

=head2 write_aln

 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in largemultifasta format
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object


=cut

sub write_aln {
    my ($self,@aln) = @_;
    my ($seq,$desc,$rseq,$name,$count,$length,$seqsub);

    foreach my $aln (@aln) {
	if( ! $aln || ! $aln->isa('Bio::Align::AlignI')  ) { 
	    $self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
	    next;
	}
	foreach $rseq ( $aln->each_seq() ) {
	    $name = $aln->displayname($rseq->get_nse());
	    $seq  = $rseq->seq();
	    $desc = $rseq->description || '';
	    $self->_print (">$name $desc\n") or return ;	
	    $count =0;
	    $length = length($seq);
	    while( ($count * 60 ) < $length ) {
		$seqsub = substr($seq,$count*60,60);
		$self->_print ("$seqsub\n") or return ;
		$count++;
	    }
	}
    }
    $self->flush if $self->_flush_on_write && defined $self->_fh;
    return 1;
}

1;
