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Bio::Tree::Node(3)    User Contributed Perl Documentation   Bio::Tree::Node(3)

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:

	 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,   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

perl v5.32.0			  2019-12-07		    Bio::Tree::Node(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | CONTRIBUTORS | APPENDIX

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Tree::Node&sektion=3&manpath=FreeBSD+12.2-RELEASE+and+Ports>

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