Bio::Taxonomy::Tree(3pm)				User Contributed Perl Documentation				  Bio::Taxonomy::Tree(3pm)

NAME

       Bio::Taxonomy::Tree - An Organism Level Implementation of TreeI interface.

SYNOPSIS

	   # NB: This module is deprecated. Use Bio::Taxon in combination with
	   # Bio::Tree::Tree instead

	   # like from a TreeIO
	   my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'treefile.dnd');
	   my $tree = $treeio->next_tree;
	   my @nodes = $tree->get_nodes;
	   my $root = $tree->get_root_node;
	   my @leaves = $tree->get_leaves;

DESCRIPTION

       This object holds handles to Taxonomic Nodes which make up a tree.

EXAMPLES

	 use Bio::Species;
	 use Bio::Taxonomy::Tree;

	 my $human=Bio::Species->new();
	 my $chimp=Bio::Species->new();
	 my $bonobo=Bio::Species->new();

	 $human->classification(qw( sapiens Homo Hominidae
				    Catarrhini Primates Eutheria
				    Mammalia Euteleostomi Vertebrata
				    Craniata Chordata
				    Metazoa Eukaryota ));
	 $chimp->classification(qw( troglodytes Pan Hominidae
				    Catarrhini Primates Eutheria
				    Mammalia Euteleostomi Vertebrata
				    Craniata Chordata
				    Metazoa Eukaryota ));
	 $bonobo->classification(qw( paniscus Pan Hominidae
				     Catarrhini Primates Eutheria
				     Mammalia Euteleostomi Vertebrata
				     Craniata Chordata
				     Metazoa Eukaryota ));

	 # ranks passed to $taxonomy match ranks of species
	 my @ranks = ('superkingdom','kingdom','phylum','subphylum',
		      'no rank 1','no rank 2','class','no rank 3','order',
		      'suborder','family','genus','species');

	 my $taxonomy=Bio::Taxonomy->new(-ranks => @ranks,
					-method => 'trust',
					-order => -1);

	 my $tree1=Bio::Taxonomy::Tree->new();
	 my $tree2=Bio::Taxonomy::Tree->new();

	 $tree1->make_species_branch($human,$taxonomy);
	 $tree2->make_species_branch($chimp,$taxonomy);

	 my ($homo_sapiens)=$tree1->get_leaves;

	 $tree1->splice($tree2);

	 $tree1->add_species($bonobo,$taxonomy);

	 my @taxa;
	 foreach my $leaf ($tree1->get_leaves) {
	    push @taxa,$leaf->taxon;
	 }
	 print join(", ",@taxa)."
";

	 @taxa=();
	 $tree1->remove_branch($homo_sapiens);
	 foreach my $leaf ($tree1->get_leaves) {
	    push @taxa,$leaf->taxon;
	 }
	 print join(", ",@taxa)."
";

FEEDBACK

       See AUTHOR

AUTHOR - Dan Kortschak
       Email kortschak@rsbs.anu.edu.au

CONTRIBUTORS

       Mainly Jason Stajich

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::Taxonomy::Tree->new();
	Function: Builds a new Bio::Taxonomy::Tree object
	Returns : Bio::Taxonomy::Tree
	Args	:

   get_nodes
	Title	: get_nodes
	Usage	: my @nodes = $tree->get_nodes()
	Function: Return list of Bio::Taxonomy::Taxon objects
	Returns : array of Bio::Taxonomy::Taxon objects
	Args	: (named values) hash with one value
		  order => 'b|breadth' first order or 'd|depth' first order

   get_root_node
	Title	: get_root_node
	Usage	: my $node = $tree->get_root_node();
	Function: Get the Top Node in the tree, in this implementation
		  Trees only have one top node.
	Returns : Bio::Taxonomy::Taxon object
	Args	: none

   set_root_node
	Title	: set_root_node
	Usage	: $tree->set_root_node($node)
	Function: Set the Root Node for the Tree
	Returns : Bio::Taxonomy::Taxon
	Args	: Bio::Taxonomy::Taxon

   get_leaves
	Title	: get_leaves
	Usage	: my @nodes = $tree->get_leaves()
	Function: Return list of Bio::Taxonomy::Taxon objects
	Returns : array of Bio::Taxonomy::Taxon objects
	Args	:

   make_species_branch
	Title	: make_species_branch
	Usage	: @nodes = $tree->make_species_branch($species,$taxonomy)
	Function: Return list of Bio::Taxonomy::Taxon objects based on a Bio::Species object
	Returns : array of Bio::Taxonomy::Taxon objects
	Args	: Bio::Species and Bio::Taxonomy objects

   make_branch
	Title	: make_branch
	Usage	: $tree->make_branch($node)
	Function: Make a linear Bio::Taxonomy::Tree object from a leafish node
	Returns :
	Args	: Bio::Taxonomy::Taxon object

   splice
	Title	: splice
	Usage	: @nodes = $tree->splice($tree)
	Function: Return a of Bio::Taxonomy::Tree object that is a fusion of two
	Returns : array of Bio::Taxonomy::Taxon added to tree
	Args	: Bio::Taxonomy::Tree object

   add_species
	Title	: add_species
	Usage	: @nodes = $tree->add_species($species,$taxonomy)
	Function: Return a of Bio::Taxonomy::Tree object with a new species added
	Returns : array of Bio::Taxonomy::Taxon added to tree
	Args	: Bio::Species object

   add_branch
	Title	: add_branch
	Usage	: $tree->add_branch($node,boolean)
	Function: Return a of Bio::Taxonomy::Tree object with a new branch added
	Returns : array of Bio::Taxonomy::Taxon objects of the resulting tree
	Args	: Bio::Taxonomy::Taxon object
		  boolean flag to force overwrite of descendent
		    (see Bio::Node->add_Descendent)

   remove_branch
	Title	: remove_branch
	Usage	: $tree->remove_branch($node)
	Function: remove a branch up to the next multifurcation
	Returns :
	Args	: Bio::Taxonomy::Taxon object

perl v5.14.2							    2012-03-02						  Bio::Taxonomy::Tree(3pm)