Bio::TreeIO::nhx - TreeIO implementation for parsing

BioPerl documentation Contained in the BioPerl distribution.

Index

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NAME

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Bio::TreeIO::nhx - TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.

SYNOPSIS

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  # do not use this module directly
  use Bio::TreeIO;
  my $treeio = Bio::TreeIO->new(-format => 'nhx', -file => 'tree.dnd');
  my $tree = $treeio->next_tree;

DESCRIPTION

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This module handles parsing and writing of Newick/New Hampshire eXtended (NHX) format.

FEEDBACK

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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 viax the web:

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

AUTHOR - Aaron Mackey

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Email amackey-at-virginia.edu

CONTRIBUTORS

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Email jason-at-bioperl-dot-org

APPENDIX

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

BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::TreeIO::nhx
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Aaron Mackey <amackey@virginia.edu>
#
# Copyright Aaron Mackey
#
# 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::nhx;
use strict;

# Object preamble - inherits from Bio::Root::Root

use Bio::Tree::NodeNHX;
use Bio::Event::EventGeneratorI;
#use XML::Handler::Subs;

use base qw(Bio::TreeIO::newick);

sub _initialize {
  my($self, %args) = @_;
  $args{-nodetype} ||= 'Bio::Tree::NodeNHX';
  $self->SUPER::_initialize(%args);
}

sub _node_as_string {
  my $self = shift;
  my $node = shift;
  my $params = shift;
  
  my $label_stringbuffer = $self->SUPER::_node_as_string($node,$params);

  my @tags = $node->get_all_tags;
  if( scalar(@tags) > 0 ) {
    @tags = sort @tags;
    $label_stringbuffer .= '[' . 
      join(":", "&&NHX",
           map { "$_=" .join(',',$node->get_tag_values($_)) } 
           @tags ) . ']';
  }
  return $label_stringbuffer;
}

1;