Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::Tree::Node - A Simple Tree Node

SYNOPSIS

           use Bio::Tree::Node;
           my $nodeA = Bio::Tree::Node->new();
           my $nodeL = Bio::Tree::Node->new();
           my $nodeR = Bio::Tree::Node->new();

           my $node = Bio::Tree::Node->new();
           $node->add_Descendent($nodeL);
           $node->add_Descendent($nodeR);

           print "node is not a leaf \n" if( $node->is_leaf);

DESCRIPTION

       Makes a Tree Node suitable for building a Tree.

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 - Jason Stajich

       Email jason-at-bioperl-dot-org

CONTRIBUTORS

       Aaron Mackey, amackey-at-virginia-dot-edu Sendu Bala,   bix@sendu.me.uk

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::Node->new();
        Function: Builds a new Bio::Tree::Node object
        Returns : Bio::Tree::Node
        Args    : -descendents   => arrayref of descendents (they will be
                                    updated s.t. their ancestor point is this
                                    node)
                  -branch_length => branch length [integer] (optional)
                  -bootstrap     => value   bootstrap value (string)
                  -description   => description of node
                  -id            => human readable id for node

   create_node_on_branch
        Title   : create_node_on_branch
        Usage   : $node->create_node_on_branch($at_length)
        Function: Create a node on the ancestral branch of the calling
                  object.
        Example :
        Returns : the created node
        Args    : -POSITION=>$absolute_branch_length_from_caller (default)
                  -FRACTION=>$fraction_of_branch_length_from_caller
                  -ANNOT=>{ -id => "the id", -desc => "the description" }
                  -FORCE, set to allow nodes with zero branch lengths

   add_Descendent
        Title   : add_Descendent
        Usage   : $node->add_Descendent($node);
        Function: Adds a descendent to a node
        Returns : number of current descendents for this node
        Args    : Bio::Node::NodeI
                  boolean flag, true if you want to ignore the fact that you are
                  adding a second node with the same unique id (typically memory
                  location reference in this implementation).  default is false and
                  will throw an error if you try and overwrite an existing node.

   each_Descendent
        Title   : each_Descendent($sortby)
        Usage   : my @nodes = $node->each_Descendent;
        Function: all the descendents for this Node (but not their descendents
                                                     i.e. not a recursive fetchall)
        Returns : Array of Bio::Tree::NodeI objects
        Args    : $sortby [optional] "height", "creation", "alpha", "revalpha",
                  or coderef to be used to sort the order of children nodes.

   remove_Descendent
        Title   : remove_Descendent
        Usage   : $node->remove_Descendent($node_foo);
        Function: Removes a specific node from being a Descendent of this node
        Returns : nothing
        Args    : An array of Bio::Node::NodeI objects which have been previously
                  passed to the add_Descendent call of this object.

   remove_all_Descendents
        Title   : remove_all_Descendents
        Usage   : $node->remove_All_Descendents()
        Function: Cleanup the node's reference to descendents and reset
                  their ancestor pointers to undef, if you don't have a reference
                  to these objects after this call they will be cleaned up - so
                  a get_nodes from the Tree object would be a safe thing to do first
        Returns : nothing
        Args    : none

   get_all_Descendents
        Title   : get_all_Descendents
        Usage   : my @nodes = $node->get_all_Descendents;
        Function: Recursively fetch all the nodes and their descendents
                  *NOTE* This is different from each_Descendent
        Returns : Array or Bio::Tree::NodeI objects
        Args    : none

   ancestor
        Title   : ancestor
        Usage   : $obj->ancestor($newval)
        Function: Set the Ancestor
        Returns : ancestral node
        Args    : newvalue (optional)

   branch_length
        Title   : branch_length
        Usage   : $obj->branch_length()
        Function: Get/Set the branch length
        Returns : value of branch_length
        Args    : newvalue (optional)

   bootstrap
        Title   : bootstrap
        Usage   : $obj->bootstrap($newval)
        Function: Get/Set the bootstrap value
        Returns : value of bootstrap
        Args    : newvalue (optional)

   description
        Title   : description
        Usage   : $obj->description($newval)
        Function: Get/Set the description string
        Returns : value of description
        Args    : newvalue (optional)

   id
        Title   : id
        Usage   : $obj->id($newval)
        Function: The human readable identifier for the node
        Returns : value of human readable id
        Args    : newvalue (optional)

       "A name can be any string of printable characters except blanks, colons, semicolons,
       parentheses, and square brackets. Because you may want to include a blank in a name, it is
       assumed that an underscore character ("_") stands for a blank; any of these in a name will
       be converted to a blank when it is read in."

       from <http://evolution.genetics.washington.edu/phylip/newicktree.html>

       Also note that these objects now support spaces, ();: because we can automatically quote
       the strings if they contain these characters.  The id_output method does this for you so
       use the id() method to get the raw string while id_output to get the pre-escaped string.

   Helper Functions
   id_output
        Title   : id_output
        Usage   : my $id = $node->id_output;
        Function: Return an id suitable for output in format like newick
                  so that if it contains spaces or ():; characters it is properly
                  quoted
        Returns : $id string if $node->id has a value
        Args    : none

   internal_id
        Title   : internal_id
        Usage   : my $internalid = $node->internal_id
        Function: Returns the internal unique id for this Node
                  (a monotonically increasing number for this in-memory implementation
                   but could be a database determined unique id in other
                   implementations)
        Returns : unique id
        Args    : none

   _creation_id
        Title   : _creation_id
        Usage   : $obj->_creation_id($newval)
        Function: a private method signifying the internal creation order
        Returns : value of _creation_id
        Args    : newvalue (optional)

   Bio::Node::NodeI decorated interface implemented
       The following methods are implemented by Bio::Node::NodeI decorated interface.

   is_Leaf
        Title   : is_Leaf
        Usage   : if( $node->is_Leaf )
        Function: Get Leaf status
        Returns : boolean
        Args    : none

   height
        Title   : height
        Usage   : my $len = $node->height
        Function: Returns the height of the tree starting at this
                  node.  Height is the maximum branchlength to get to the tip.
        Returns : The longest length (weighting branches with branch_length) to a leaf
        Args    : none

   invalidate_height
        Title   : invalidate_height
        Usage   : private helper method
        Function: Invalidate our cached value of the node height in the tree
        Returns : nothing
        Args    : none

   set_tag_value
        Title   : set_tag_value
        Usage   : $node->set_tag_value($tag,$value)
                  $node->set_tag_value($tag,@values)
        Function: Sets a tag value(s) to a node. Replaces old values.
        Returns : number of values stored for this tag
        Args    : $tag   - tag name
                  $value - value to store for the tag

   add_tag_value
        Title   : add_tag_value
        Usage   : $node->add_tag_value($tag,$value)
        Function: Adds a tag value to a node
        Returns : number of values stored for this tag
        Args    : $tag   - tag name
                  $value - value to store for the tag

   remove_tag
        Title   : remove_tag
        Usage   : $node->remove_tag($tag)
        Function: Remove the tag and all values for this tag
        Returns : boolean representing success (0 if tag does not exist)
        Args    : $tag - tagname to remove

   remove_all_tags
        Title   : remove_all_tags
        Usage   : $node->remove_all_tags()
        Function: Removes all tags
        Returns : None
        Args    : None

   get_all_tags
        Title   : get_all_tags
        Usage   : my @tags = $node->get_all_tags()
        Function: Gets all the tag names for this Node
        Returns : Array of tagnames
        Args    : None

   get_tag_values
        Title   : get_tag_values
        Usage   : my @values = $node->get_tag_values($tag)
        Function: Gets the values for given tag ($tag)
        Returns : In array context returns an array of values
                  or an empty list if tag does not exist.
                  In scalar context returns the first value or undef.
        Args    : $tag - tag name

   has_tag
        Title   : has_tag
        Usage   : $node->has_tag($tag)
        Function: Boolean test if tag exists in the Node
        Returns : Boolean
        Args    : $tag - tagname

   reverse_edge
        Title   : reverse_edge
        Usage   : $node->reverse_edge(child);
        Function: makes child be a parent of node
        Requires: child must be a direct descendent of node
        Returns : 1 on success, 0 on failure
        Args    : Bio::Tree::NodeI that is in the tree