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Bio::Tree::NodeNHX.3pm

NAME

Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags

SYNOPSIS

     use Bio::Tree::NodeNHX;
     my $nodeA = new Bio::Tree::NodeNHX();
     my $nodeL = new Bio::Tree::NodeNHX();
     my $nodeR = new Bio::Tree::NodeNHX();
 
 

     my $node = new Bio::Tree::NodeNHX();
     $node->add_Descendents($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
 
 

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://www.genetics.wustl.edu/eddy/forester/NHX.html
 
 

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 = new Bio::Tree::NodeNHX();
  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