Class: Bio::PhyloXML::ProteinDomain

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

Overview

Description

To represent an individual domain in a domain architecture. The name/unique identifier is described via the ‘id’ attribute.

Instance Attribute Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#confidence ⇒ Object

Float, for example to store E-values 4.7E-14



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 870

def confidence
  @confidence
end

#from ⇒ Object

Integer. Beginning of the domain.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 876

def from
  @from
end

#id ⇒ Object

String



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 873

def id
  @id
end

#to ⇒ Object

Integer. End of the domain.



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 879

def to
  @to
end

#value ⇒ Object

String



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 873

def value
  @value
end

Instance Method Details

#to_xml ⇒ Object

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



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# File 'lib/bio-phyloxml/phyloxml_elements.rb', line 897

def to_xml
  if @from == nil
    raise "from attribute of ProteinDomain class is required."
  elsif @to == nil
    raise "to attribute of ProteinDomain class is required."
  else
    xml_node = LibXML::XML::Node.new('domain', @value)
    xml_node["from"] = @from.to_s
    xml_node["to"] = @to.to_s
    xml_node["id"] = @id if (defined? @id) && @id
    xml_node["confidence"] = @confidence.to_s

    return xml_node
  end

end