Provided by: libbio-perl-perl_1.7.2-3_all bug

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