Bio::TreeIO nhx
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Summary
Bio::TreeIO::nhx - TreeIO implementation for parsing
Newick/New Hampshire eXtendend (NHX) format.
Package variables
No package variables defined.
Included modules
Bio::Event::EventGeneratorI
Bio::Tree::NodeNHX
Inherit
Bio::TreeIO::newick
Synopsis
  # do not use this module directly
use Bio::TreeIO;
my $treeio = Bio::TreeIO->new(-format => 'nhx', -file => 'tree.dnd');
my $tree = $treeio->next_tree;
Description
This module handles parsing and writing of Newick/New Hampshire eXtended (NHX) format.
Methods
_initialize
No description
Code
_node_as_string
No description
Code
Methods description
None available.
Methods code
_initializedescriptionprevnextTop
sub _initialize {
  my($self, %args) = @_;
  $args{-nodetype} ||= 'Bio::Tree::NodeNHX';
  $self->SUPER::_initialize(%args);
}
_node_as_stringdescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 MackeyTop
Email amackey-at-virginia.edu
CONTRIBUTORSTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _