Bio::SeqIO::nexml - NeXML sequence input/output stream

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 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : L<Bio::Seq> object
 Args    : NONE

 Title   : rewind
 Usage   : $seqio->rewind
 Function: Resets the stream
 Returns : none
 Args    : none

 Title   : doc
 Usage   : $treeio->doc
 Function: Returns the biophylo nexml document object
 Returns : Bio::Phylo::Project
 Args    : none or Bio::Phylo::Project object

 Title   : write_seq
 Usage   : $stream->write_seq(@seq)
 Function: Writes the $seq object into the stream
 Returns : 1 for success and 0 for error
 Args    : Array of 1 or more L<Bio::PrimarySeqI> objects

# BioPerl module for Bio::SeqIO::nexml
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Chase Miller <chmille4@gmail.com>
#
# Copyright Chase Miller
#
# You may distribute this module under the same terms as perl itself
# _history
# May, 2009  Largely written by Chase Miller

# POD documentation - main docs before the code

# Let the code begin...

package Bio::SeqIO::nexml;

use strict;

use lib '../..';
use Bio::Seq;
use Bio::Seq::SeqFactory;
use Bio::Nexml::Factory;
use Bio::Phylo::IO qw (parse unparse);

use base qw(Bio::SeqIO);

sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args); 
  $self->{_doc} = undef; 
}

sub next_seq {
	my ($self) = @_;
    unless ( $self->{'_parsed'} ) {
    	#use a parse function to load all the sequence objects found in the nexml file at once
        $self->_parse;
    }
    return $self->{'_seqs'}->[ $self->{'_seqiter'}++ ];
}

sub rewind {
    my $self = shift;
    $self->{'_seqiter'} = 0;
}

sub doc {
	my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_doc'} = $value;
	}
	return $obj->{'_doc'};
}

sub _parse {
	my ($self) = @_;
	my $fac = Bio::Nexml::Factory->new();
	
    $self->{'_parsed'}   = 1;
    $self->{'_seqiter'} = 0;
	
	$self->doc(Bio::Phylo::IO->parse(
 	'-file'       => $self->{'_file'},
 	'-format'     => 'nexml',
 	'-as_project' => '1'
 	));
 
 	
 		
 	$self->{'_seqs'} = $fac->create_bperl_seq($self);
 		
 	
 	unless(@{ $self->{'_seqs'} } == 0)
 	{
# 		self->debug("no seqs in $self->{_file}");
 	}
 }
 
 
 

sub write_seq {
	
	my ($self, $bp_seq) = @_;
	
	my $fac = Bio::Nexml::Factory->new();
	my $taxa = $fac->create_bphylo_taxa($bp_seq);
	my ($seq) = $fac->create_bphylo_seq($bp_seq, $taxa);
	
	my $matrix = Bio::Phylo::Factory->create_matrix('-type' => $seq->get_type());
	$matrix->insert($seq);
	$matrix->set_taxa($taxa);
	
	#set matrix label
	my $feat = ($bp_seq->get_SeqFeatures())[0];
	$matrix->set_name($feat->get_tag_values('matrix_label'));
	
	$self->doc(Bio::Phylo::Factory->create_project());
	
	$self->doc->insert($matrix);
	
	my $ret = $self->_print($self->doc->to_xml());
	$self->flush;
	return $ret
}


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