table of contents
Bio::Tree::TreeI(3pm) | User Contributed Perl Documentation | Bio::Tree::TreeI(3pm) |
NAME¶
Bio::Tree::TreeI - A Tree object suitable for lots of things,
designed
originally for Phylogenetic Trees.
SYNOPSIS¶
# 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;
DESCRIPTION¶
This object holds a pointer to the Root of a Tree which is a Bio::Tree::NodeI.
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://github.com/bioperl/bioperl-live/issues
AUTHOR - Jason Stajich¶
Email jason@bioperl.org
CONTRIBUTORS¶
Aaron Mackey, amackey@virginia.edu Elia Stupka, elia@fugu-sg.org Sendu Bala, bix@sendu.me.uk
APPENDIX¶
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
get_nodes¶
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
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
number_nodes¶
Title : number_nodes Usage : my $size = $tree->number_nodes Function: Find the number of nodes in the tree. Returns : int Args : none
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 : integer Args : none
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
id¶
Title : id Usage : my $id = $tree->id(); Function: An id value for the tree Returns : scalar Args :
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)
get_leaf_nodes¶
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
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
2020-10-28 | perl v5.30.3 |