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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:

   http://bugzilla.open-bio.org/
 
 

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