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(); $node->add_Descendents($nodeL); $node->add_Descendents($nodeR); print "node is not a leaf \n" if( $node->is_leaf);
Makes a Tree Node suitable for building a Tree.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = new Bio::Tree::Node(); Function: Builds a new Bio::Tree::Node object Returns : Bio::Tree::Node Args : -left => pointer to Left descendent (optional) -right => pointer to Right descenent (optional) -branch_length => branch length [integer] (optional) -bootstrap => value bootstrap value (string) -description => description of node -id => unique id for node
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.
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.
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.
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 cleanedup - so a get_nodes from the Tree object would be a safe thing to do first Returns : nothing Args : none
Title : get_Descendents Usage : my @nodes = $node->get_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
Title : ancestor Usage : $obj->ancestor($newval) Function: Set the Ancestor Returns : value of ancestor Args : newvalue (optional)
Title : branch_length Usage : $obj->branch_length($newval) Function: Example : Returns : value of branch_length Args : newvalue (optional)
Title : bootstrap Usage : $obj->bootstrap($newval) Function: Example : Returns : value of bootstrap Args : newvalue (optional)
Title : description Usage : $obj->description($newval) Function: Example : Returns : value of description Args : newvalue (optional)
Title : id Usage : $obj->id($newval) Function: Example : Returns : value of id Args : newvalue (optional)
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
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)
Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean Args : none
Title : to_string Usage : my $str = $node->to_string() Function: For debugging, provide a node as a string Returns : string Args : none
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
Title : invalidate_height Usage : private helper method Function: Invalidate our cached value of the node'e height in the tree Returns : nothing Args : none
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.