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.\" ========================================================================
.\"
.IX Title "Bio::Taxonomy::Tree 3pm"
.TH Bio::Taxonomy::Tree 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Taxonomy::Tree \- An Organism Level Implementation of TreeI interface.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&    # 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 => \*(Aqnewick\*(Aq, \-file => \*(Aqtreefile.dnd\*(Aq);
\&    my $tree = $treeio\->next_tree;
\&    my @nodes = $tree\->get_nodes;
\&    my $root = $tree\->get_root_node;
\&    my @leaves = $tree\->get_leaves;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object holds handles to Taxonomic Nodes which make up a tree.
.SH "EXAMPLES"
.IX Header "EXAMPLES"
.Vb 2
\&  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 = (\*(Aqsuperkingdom\*(Aq,\*(Aqkingdom\*(Aq,\*(Aqphylum\*(Aq,\*(Aqsubphylum\*(Aq,
\&               \*(Aqno rank 1\*(Aq,\*(Aqno rank 2\*(Aq,\*(Aqclass\*(Aq,\*(Aqno rank 3\*(Aq,\*(Aqorder\*(Aq,
\&               \*(Aqsuborder\*(Aq,\*(Aqfamily\*(Aq,\*(Aqgenus\*(Aq,\*(Aqspecies\*(Aq);
\&
\&  my $taxonomy=Bio::Taxonomy\->new(\-ranks => \e@ranks,
\&                                 \-method => \*(Aqtrust\*(Aq,
\&                                 \-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)."\en";
\&
\&  @taxa=();
\&  $tree1\->remove_branch($homo_sapiens);
\&  foreach my $leaf ($tree1\->get_leaves) {
\&     push @taxa,$leaf\->taxon;
\&  }
\&  print join(", ",@taxa)."\en";
.Ve
.SH "FEEDBACK"
.IX Header "FEEDBACK"
See \s-1AUTHOR\s0
.SH "AUTHOR \- Dan Kortschak"
.IX Header "AUTHOR - Dan Kortschak"
Email kortschak@rsbs.anu.edu.au
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Mainly Jason Stajich
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : my $obj = Bio::Taxonomy::Tree\->new();
\& Function: Builds a new Bio::Taxonomy::Tree object 
\& Returns : Bio::Taxonomy::Tree
\& Args    :
.Ve
.SS "get_nodes"
.IX Subsection "get_nodes"
.Vb 6
\& 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 => \*(Aqb|breadth\*(Aq first order or \*(Aqd|depth\*(Aq first order
.Ve
.SS "get_root_node"
.IX Subsection "get_root_node"
.Vb 6
\& 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
.Ve
.SS "set_root_node"
.IX Subsection "set_root_node"
.Vb 5
\& 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
.Ve
.SS "get_leaves"
.IX Subsection "get_leaves"
.Vb 5
\& 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    :
.Ve
.SS "make_species_branch"
.IX Subsection "make_species_branch"
.Vb 5
\& 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
.Ve
.SS "make_branch"
.IX Subsection "make_branch"
.Vb 5
\& 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
.Ve
.SS "splice"
.IX Subsection "splice"
.Vb 5
\& 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
.Ve
.SS "add_species"
.IX Subsection "add_species"
.Vb 5
\& 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
.Ve
.SS "add_branch"
.IX Subsection "add_branch"
.Vb 7
\& 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)
.Ve
.SS "remove_branch"
.IX Subsection "remove_branch"
.Vb 5
\& Title   : remove_branch
\& Usage   : $tree\->remove_branch($node)
\& Function: remove a branch up to the next multifurcation
\& Returns :
\& Args    : Bio::Taxonomy::Taxon object
.Ve