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

NAME
       Bio::Tree::NodeI	- Interface describing a Tree Node

SYNOPSIS
	   # get a Tree::NodeI somehow
	   # like from a TreeIO
	   use Bio::TreeIO;
	   # read in a clustalw	NJ in phylip/newick format
	   my $treeio =	Bio::TreeIO->new(-format => 'newick', -file => 'file.dnd');

	   my $tree = $treeio->next_tree; # we'll assume it worked for demo purposes
					  # you	might want to test that	it was defined

	   my $rootnode	= $tree->get_root_node;

	   # process just the next generation
	   foreach my $node ( $rootnode->each_Descendent() ) {
	       print "branch len is ", $node->branch_length, "\n";
	   }

	   # process all the children
	   my $example_leaf_node;
	   foreach my $node ( $rootnode->get_all_Descendents() ) {
	       if( $node->is_Leaf ) {
		   print "node is a leaf ... ";
		   # for example use below
		   $example_leaf_node =	$node unless defined $example_leaf_node;
	       }
	       print "branch len is ", $node->branch_length, "\n";
	   }

	   # The ancestor() method points to the parent	of a node
	   # A node can	only have one parent

	   my $parent =	$example_leaf_node->ancestor;

	   # parent won't likely have an description because it	is an internal node
	   # but child will because it is a leaf

	   print "Parent id: ",	$parent->id," child id:	",
		 $example_leaf_node->id, "\n";

DESCRIPTION
       A NodeI is capable of the basic structure of building a tree and
       storing the branch length between nodes.	 The branch length is the
       length of the branch between the	node and its ancestor, thus a root
       node in a Tree will not typically have a	valid branch length.

       Various implementations of NodeI	may extend the basic functions and
       allow storing of	other information (like	attaching a species object or
       full sequences used to build a tree or alternative sequences).  If you
       don't know how to extend	a Bioperl object please	ask, happy to help, we
       would also greatly appreciate contributions with	improvements or
       extensions of the objects back to the Bioperl code base so that others
       don't have to reinvent your ideas.

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@bioperl.org

CONTRIBUTORS
       Aaron Mackey amackey@virginia.edu

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   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

   each_Descendent
	Title	: each_Descendent
	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	: none

   Decorated Interface methods
   get_all_Descendents
	Title	: get_all_Descendents($sortby)
	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	: $sortby [optional] "height", "creation", "alpha", "revalpha",
		  or a coderef to be used to sort the order of children	nodes.

   is_Leaf
	Title	: is_Leaf
	Usage	: if( $node->is_Leaf )
	Function: Get Leaf status
	Returns	: boolean
	Args	: none

   descendent_count
	Title	: descendent_count
	Usage	: my $count = $node->descendent_count;
	Function: Counts the number of descendents a node has
		  (and all of their subnodes)
	Returns	: integer
	Args	: none

   to_string
	Title	: to_string
	Usage	: my $str = $node->to_string()
	Function: For debugging, provide a node	as a string
	Returns	: string
	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

   depth
	Title	: depth
	Usage	: my $len = $node->depth
	Function: Returns the depth of the tree	starting at this
		  node.	 Depth is the distance from this node to the root.
	Returns	: The branch length to the root.
	Args	: none

   Get/Set methods
   branch_length
	Title	: branch_length
	Usage	: $obj->branch_length()
	Function: Get/Set the branch length
	Returns	: value	of branch_length
	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)

   internal_id
	Title	: internal_id
	Usage	: my $internalid = $node->internal_id
	Function: Returns the internal unique id for this Node
	Returns	: unique id
	Args	: none

   description
	Title	: description
	Usage	: $obj->description($newval)
	Function: Get/Set the description string
	Returns	: value	of description
	Args	: newvalue (optional)

   bootstrap
	Title	: bootstrap
	Usage	: $obj->bootstrap($newval)
	Function: Get/Set the bootstrap	value
	Returns	: value	of bootstrap
	Args	: newvalue (optional)

   ancestor
	Title	: ancestor
	Usage	: my $node = $node->ancestor;
	Function: Get/Set the ancestor node pointer for	a Node
	Returns	: Null if this is top level node
	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

   Methods for associating Tag/Values with a Node
       These methods associate tag/value pairs with a Node

   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	: Array	of values or empty list	if tag does not	exist
	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

   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

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

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

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