diff variant_effect_predictor/Bio/Tree/TreeI.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tree/TreeI.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,218 @@
+# $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');
+}
+
+
+1;