Class: Bio::PhyloXML::Tree

Inherits:
Tree
  • Object
show all
Defined in:
lib/bio-phyloxml/phyloxml_elements.rb

Overview

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Tree

Returns a new instance of Tree.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 143

def initialize
  super
  @sequence_relations = []
  @clade_relations = []
  @confidences = []
  @properties = []
  @other = []
end

Instance Attribute Details

#branch_length_unit ⇒ Object

String.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 131

def branch_length_unit
  @branch_length_unit
end

#clade_relations ⇒ Object

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.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 122

def clade_relations
  @clade_relations
end

#confidences ⇒ Object

Array of confidence object



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 128

def confidences
  @confidences
end

#date ⇒ Object

String. Date



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 137

def date
  @date
end

#description ⇒ Object

String. Description of tree.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 110

def description
  @description
end

#name ⇒ Object

String. Name of tree (name subelement of phylogeny element).



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 104

def name
  @name
end

#other ⇒ Object

Array of Other objects. Used to save additional information from other than PhyloXML namspace.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 141

def other
  @other
end

#phylogeny_id ⇒ Object

Id object.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 107

def phylogeny_id
  @phylogeny_id
end

#properties ⇒ Object

Array of Property object. Allows for typed and referenced properties from external resources to be attached.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 119

def properties
  @properties
end

#rerootable ⇒ Object

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).



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 113

def rerootable
  @rerootable
end

#rooted ⇒ Object

Boolean. Required element.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 116

def rooted
  @rooted
end

#sequence_relations ⇒ Object

SequenceRelation object. This is used to express a typed relationship between two sequences. For example it could be used to describe an orthology.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 125

def sequence_relations
  @sequence_relations
end

#type ⇒ Object

String. Indicate the type of phylogeny (i.e. ‘gene tree’).



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 134

def type
  @type
end