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://github.com/bioperl/bioperl-live/issues

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
           sortby => [optional] "height", "creation", "alpha", "revalpha",
           or coderef to be used to sort the order of children nodes. See L<Bio::Tree::Node> for details

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, e.g.: 'newick', 'nhx' or 'tabtree' (the default)
 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
 Returns : Bio::Tree::Tree object
 Args    : [optional] $start_node, Bio::Tree::Node object