Bio::Tree::NodeI - Interface describing a Tree Node # get a Tree::NodeI somehow # like from a TreeIO use Bio::TreeIO; # read in a clustalw NJ in phylip/newick format my $treeio = new Bio::TreeIO(-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"; 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 attatching 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.

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/MailList.shtml - About the mailing lists

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.bioperl.org/ Email jason@bioperl.org Aaron Mackey amackey@virginia.edu The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

add_Descendent
Title : add_Descendent Usage : $node->add_Descendant($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" or 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. Returns : The longest length (weighting branches with branch_length) to a leaf 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

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 = $node->get_tag_value($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