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Bio::Tree::Tree.3pm

NAME

Bio::Tree::Tree - An Implementation of TreeI interface.

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.

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 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 _

new

  Title   : new
  Usage   : my $obj = new Bio::Tree::Tree();
  Function: Builds a new Bio::Tree::Tree object 
  Returns : Bio::Tree::Tree
  Args    : -root     => L<Bio::Tree::NodeI> object which is the root
              OR
            -node     => L<Bio::Tree::NodeI> object from which the root will be
                         determined
 
 

            -nodelete => boolean, whether or not to try and cleanup all
                                  the nodes when this this tree goes out
                                  of scope.
            -id       => optional tree ID
            -score    => optional tree score value
 
 

nodelete

  Title   : nodelete
  Usage   : $obj->nodelete($newval)
  Function: Get/Set Boolean whether or not to delete the underlying
            nodes when it goes out of scope.  By default this is false
            meaning trees are cleaned up.
  Returns : boolean
  Args    : on set, new boolean value
 
 

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
 
 

set_root_node

  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_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
 
 

id

  Title   : id
  Usage   : my $id = $tree->id();
  Function: An id value for the tree
  Returns : scalar
  Args    : [optional] new value to set
 
 

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)
 
 

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
 
 

number_nodes

  Title   : number_nodes
  Usage   : my $size = $tree->number_nodes
  Function: Returns the number of nodes in the tree
  Returns : integer
  Args    : none