class Bio::PhyloXML::Property
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>
Attributes
String
String
String
String
String
String
Public Instance Methods
# File lib/bio-phyloxml/phyloxml_elements.rb 950 def applies_to=(str) 951 unless ['phylogeny','clade','node','annotation','parent_branch','other'].include?(str) 952 puts "Warning: #{str} is not in the list of allowed values." 953 end 954 @applies_to = str 955 end
# File lib/bio-phyloxml/phyloxml_elements.rb 935 def datatype=(str) 936 #@todo add unit test or maybe remove, if assume that xml is valid. 937 unless ['xsd:string','xsd:boolean','xsd:decimal','xsd:float','xsd:double', 938 'xsd:duration','xsd:dateTime','xsd:time','xsd:date','xsd:gYearMonth', 939 'xsd:gYear','xsd:gMonthDay','xsd:gDay','xsd:gMonth','xsd:hexBinary', 940 'xsd:base64Binary','xsd:anyURI','xsd:normalizedString','xsd:token', 941 'xsd:integer','xsd:nonPositiveInteger','xsd:negativeInteger', 942 'xsd:long','xsd:int','xsd:short','xsd:byte','xsd:nonNegativeInteger', 943 'xsd:unsignedLong','xsd:unsignedInt','xsd:unsignedShort', 944 'xsd:unsignedByte','xsd:positiveInteger'].include?(str) 945 raise "Warning: #{str} is not in the list of allowed values." 946 end 947 @datatype = str 948 end
Converts elements to xml representation. Called by PhyloXML::Writer
class.
# File lib/bio-phyloxml/phyloxml_elements.rb 958 def to_xml 959 #@todo write unit test for this 960 raise "ref is an required element of property" if @ref.nil? 961 raise "datatype is an required element of property" if @datatype.nil? 962 raise "applies_to is an required element of property" if @applies_to.nil? 963 964 property = LibXML::XML::Node.new('property') 965 Writer.generate_xml(property, self, [ 966 [:attr, 'ref'], 967 [:attr, 'unit'], 968 [:attr, 'datatype'], 969 [:attr, 'applies_to'], 970 [:attr, 'id_ref']]) 971 972 property << @value if @value != nil 973 return property 974 end