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

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

Public Instance Methods

applies_to=(str) click to toggle source
# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 961
def applies_to=(str)
  unless ['phylogeny','clade','node','annotation','parent_branch','other'].include?(str)
    puts "Warning: #{str} is not in the list of allowed values."
  end
  @applies_to = str
end
datatype=(str) click to toggle source
# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 946
def datatype=(str)
   #@todo add unit test or maybe remove, if assume that xml is valid.
  unless ['xsd:string','xsd:boolean','xsd:decimal','xsd:float','xsd:double',
      'xsd:duration','xsd:dateTime','xsd:time','xsd:date','xsd:gYearMonth',
      'xsd:gYear','xsd:gMonthDay','xsd:gDay','xsd:gMonth','xsd:hexBinary',
      'xsd:base64Binary','xsd:anyURI','xsd:normalizedString','xsd:token',
      'xsd:integer','xsd:nonPositiveInteger','xsd:negativeInteger',
      'xsd:long','xsd:int','xsd:short','xsd:byte','xsd:nonNegativeInteger',
      'xsd:unsignedLong','xsd:unsignedInt','xsd:unsignedShort',
      'xsd:unsignedByte','xsd:positiveInteger'].include?(str)
    raise "Warning: #{str} is not in the list of allowed values."
  end
  @datatype = str
end
to_xml() click to toggle source

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

# File lib/bio/db/phyloxml/phyloxml_elements.rb, line 969
def to_xml
  #@todo  write unit test for this
  raise "ref is an required element of property"  if @ref.nil?
  raise "datatype is an required element of property" if @datatype.nil?
  raise "applies_to is an required element of property" if @applies_to.nil?

  property = LibXML::XML::Node.new('property')
  Writer.generate_xml(property, self, [
      [:attr, 'ref'],
      [:attr, 'unit'],
      [:attr, 'datatype'],
      [:attr, 'applies_to'],
      [:attr, 'id_ref']])

  property << @value if @value != nil
  return property
end