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)."\n";

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

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