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Summary

Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver

Package variables

Included modules

Inherit

Bio::AlignIO

Synopsis

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

Description

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

Methods

Methods description

 Title   : next_aln
 Usage   : $aln = $stream->next_aln
 Function: returns the next alignment in the stream.
 Returns : Bio::Align::AlignI object - returns 0 on end of file
	        or on error
 Args    : 

 Title   : rewind
 Usage   : $alnio->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_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the $aln object into the stream in nexml format
 Returns : 1 for success and 0 for error
 Args    : Bio::Align::AlignI object

Methods code

sub _initialize {

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

}

sub next_aln {

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

}

sub rewind {

    my $self = shift;
    $self->{'_alniter'} = 0;

}

sub doc {

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

}

sub _parse {

	my ($self) = @_;

    $self->{'_parsed'}   = 1;
    $self->{'_alnsiter'} = 0;
    my $fac = Bio::Nexml::Factory->new();
	
	$self->doc(parse(
 	'-file'       => $self->{'_file'},
 	'-format'     => 'nexml',
 	'-as_project' => '1'
 	));

	$self->{'_alns'} = $fac->create_bperl_aln($self);
 	if(@{ $self->{'_alns'} } == 0)
 	{
 		self->debug("no seqs in $self->{_file}");
 	}

}

sub write_aln {

	my ($self, $aln) = @_;
	
    my $fac = Bio::Nexml::Factory->new();
    my $taxa = $fac->create_bphylo_taxa($aln);
	my ($matrix) = $fac->create_bphylo_aln($aln, $taxa);
	$matrix->set_taxa($taxa);
	
	$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

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/

Chase Miller

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 _