--- name: "Bio::Tree::NodeI" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Tree::NodeI" --- # Bio::Tree::NodeI(3pm) Interface describing a Tree Node ## 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 ```