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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

Top

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

SYNOPSIS

Top

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

DESCRIPTION

Top

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

FEEDBACK

Top

Mailing Lists

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

Support

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.

Reporting Bugs

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/

AUTHOR - Chase Miller

Top

Email chmille4@gmail.com

APPENDIX

Top

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

next_tree

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

doc

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

rewind

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

write_tree

 Title   : write_tree
 Usage   : $treeio->write_tree($tree);
 Function: Writes a tree onto the stream
 Returns : none
 Args    : L<Bio::Tree::TreeI>
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::TreeIO::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

# POD documentation - main docs before the code


# Let the code begin...

package Bio::TreeIO::nexml;
use strict;

use lib '../..';
use Bio::Event::EventGeneratorI;
use IO::String;
use Bio::Nexml::Factory;
use Bio::Phylo::IO qw (parse unparse);


use base qw(Bio::TreeIO);


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;