Bio::Taxonomy Tree
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Summary
Bio::Taxonomy::Tree - An Organism Level Implementation of TreeI interface.
Package variables
No package variables defined.
Included modules
Bio::Taxonomy::Taxon
Inherit
Bio::Root::Root Bio::Tree::TreeFunctionsI Bio::Tree::TreeI
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.
Methods
newDescriptionCode
get_nodesDescriptionCode
get_root_nodeDescriptionCode
set_root_nodeDescriptionCode
get_leavesDescriptionCode
make_species_branchDescriptionCode
make_branchDescriptionCode
spliceDescriptionCode
add_speciesDescriptionCode
add_branchDescriptionCode
remove_branchDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Taxonomy::Tree->new();
Function: Builds a new Bio::Taxonomy::Tree object
Returns : Bio::Taxonomy::Tree
Args :
get_nodescodeprevnextTop
 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_nodecodeprevnextTop
 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_nodecodeprevnextTop
 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_leavescodeprevnextTop
 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_branchcodeprevnextTop
 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_branchcodeprevnextTop
 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
splicecodeprevnextTop
 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_speciescodeprevnextTop
 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_branchcodeprevnextTop
 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_branchcodeprevnextTop
 Title   : remove_branch
Usage : $tree->remove_branch($node)
Function: remove a branch up to the next multifurcation
Returns :
Args : Bio::Taxonomy::Taxon object
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  
  my $self = $class->SUPER::new(@args);
  $self->warn("Bio::Taxonomy::Tree is deprecated. Use Bio::Taxon in combination with Bio::Tree::Tree instead.");
  
  $self->{'_rootnode'} = undef;
  $self->{'_maxbranchlen'} = 0;

  my ($root)= $self->_rearrange([qw(ROOT)], @args);
  if( $root ) { $self->set_root_node($root); }
  return $self;
}
get_nodesdescriptionprevnextTop
sub get_nodes {
   my ($self, @args) = @_;
   
   my ($order, $sortby) = $self->_rearrange([qw(ORDER SORTBY)],@args);
   $order ||= 'depth';
   $sortby ||= 'height';

   if ($order =~ m/^b|(breadth)$/oi) {
my $node = $self->get_root_node;
my @children = ($node); for (@children) { push @children, $_->each_Descendent($sortby); } return @children; } if ($order =~ m/^d|(depth)$/oi) {
# this is depth-first search I believe
my $node = $self->get_root_node;
my @children = ($node,$node->get_Descendents($sortby)); return @children; }
}
get_root_nodedescriptionprevnextTop
sub get_root_node {
   my ($self) = @_;
   return $self->{'_rootnode'};
}
set_root_nodedescriptionprevnextTop
sub set_root_node {
   my ($self,$value) = @_;
   if( defined $value ) { 
      if( ! $value->isa('Bio::Taxonomy::Taxon') ) { 
	   $self->warn("Trying to set the root node to $value which is not a Bio::Taxonomy::Taxon");
	   return $self->get_root_node;
      }
      $self->{'_rootnode'} = $value;
   }
   return $self->get_root_node;
}
get_leavesdescriptionprevnextTop
sub get_leaves {
   my ($self) = @_;
   
   my $node = $self->get_root_node;
   my @leaves;
   my @children = ($node);
   for (@children) {
      push @children, $_->each_Descendent();
   }
   for (@children) {
      push @leaves, $_ if $_->is_Leaf;
   }
   return @leaves;
}
make_species_branchdescriptionprevnextTop
sub make_species_branch {
   my ($self,$species,$taxonomy) = @_;
   
   if (! $species->isa('Bio::Species') ) {
      $self->throw("Trying to classify $species which is not a Bio::Species object");
   }
   if (! $taxonomy->isa('Bio::Taxonomy') ) {
      $self->throw("Trying to classify with $taxonomy which is not a Bio::Taxonomy object");
   }

   # this is done to make sure we aren't duplicating a path (let God sort them out)
if (defined $self->get_root_node) { $self->get_root_node->remove_all_Descendents; } my @nodes; # nb taxa in [i][0] and ranks in [i][1]
my @taxa=$taxonomy->classify($species); for (my $i = 0; $i < @taxa; $i++) { $nodes[$i]=Bio::Taxonomy::Taxon->new(-taxon => $taxa[$i][0], -rank => $taxa[$i][1]); } for (my $i = 0; $i < @taxa-1; $i++) { $nodes[$i]->add_Descendent($nodes[$i+1]); } $self->set_root_node($nodes[0]); return @nodes;
}
make_branchdescriptionprevnextTop
sub make_branch {
   my ($self,$node) = @_;

   # this is done to make sure we aren't duplicating a path (let God sort them out)
# note that if you are using a linked set of node which include node
# already in the tree, this will break
$self->get_root_node->remove_all_Descendents; while (defined $node->ancestor) { $self->set_root_node($node); $node=$node->ancestor; }
}
splicedescriptionprevnextTop
sub splice {
   my ($self,$tree) = @_;

   my @nodes;

   my @newleaves = $tree->get_leaves;
   foreach my $leaf (@newleaves) {
      push @nodes,$self->add_branch($leaf);
   }

   return @nodes;
}
add_speciesdescriptionprevnextTop
sub add_species {
   my ($self,$species,$taxonomy) = @_;

   my $branch=Bio::Taxonomy::Tree->new;
   my @nodes=$branch->make_species_branch($species,$taxonomy);

   my ($newleaf)=$branch->get_leaves;
  
   return $self->add_branch($newleaf);
}
add_branchdescriptionprevnextTop
sub add_branch {
   my ($self,$node,$force) = @_;

   my $best_node_level=0;
   my ($best_node,@nodes,$common);

   my @leaves=$self->get_leaves;
   foreach my $leaf (@leaves) {
      $common=$node->recent_common_ancestor($leaf); # the root of the part to add
if (defined $common && ($common->distance_to_root > $best_node_level)) { $best_node_level = $common->distance_to_root; $best_node = $common; } } return unless defined $best_node; push @nodes,($self->get_root_node,$self->get_root_node->get_Descendents); foreach my $node (@nodes) { if ((defined $best_node->id && $best_node->id == $node->id) || ($best_node->rank eq $node->rank && $best_node->taxon eq $node->taxon) && ($best_node->rank ne 'no rank')) { foreach my $descendent ($common->each_Descendent) { $node->add_Descendent($descendent,$force); } } $self->set_root_node($node) if $node->distance_to_root==0; } return ($common->get_Descendents);
}
remove_branchdescriptionprevnextTop
sub remove_branch {
   my ($self,$node) = @_;

   # we can define a branch at any point along it
while (defined $node->ancestor) { last if $node->ancestor->each_Descendent > 1; $node=$node->ancestor; } $node->remove_all_Descendents; # I'm not sure if this is necessary,
# but I don't see that remove_Descendent
# has the side effect of deleting
# descendent nodes of the deletee
$node->ancestor->remove_Descendent($node); } 1;
}
General documentation
EXAMPLESTop
  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";
FEEDBACKTop
See AUTHOR
AUTHOR - Dan KortschakTop
Email kortschak@rsbs.anu.edu.au
CONTRIBUTORSTop
Mainly Jason Stajich
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _