Bio::Tree::Node - A Simple Tree Node use Bio::Tree::Node; my $nodeA = new Bio::Tree::Node(); my $nodeL = new Bio::Tree::Node(); my $nodeR = new Bio::Tree::Node(); my $node = new Bio::Tree::Node(); $node->add_Descendent($nodeL); $node->add_Descendent($nodeR); print "node is not a leaf \n" if( $node->is_leaf); Makes a Tree Node suitable for building a Tree.

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/MailList.shtml - 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.bioperl.org/ Email jason@bioperl.org Aaron Mackey amackey@virginia.edu 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::Node(); 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

add_Descendent
Title : add_Descendent Usage : $node->add_Descendant($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" or coderef to be used to sort the order of children nodes.

remove_Descendent
Title : remove_Descendent Usage : $node->remove_Descedent($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 be 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 : value of ancestor 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) Note : id cannot contain the chracters '();:' "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>

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

to_string
Title : to_string Usage : my $str = $node->to_string() Function: For debugging, provide a node as a string Returns : string 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. 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's height in the tree Returns : nothing Args : none

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 = $node->get_tag_value($tag) Function: Gets the values for given tag ($tag) Returns : Array of values or empty list if tag does not exist 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