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

#distance ⇒ Object

Float



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1132

def distance
  @distance
end

#id_ref_0 ⇒ Object

String



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1124

def id_ref_0
  @id_ref_0
end

#id_ref_1 ⇒ Object

String



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1124

def id_ref_1
  @id_ref_1
end

#type ⇒ Object

String. Allowed values: “orthology”, “one_to_one_orthology”, “super_orthology”, “paralogy”, “ultra_paralogy”, “xenology”, “unknown”, “other”



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1129

def type
  @type
end

Instance Method Details

#to_xml ⇒ Object

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



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# File 'lib/bio/db/phyloxml/phyloxml_elements.rb', line 1156

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 (defined? @distance) && @distance
    sr['type'] = @type
    return sr
  end
end