Bio::Tree::Tree(3pm) User Contributed Perl Documentation Bio::Tree::Tree(3pm)
NAME
Bio::Tree::Tree - An Implementation of TreeI interface.
SYNOPSIS
# 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 $root = $tree->get_root_node;
DESCRIPTION
This object holds handles to Nodes which make up a tree.
IMPLEMENTATION NOTE
This implementation of Bio::Tree::Tree contains Bio::Tree:::NodeI; mainly linked via the root node. As NodeI can potentially contain
circular references (as nodes will need to refer to both parent and child nodes), Bio::Tree::Tree will remove those circular references
when the object is garbage-collected. This has some side effects; primarily, one must keep the Tree in scope or have at least one reference
to it if working with nodes. The fix is to count the references to the nodes and if it is greater than expected retain all of them, but it
requires an additional prereq and thus may not be worth the effort. This only shows up in minor edge cases, though (see Bug #2869).
Example of issue:
# tree is not assigned to a variable, so passes from memory after
# root node is passed
my $root = Bio::TreeIO->new(-format => 'newick', -file => 'foo.txt')->next_tree
->get_root_node;
# gets nothing, as all Node links are broken when Tree is garbage-collected above
my @descendents = $root->get_all_Descendents;
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
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
Email jason@bioperl.org
CONTRIBUTORS
Aaron Mackey amackey@virginia.edu Sendu Bala bix@sendu.me.uk Mark A. Jensen maj@fortinbras.us
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 = Bio::Tree::Tree->new();
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 Bio::Tree::NodeI objects
Returns : array of Bio::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 : real
Args : none
subtree_length
Title : subtree_length
Usage : my $subtree_size = $tree->subtree_length($internal_node)
Function: Returns the sum of the length of all branches in a subtree
under the node. Calculates the size of the whole tree
without an argument (but only if root node is defined)
Returns : real or undef
Args : Bio::Tree::NodeI object, defaults to the root node
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
as_text
Title : as_text
Usage : my $tree_as_string = $tree->as_text($format)
Function: Returns the tree as a string representation in the
desired format (currently 'newick', 'nhx', or
'tabtree')
Returns : scalar string
Args : format type as specified by Bio::TreeIO
Note : This method loads the Bio::TreeIO::$format module
on the fly, and commandeers the _write_tree_Helper
routine therein to create the tree string.
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
clone()
Title : clone
Alias : _clone
Usage : $tree_copy = $tree->clone();
$subtree_copy = $tree->clone($internal_node);
Function: Safe tree clone that doesn't segfault
(of Sendu)
Returns : Bio::Tree::Tree object
Args : [optional] $start_node, Bio::Tree::Node object
perl v5.14.2 2012-03-02 Bio::Tree::Tree(3pm)