Reference

Bio::Tree::Node(3pm)

A Simple Tree Node

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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, [email protected]

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

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