| Bio::Tree::TreeI(3pm) | User Contributed Perl Documentation | Bio::Tree::TreeI(3pm) |
Bio::Tree::TreeI - A Tree object suitable for lots of things,
designed
originally for Phylogenetic Trees.
# 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;
This object holds a pointer to the Root of a Tree which is a Bio::Tree::NodeI.
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
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.
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
Email jason@bioperl.org
Aaron Mackey, amackey@virginia.edu Elia Stupka, elia@fugu-sg.org Sendu Bala, bix@sendu.me.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
Title : number_nodes Usage : my $size = $tree->number_nodes Function: Find the number of nodes in the tree. Returns : int Args : none
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
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
Title : id Usage : my $id = $tree->id(); Function: An id value for the tree Returns : scalar Args :
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)
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
These methods associate tag/value pairs with a Tree
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
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
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
Title : remove_all_tags Usage : $tree->remove_all_tags() Function: Removes all tags Returns : None Args : None
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
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
Title : has_tag Usage : $tree->has_tag($tag) Function: Boolean test if tag exists in the Tree Returns : Boolean Args : $tag - tagname
| 2021-08-15 | perl v5.32.1 |