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Summary

Bio::TreeIO::nexml - A TreeIO driver module for parsing NeXML tree files

Package variables

Included modules

Inherit

Bio::TreeIO

Synopsis

  use Bio::TreeIO;
  my $in = Bio::TreeIO->new(-file => 'data.nexml' -format => 'Nexml');
  while( my $tree = $in->next_tree ) {
  }

Description

This is a driver module for parsing tree data in a NeXML format. For
more information on NeXML, visit http://www.nexml.org.

Methods

Methods description

 Title   : next_tree
 Usage   : my $tree = $treeio->next_tree
 Function: Gets the next tree in the stream
 Returns : Bio::Tree::TreeI
 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   : rewind
 Usage   : $treeio->rewind
 Function: Resets the stream
 Returns : none
 Args    : none

 Title   : write_tree
 Usage   : $treeio->write_tree($tree);
 Function: Writes a tree onto the stream
 Returns : none
 Args    : Bio::Tree::TreeI

Methods code

sub _initialize {

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

}

sub next_tree {

    my ($self) = @_;
    unless ( $self->{'_parsed'} ) {
        $self->_parse;
    }
    return $self->{'_trees'}->[ $self->{'_treeiter'}++ ];

}

sub doc {

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

}

sub rewind {

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

}

sub _parse {

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

}

sub write_tree {

	my ($self, $bp_tree) = @_;
	
	my $fac = Bio::Nexml::Factory->new();
	my $taxa = $fac->create_bphylo_taxa($bp_tree);
	my ($tree) = $fac->create_bphylo_tree($bp_tree, $taxa);
	
	my $forest = Bio::Phylo::Factory->create_forest();
	$self->doc(Bio::Phylo::Factory->create_project());
	
	$forest->set_taxa($taxa);
	$forest->insert($tree);
	
	$self->doc->insert($forest);
	
	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
the Bioperl mailing list. 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
of the bugs and their resolution. Bug reports can be submitted via
the web:

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

Email chmille4@gmail.com

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