Class: Bio::PhyloXML::SequenceRelation

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 sequences. For example it could be used to describe an orthology (in which case attribute 'type' is 'orthology').

Instance Attribute Summary (collapse)

Instance Method Summary (collapse)

Instance Attribute Details

- (Object) distance

Float



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1112

def distance
  @distance
end

- (Object) id_ref_0

String



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1110

def id_ref_0
  @id_ref_0
end

- (Object) id_ref_1

String



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1110

def id_ref_1
  @id_ref_1
end

- (Object) type

String



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1110

def type
  @type
end

Instance Method Details

- (Object) to_xml

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



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1133

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
    sr = LibXML::XML::Node.new('sequence_relation')
    sr['id_ref_0'] = @id_ref_0
    sr['id_ref_1'] = @id_ref_1
    sr['distance'] = @distance.to_s if @distance != nil
    sr['type'] = @type
    return sr
  end
end