Bio::Tree::TreeI - A Tree object suitable for lots of things, designed

BioPerl documentation Contained in the BioPerl distribution.

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NAME

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

SYNOPSIS

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  # get a Bio::Tree::TreeI somehow
  # like from a TreeIO
  my $treeio = Bio::TreeIO->new(-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

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

FEEDBACK

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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

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

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Email jason@bioperl.org

CONTRIBUTORS

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Aaron Mackey, amackey@virginia.edu Elia Stupka, elia@fugu-sg.org Sendu Bala, bix@sendu.me.uk

APPENDIX

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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

Methods for associating Tag/Values with a Tree

These methods associate tag/value pairs with a Tree

set_tag_value

 Title   : set_tag_value
 Usage   : $tree->set_tag_value($tag,$value)
           $tree->set_tag_value($tag,@values)
 Function: Sets a tag value(s) to a tree. Replaces old values.
 Returns : number of values stored for this tag
 Args    : $tag   - tag name
           $value - value to store for the tag

add_tag_value

 Title   : add_tag_value
 Usage   : $tree->add_tag_value($tag,$value)
 Function: Adds a tag value to a tree 
 Returns : number of values stored for this tag
 Args    : $tag   - tag name
           $value - value to store for the tag

remove_tag

 Title   : remove_tag
 Usage   : $tree->remove_tag($tag)
 Function: Remove the tag and all values for this tag
 Returns : boolean representing success (0 if tag does not exist)
 Args    : $tag - tagname to remove

remove_all_tags

 Title   : remove_all_tags
 Usage   : $tree->remove_all_tags()
 Function: Removes all tags 
 Returns : None
 Args    : None

get_all_tags

 Title   : get_all_tags
 Usage   : my @tags = $tree->get_all_tags()
 Function: Gets all the tag names for this Tree
 Returns : Array of tagnames
 Args    : None

get_tag_values

 Title   : get_tag_values
 Usage   : my @values = $tree->get_tag_values($tag)
 Function: Gets the values for given tag ($tag)
 Returns : Array of values or empty list if tag does not exist
 Args    : $tag - tag name

has_tag

 Title   : has_tag
 Usage   : $tree->has_tag($tag)
 Function: Boolean test if tag exists in the Tree
 Returns : Boolean
 Args    : $tag - tagname
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Tree::TreeI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::Tree::TreeI;
use strict;

use base qw(Bio::Root::RootI);


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


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


sub number_nodes{
   my ($self) = @_;
   my $root = $self->get_root_node;
   if( defined $root && $root->isa('Bio::Tree::NodeI'))  {
       return ($root->descendent_count + 1);
   }
   return 0;
}


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


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


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


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


sub get_leaf_nodes{
   my ($self) = @_;
   return grep { $_->is_Leaf() } $self->get_nodes(-sortby  => 'none');
}



sub set_tag_value{
    shift->throw_not_implemented();
}


sub add_tag_value{
    shift->throw_not_implemented();
}


sub remove_tag {
    shift->throw_not_implemented();
}


sub remove_all_tags{
    shift->throw_not_implemented();
}


sub get_all_tags {
    shift->throw_not_implemented();
}


sub get_tag_values{
    shift->throw_not_implemented();
}


sub has_tag{
    shift->throw_not_implemented();
}

1;