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Summary

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

Package variables

Included modules

Inherit

Bio::SeqIO

Synopsis

Do not use this module directly. Use it via the Bio::SeqIO class.

Description

This object can transform Bio::Seq objects to and from NeXML format.
For more information on the NeXML standard, visit http://www.nexml.org.

Methods

Methods description

 Title   : next_seq
 Usage   : $seq = $stream->next_seq()
 Function: returns the next sequence in the stream
 Returns : 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 Bio::PrimarySeqI objects

Methods code

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
}


1;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
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.

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:

  https://redmine.open-bio.org/projects/bioperl/

Email: chmille4@gmail.com

Mark Jensen, maj@fortinbras.us
Rutger Vos, rutgeraldo@gmail.com

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _