class Bio::PhyloXML::Tree

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

Attributes

branch_length_unit[RW]
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]
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

new() click to toggle source
Calls superclass method Bio::Tree.new
# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 154
def initialize
  super
  @sequence_relations = []
  @clade_relations = []
  @confidences = []
  @properties = []
  @other = []
end