Class Bio::PhyloXML::ProteinDomain
In: lib/bio/db/phyloxml/phyloxml_elements.rb
Parent: Object

Description

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

Methods

confidence=   from=   to=   to_xml  

Attributes

confidence  [RW]  Float, for example to store E-values 4.7E-14
from  [R]  Integer. Beginning of the domain.
id  [RW]  String
to  [R]  Integer. End of the domain.
value  [RW]  String

Public Instance methods

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 890
890:       def confidence=(str)
891:         @confidence = str.to_f
892:       end

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 882
882:       def from=(str)
883:         @from = str.to_i
884:       end

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 886
886:       def to=(str)
887:         @to = str.to_i
888:       end

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

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 895
895:       def to_xml
896:         if @from == nil
897:           raise "from attribute of ProteinDomain class is required."
898:         elsif @to == nil
899:           raise "to attribute of ProteinDomain class is required."
900:         else
901:           xml_node = LibXML::XML::Node.new('domain', @value)
902:           xml_node["from"] = @from.to_s
903:           xml_node["to"] = @to.to_s
904:           xml_node["id"] = @id if @id != nil
905:           xml_node["confidence"] = @confidence.to_s
906: 
907:           return xml_node
908:         end
909: 
910:       end

[Validate]