Bio::Taxonomy::Tree(3)User Contributed Perl DocumentatioBio::Taxonomy::Tree(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::Taxonomy::Tree(3)
