Class Bio::PhyloXML::Tree
In: lib/bio/db/phyloxml/phyloxml_elements.rb
Parent: Bio::Tree

Object to hold one phylogeny element (and its subelements.) Extended version of Bio::Tree.

Methods

new  

Attributes

branch_length_unit  [RW]  String.
clade_relations  [RW]  CladeRelation object. This is used to express a typed relationship between two clades. For example it could be used to describe multiple parents of a clade.
confidences  [RW]  Array of confidence object
date  [RW]  String. Date
description  [RW]  String. Description of tree.
name  [RW]  String. Name of tree (name subelement of phylogeny element).
other  [RW]  Array of Other objects. Used to save additional information from other than PhyloXML namspace.
phylogeny_id  [RW]  Id object.
properties  [RW]  Array of Property object. Allows for typed and referenced properties from external resources to be attached.
rerootable  [RW]  Boolean. Can be used to indicate that the phylogeny is not allowed to be rooted differently (i.e. because it is associated with root dependent data, such as gene duplications).
rooted  [RW]  Boolean. Required element.
sequence_relations  [RW]  SequenceRelation object. This is used to express a typed relationship between two sequences. For example it could be used to describe an orthology.
type  [RW]  String. Indicate the type of phylogeny (i.e. ‘gene tree’).

Public Class methods

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 155
155:    def initialize
156:      super
157:      @sequence_relations = []
158:      @clade_relations = []
159:      @confidences = []
160:      @properties = []
161:      @other = []
162:    end

[Validate]