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

Property allows for typed and referenced properties from external resources to be attached to ‘Phylogeny’, ‘Clade’, and ‘Annotation’. The value of a property is its mixed (free text) content. Attribute ‘datatype’ indicates the type of a property and is limited to xsd-datatypes (e.g. ‘xsd:string’, ‘xsd:boolean’, ‘xsd:integer’, ‘xsd:decimal’, ‘xsd:float’, ‘xsd:double’, ‘xsd:date’, ‘xsd:anyURI’). Attribute ‘applies_to’ indicates the item to which a property applies to (e.g. ‘node’ for the parent node of a clade, ‘parent_branch’ for the parent branch of a clade). Attribute ‘id_ref’ allows to attached a property specifically to one element (on the xml-level). Optional attribute ‘unit’ is used to indicate the unit of the property. An example: <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade" unit="METRIC:m"> 200 </property>

Methods

Attributes

applies_to  [R]  String
datatype  [R]  String
id_ref  [RW]  String
ref  [RW]  String
unit  [RW]  String
value  [RW]  String

Public Instance methods

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 948
948:       def applies_to=(str)
949:         unless ['phylogeny','clade','node','annotation','parent_branch','other'].include?(str)
950:           puts "Warning: #{str} is not in the list of allowed values."
951:         end
952:         @applies_to = str
953:       end

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 933
933:       def datatype=(str)
934:          #@todo add unit test or maybe remove, if assume that xml is valid.
935:         unless ['xsd:string','xsd:boolean','xsd:decimal','xsd:float','xsd:double',
936:             'xsd:duration','xsd:dateTime','xsd:time','xsd:date','xsd:gYearMonth',
937:             'xsd:gYear','xsd:gMonthDay','xsd:gDay','xsd:gMonth','xsd:hexBinary',
938:             'xsd:base64Binary','xsd:anyURI','xsd:normalizedString','xsd:token',
939:             'xsd:integer','xsd:nonPositiveInteger','xsd:negativeInteger',
940:             'xsd:long','xsd:int','xsd:short','xsd:byte','xsd:nonNegativeInteger',
941:             'xsd:unsignedLong','xsd:unsignedInt','xsd:unsignedShort',
942:             'xsd:unsignedByte','xsd:positiveInteger'].include?(str)
943:           raise "Warning: #{str} is not in the list of allowed values."
944:         end
945:         @datatype = str
946:       end

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

[Source]

     # File lib/bio/db/phyloxml/phyloxml_elements.rb, line 956
956:       def to_xml
957:         #@todo  write unit test for this
958:         raise "ref is an required element of property"  if @ref.nil?
959:         raise "datatype is an required element of property" if @datatype.nil?
960:         raise "applies_to is an required element of property" if @applies_to.nil?
961: 
962:         property = LibXML::XML::Node.new('property')
963:         Writer.generate_xml(property, self, [
964:             [:attr, 'ref'],
965:             [:attr, 'unit'],
966:             [:attr, 'datatype'],
967:             [:attr, 'applies_to'],
968:             [:attr, 'id_ref']])
969: 
970:         property << @value if @value != nil
971:         return property
972:       end

[Validate]