Mailing Lists¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support¶

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¶

  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¶

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