Bio::Tree TreeI
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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 @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.
Methods
get_leaf_nodesDescriptionCode
get_nodesDescriptionCode
get_root_nodeDescriptionCode
heightDescriptionCode
idDescriptionCode
number_nodesDescriptionCode
scoreDescriptionCode
total_branch_lengthDescriptionCode
Methods description
get_leaf_nodescode    nextTop
 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
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
heightcodeprevnextTop
 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
idcodeprevnextTop
 Title   : id
 Usage   : my $id = $tree->id();
 Function: An id value for the tree
 Returns : scalar
 Args    :
number_nodescodeprevnextTop
 Title   : number_nodes
 Usage   : my $size = $tree->number_nodes
 Function: Returns the number of nodes
 Example :
 Returns : 
 Args    :
scorecodeprevnextTop
 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)
total_branch_lengthcodeprevnextTop
 Title   : total_branch_length
 Usage   : my $size = $tree->total_branch_length
 Function: Returns the sum of the length of all branches
 Returns : integer
 Args    : none
Methods code
get_leaf_nodesdescriptionprevnextTop
sub get_leaf_nodes {
   my ($self) = @_;
   return grep { $_->is_Leaf() } $self->get_nodes(-sortby => 'creation');
}


1;
}
get_nodesdescriptionprevnextTop
sub get_nodes {
   my ($self) = @_;
   $self->throw_not_implemented();
}
get_root_nodedescriptionprevnextTop
sub get_root_node {
   my ($self) = @_;
   $self->throw_not_implemented();
}
heightdescriptionprevnextTop
sub height {
   my ($self) = @_;
   my $nodect =  $self->number_nodes;
   return 0 if( ! $nodect ); 
   return log($nodect) / log(2);
}
iddescriptionprevnextTop
sub id {
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}
number_nodesdescriptionprevnextTop
sub number_nodes {
   my ($self) = @_;
   my $root = $self->get_root_node;
   if( defined $root && $root->isa('Bio::Tree::NodeI'))  {
       return $root->descendent_count;
   }
   return 0;
}
scoredescriptionprevnextTop
sub score {
   my ($self,$value) = @_;
   $self->throw_not_implemented();
}
total_branch_lengthdescriptionprevnextTop
sub total_branch_length {
   my ($self) = @_;
   $self->throw_not_implemented();
}
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
the web:
  http://bugzilla.bioperl.org/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
CONTRIBUTORSTop
Aaron Mackey amackey@virginia.edu
Elia Stupka, elia@fugu-sg.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _