Bio::Tree Tree
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Tree::Tree - An Implementation of TreeI interface.
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::Tree::TreeI
Inherit
Bio::Root::Root Bio::Tree::TreeI
Synopsis
    # like from a TreeIO
    my $treeio = new Bio::TreeIO(-format => 'newick', -file => 'treefile.dnd');
    my $tree = $treeio->next_tree;
    my @nodes = $tree->get_nodes;
    my $root = $tree->get_root_node;
Description
This object holds handles to Nodes which make up a tree.
Methods
newDescriptionCode
get_nodesDescriptionCode
get_root_nodeDescriptionCode
set_root_nodeDescriptionCode
total_branch_lengthDescriptionCode
Methods description
newcode    nextTop
 Title   : new
 Usage   : my $obj = new Bio::Tree::Tree();
 Function: Builds a new Bio::Tree::Tree object 
 Returns : Bio::Tree::Tree
 Args    :
get_nodescodeprevnextTop
 Title   : get_nodes
 Usage   : my @nodes = $tree->get_nodes()
 Function: Return list of Tree::NodeI objects
 Returns : array of Tree::NodeI 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::Tree::NodeI 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::Tree::NodeI
 Args    : Bio::Tree::NodeI
total_branch_lengthcodeprevnextTop
 Title   : total_branch_length
 Usage   : my $size = $tree->total_branch_length
 Function: Returns the sum of the length of all branches
 Returns : integer
 Args    : none
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  
  my $self = $class->SUPER::new(@args);
  $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) = $self->_rearrange([qw(ORDER)],@args);

   # this is depth search I believe
   my $node = $self->get_root_node;
   my @children = ($node,$node->get_Descendents);
   return @children;
}
get_root_nodedescriptionprevnextTop
sub get_root_node {
   my ($self) = @_;
   return $self->{'_rootnode'};
}
set_root_nodedescriptionprevnextTop
sub set_root_node {
   my ($self,$value) = @_;
   if( defined $value ) { 
       if( ! $value->isa('Bio::Tree::NodeI') ) { 
	   $self->warn("Trying to set the root node to $value which is not a Bio::Tree::NodeI");
	   return $self->get_root_node;
       }
       $self->{'_rootnode'} = $value;
   }
   return $self->get_root_node;
}
total_branch_lengthdescriptionprevnextTop
sub total_branch_length {
   my ($self) = @_;
   my $sum = 0;
   map { $sum += $_->branch_length || 0 } $self->get_root_node->get_Descendents();
   return $sum;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
heightTop
 Title   : height
 Usage   : my $height = $tree->height
 Function: Gets the height of tree - this LOG_2($number_nodes)
 Returns : integer
 Args    : none
number_nodesTop
 Title   : number_nodes
 Usage   : my $size = $tree->number_nodes
 Function: Returns the number of nodes
 Example :
 Returns : 
 Args    :