comparison variant_effect_predictor/Bio/Tree/TreeI.pm @ 0:1f6dce3d34e0

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# $Id: TreeI.pm,v 1.11.2.1 2003/09/14 20:21:10 jason Exp $
#
# BioPerl module for Bio::Tree::TreeI
#
# Cared for by Jason Stajich <[e-mail]>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

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

=head1 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;

=head1 DESCRIPTION

This object holds a pointer to the Root of a Tree which is a
Bio::Tree::NodeI.

=head1 FEEDBACK

=head2 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.

  [e-mail]              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

=head2 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.bioperl.org/

=head1 AUTHOR - Jason Stajich

Email [e-mail]

=head1 CONTRIBUTORS

Aaron Mackey [e-mail]
Elia Stupka, [e-mail]

=head1 APPENDIX

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

=cut


# Let the code begin...


package Bio::Tree::TreeI;
use Bio::Tree::NodeI;
use vars qw(@ISA);
use strict;

@ISA = qw(Bio::Tree::NodeI);

=head2 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

=cut

sub get_nodes{
   my ($self) = @_;
   $self->throw_not_implemented();
}

=head2 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

=cut

sub get_root_node{
   my ($self) = @_;
   $self->throw_not_implemented();
}

=head2 number_nodes

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


=cut

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;
}

=head2 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

=cut

sub total_branch_length {
   my ($self) = @_;
   $self->throw_not_implemented();
}

=head2 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

=cut

sub height{
   my ($self) = @_;
   my $nodect =  $self->number_nodes;
   return 0 if( ! $nodect ); 
   return log($nodect) / log(2);
}

=head2 id

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


=cut

sub id{
   my ($self,@args) = @_;
   $self->throw_not_implemented();
}

=head2 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)


=cut

sub score{
   my ($self,$value) = @_;
   $self->throw_not_implemented();
}

=head2 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


=cut

sub get_leaf_nodes{
   my ($self) = @_;
   return grep { $_->is_Leaf() } $self->get_nodes(-sortby => 'creation');
}


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