Ewan Birney

NAME

Bio::Tree::TreeI - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.

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.

FEEDBACK

Mailing Lists

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 Bugs

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 Stajich

Email jason@bioperl.org

CONTRIBUTORS

Elia Stupka, elia@ebi.ac.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

get_nodes

 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_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::Tree::NodeI object
 Args    : none

number_nodes

 Title   : number_nodes
 Usage   : my $size = $tree->number_nodes
 Function: Returns the number of nodes
 Example :
 Returns : 
 Args    :

total_branch_length

 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

height

 Title   : height
 Usage   : my $height = $tree->height
 Function: Gets the height of tree - this LOG_2($number_nodes)
 Returns : integer
 Args    : none