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Bio::Tree::TreeI.3pm

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 @leaves = $tree->get_leaf_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/wiki/Mailing_lists  - 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 the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Aaron Mackey, amackey@virginia.edu Elia Stupka, elia@fugu-sg.org Sendu Bala, bix@sendu.me.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: Find the number of nodes in the tree.
  Returns : int
  Args    : none
 
 

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)
            WARNING: this is only true for strict binary trees.  The TreeIO
            system is capable of building non-binary trees, for which this
            method will currently return an incorrect value!!
  Returns : integer
  Args    : none
 
 

id

  Title   : id
  Usage   : my $id = $tree->id();
  Function: An id value for the tree
  Returns : scalar
  Args    :
 
 

score

  Title   : score
  Usage   : $obj->score($newval)
  Function: Sets the associated score with this tree
            This is a generic slot which is probably best used 
            for log likelihood or other overall tree score
  Returns : value of score
  Args    : newvalue (optional)
 
 

get_leaf_nodes

  Title   : get_leaf_nodes
  Usage   : my @leaves = $tree->get_leaf_nodes()
  Function: Returns the leaves (tips) of the tree
  Returns : Array of Bio::Tree::NodeI objects
  Args    : none