| Bio::Tree::Node(3pm) | User Contributed Perl Documentation | Bio::Tree::Node(3pm) |
Bio::Tree::Node - A Simple Tree Node
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);
Makes a Tree Node suitable for building a Tree.
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Aaron Mackey, amackey-at-virginia-dot-edu Sendu Bala, bix@sendu.me.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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.
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.
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.
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
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
Title : ancestor Usage : $obj->ancestor($newval) Function: Set the Ancestor Returns : ancestral node Args : newvalue (optional)
Title : branch_length Usage : $obj->branch_length() Function: Get/Set the branch length Returns : value of branch_length Args : newvalue (optional)
Title : bootstrap Usage : $obj->bootstrap($newval) Function: Get/Set the bootstrap value Returns : value of bootstrap Args : newvalue (optional)
Title : description Usage : $obj->description($newval) Function: Get/Set the description string Returns : value of description Args : newvalue (optional)
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.
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
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)
The following methods are implemented by Bio::Node::NodeI decorated interface.
Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean 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 to get to the tip.
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 height in the tree Returns : nothing Args : none
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
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
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
Title : remove_all_tags Usage : $node->remove_all_tags() Function: Removes all tags Returns : None Args : None
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
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
Title : has_tag Usage : $node->has_tag($tag) Function: Boolean test if tag exists in the Node Returns : Boolean Args : $tag - tagname
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
| 2020-10-28 | perl v5.30.3 |