Bio::Tree TreeI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Tree::TreeI - A Tree object suitable for lots of things, designed
originally for Phylogenetic Trees.
Package variables
No package variables defined.
Included modules
Bio::Tree::NodeI
strict
Inherit
Bio::Tree::NodeI
Synopsis
  # get a Bio::Tree::TreeI somehow
  # 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 a pointer to the Root of a Tree which is a
Bio::Tree::NodeI.
Methods
get_nodesDescriptionCode
get_root_nodeDescriptionCode
number_nodesDescriptionCode
branch_length
No description
Code
heightDescriptionCode
Methods description
get_nodescode    nextTop
 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
number_nodescodeprevnextTop
 Title   : number_nodes
 Usage   : my $size = $tree->number_nodes
 Function: Returns the number of nodes
 Example :
 Returns : 
 Args    :
heightcodeprevnextTop
 Title   : height
 Usage   : my $height = $tree->height
 Function: Gets the height of tree - this LOG_2($number_nodes)
 Returns : integer
 Args    : none
Methods code
get_nodesdescriptionprevnextTop
sub get_nodes {
   my ($self) = @_;
   $self->_abstractDeath('get_nodes');
}
get_root_nodedescriptionprevnextTop
sub get_root_node {
   my ($self) = @_;
   $self->_abstractDeath('get_root_node');
}
number_nodesdescriptionprevnextTop
sub number_nodes {
   my ($self) = @_;
   my $root = $self->get_root_node;
   if( defined $root && $root->isa('Bio::Tree::NodeI'))  {
       return $root->descendent_count;
   }
   return 0;
}
branch_lengthdescriptionprevnextTop
sub branch_length {
   my ($self) = @_;
   $self->_abstractDeath('branch_length');
}
heightdescriptionprevnextTop
sub height {
   my ($self) = @_;
   my $nodect =  $self->number_nodes;
   return 0 if( ! $nodect ); 
   return log($nodect) / log(2);
}
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
CONTRIBUTORSTop
Elia Stupka, elia@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
total_branch_lengthTop
 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