NAME¶
Bio::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:
https://github.com/bioperl/bioperl-live/issues
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