Bio::Tree::Node.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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