Class: Bio::PhyloXML::CladeRelation

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

Overview

Description

This is used to express a typed relationship between two clades. For example it could be used to describe multiple parents of a clade.

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#confidenceObject

Confidence object


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1021

def confidence
  @confidence
end

#distanceObject

Float


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1015

def distance
  @distance
end

#id_ref_0Object

String. Id of the referenced parents of a clade.


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1017

def id_ref_0
  @id_ref_0
end

#id_ref_1Object

String. Id of the referenced parents of a clade.


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1017

def id_ref_1
  @id_ref_1
end

#typeObject

String


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1019

def type
  @type
end

Instance Method Details

#to_xmlObject

Converts elements to xml representation. Called by PhyloXML::Writer class.


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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1029

def to_xml
  if @id_ref_0 == nil or @id_ref_1 == nil or @type == nil
    raise "Attributes id_ref_0, id_ref_1, type are required elements by SequenceRelation element."
  else
    cr = LibXML::XML::Node.new('clade_relation')
    Writer.generate_xml(cr, self, [
        [:attr, 'id_ref_0'],
        [:attr, 'id_ref_1'],
        [:attr, 'distance'],
        [:attr, 'type'],
        [:complex, 'confidence', (defined? @confidnece) ? @confidnece : nil]])

    return cr
  end
end