Bio::Tree::NodeNHX(3) User Contributed Perl DocumentationBio::Tree::NodeNHX(3)NAMEBio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags
SYNOPSIS
use Bio::Tree::NodeNHX;
my $nodeA = Bio::Tree::NodeNHX->new();
my $nodeL = Bio::Tree::NodeNHX->new();
my $nodeR = Bio::Tree::NodeNHX->new();
my $node = Bio::Tree::NodeNHX->new();
$node->add_Descendents($nodeL);
$node->add_Descendents($nodeR);
print "node is not a leaf \n" if( $node->is_leaf);
DESCRIPTION
Makes a Tree Node with NHX tags, suitable for building a Tree. See
Bio::Tree::Node for a full list of functionality.
FEEDBACK
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:
http://bugzilla.open-bio.org/
AUTHOR - Aaron Mackey
Email amackey@virginia.edu
CONTRIBUTORS
The NHX (New Hampshire eXtended) format was created by Chris Zmasek,
and is described at:
http://sourceforge.net/projects/forester-atv/
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Tree::NodeNHX->new();
Function: Builds a new Bio::Tree::NodeNHX object
Returns : Bio::Tree::NodeNHX
Args : -left => pointer to Left descendent (optional)
-right => pointer to Right descenent (optional)
-branch_length => branch length [integer] (optional)
-bootstrap => bootstrap value (string)
-description => description of node
-id => unique id for node
-nhx => hashref of NHX tags and values
nhx_tag
Title : nhx_tag
Usage : my $tag = $nodenhx->nhx_tag(%tags);
Function: Set tag-value pairs for NHX nodes
Returns : none
Args : hashref to update the tags/value pairs
OR
with a scalar value update the bootstrap value by default
perl v5.14.1 2011-07-22 Bio::Tree::NodeNHX(3)
