How to use

NamedProperty

method

in

uk.ac.ncl.intbio.core.datatree.Datatree

private static void formatModelProperties(Set<URI> models, List<NamedProperty<QName>> list)
{
  for(URI m : models)
  {
    list.add(NamedProperty(Sbol2Terms.ModuleDefinition.hasModels, m));
  }
}

private static void formatSequence(URI sequence, List<NamedProperty<QName>> list)
{
  list.add(NamedProperty(Sbol2Terms.ComponentDefinition.hasSequence, sequence));
}

private static void formatWasInformedByProperties(Set<URI> wasInformedBys, List<NamedProperty<QName>> list)
{
  for(URI wib : wasInformedBys)
  {
    list.add(NamedProperty(Sbol2Terms.Activity.wasInformedBy, wib));
  }
}

/**
 * Create a value property from a Boolean value.
 *
 * @param name    the property name
 * @param value   the property value
 * @param <N>     the property name type
 * @return  a new NamedProperty with the supplied name and value
 */
public static <N> NamedProperty<N> NamedProperty(final N name, final Boolean value) {
 return NamedProperty(name, Datatree.<N>Literal(value));
}

/**
 * Create a value property from an int value.
 *
 * @param name    the property name
 * @param value   the property value
 * @param <N>     the property name type
 * @return  a new NamedProperty with the supplied name and value
 */
public static <N> NamedProperty<N> NamedProperty(final N name, final int value) {
 return NamedProperty(name, Datatree.<N>Literal(value));
}

/**
 * Create a value property from a Double value.
 *
 * @param name    the property name
 * @param value   the property value
 * @param <N>     the property name type
 * @return  a new NamedProperty with the supplied name and value
 */
public static <N> NamedProperty<N> NamedProperty(final N name, final Double value) {
 return NamedProperty(name, Datatree.<N>Literal(value));
}

/**
 * Create a value property from a string value.
 *
 * @param name    the property name
 * @param value   the property value
 * @param <N>     the property name type
 * @return  a new NamedProperty with the supplied name and value
 */
public static <N> NamedProperty<N> NamedProperty(final N name, final String value) {
 return NamedProperty(name, Datatree.<N>Literal(value));
}

/**
 * Create a value property from a URI value.
 *
 * @param name    the property name
 * @param value   the property value
 * @param <N>     the property name type
 * @return  a new NamedProperty with the supplied name and value
 */
public static <N> NamedProperty<N> NamedProperty(final N name, final URI value) {
 return NamedProperty(name, Datatree.<N>Literal(value));
}

private static void formatModels (Set<Model> models, List<TopLevelDocument<QName>> topLevelDoc)
{
  for(Model m : models)
  {
    List<NamedProperty<QName>> list = new ArrayList<>();
    formatCommonTopLevelData(list,m);
    list.add(NamedProperty(Sbol2Terms.Model.source, m.getSource()));
    list.add(NamedProperty(Sbol2Terms.Model.language, m.getLanguage()));
    list.add(NamedProperty(Sbol2Terms.Model.framework, m.getFramework()));
    topLevelDoc.add(TopLevelDocument(Sbol2Terms.Model.Model, m.getIdentity(), NamedProperties(list)));
  }
}

private static void formatSequenceConstraints(Set<SequenceConstraint> sequenceConstraint,
    List<NamedProperty<QName>> properties)
{
  for(SequenceConstraint s : sequenceConstraint)
  {
    List<NamedProperty<QName>> list = new ArrayList<>();
    formatCommonIdentifiedData(list, s);
    list.add(NamedProperty(Sbol2Terms.SequenceConstraint.restriction, s.getRestrictionURI()));
    list.add(NamedProperty(Sbol2Terms.SequenceConstraint.hasSubject, s.getSubjectURI()));
    list.add(NamedProperty(Sbol2Terms.SequenceConstraint.hasObject, s.getObjectURI()));
    properties.add(NamedProperty(Sbol2Terms.ComponentDefinition.hasSequenceConstraints,
        NestedDocument( Sbol2Terms.SequenceConstraint.SequenceConstraint,
            s.getIdentity(), NamedProperties(list))));
  }
}

private static void formatCommonTopLevelData (List<NamedProperty<QName>> list, TopLevel t)
{
  formatCommonIdentifiedData(list,t);
  for(URI attachment : t.getAttachmentURIs()) {
    list.add(NamedProperty(Sbol2Terms.TopLevel.hasAttachment, attachment));
  }
}

private static List<NestedDocument<QName>> getMapsTo(Set<MapsTo> references)
{
  List<NestedDocument<QName>> nestedDoc = new ArrayList<>();
  for(MapsTo m : references)
  {
    List<NamedProperty<QName>> list = new ArrayList<>();
    formatCommonIdentifiedData(list, m);
    list.add(NamedProperty(Sbol2Terms.MapsTo.refinement, RefinementType.convertToURI(m.getRefinement())));
    list.add(NamedProperty(Sbol2Terms.MapsTo.hasRemote, m.getRemoteURI()));
    list.add(NamedProperty(Sbol2Terms.MapsTo.hasLocal, m.getLocalURI()));
    nestedDoc.add(NestedDocument(Sbol2Terms.MapsTo.MapsTo, m.getIdentity(), NamedProperties(list)));
  }
  return nestedDoc;
}

private static void formatSequences (Set<Sequence> sequences, List<TopLevelDocument<QName>> topLevelDoc)
{
  for(Sequence s : sequences)
  {
    List<NamedProperty<QName>> list = new ArrayList<>();
    formatCommonTopLevelData(list, s);
    list.add(NamedProperty(Sbol2Terms.Sequence.elements, s.getElements()));
    list.add(NamedProperty(Sbol2Terms.Sequence.encoding, s.getEncoding()));
    topLevelDoc.add(TopLevelDocument(Sbol2Terms.Sequence.Sequence, s.getIdentity(), NamedProperties(list)));
  }
}

private static List<NestedDocument<QName>> formatParticipations(Set<Participation> participations)
{
  List<NestedDocument<QName>> nestedDoc = new ArrayList<>();
  for(Participation p : participations)
  {
    List<NamedProperty<QName>> list = new ArrayList<>();
    formatCommonIdentifiedData(list, p);
    for(URI r : p.getRoles())
      list.add(NamedProperty(Sbol2Terms.Participation.role, r));
    list.add(NamedProperty(Sbol2Terms.Participation.hasParticipant, p.getParticipantURI()));
    nestedDoc.add(NestedDocument(Sbol2Terms.Participation.Participation, p.getIdentity(), NamedProperties(list)));
  }
  return nestedDoc;
}

private static void formatDNASequence(Sequence sequence, List<TopLevelDocument<QName>> topLevelDoc)
{
  List<NamedProperty<QName>> list = new ArrayList<>();
  list.add(NamedProperty(Sbol1Terms.DNASequence.nucleotides, sequence.getElements()));
  topLevelDoc.add(TopLevelDocument(Sbol1Terms.DNASequence.DNASequence, sequence.getIdentity(), NamedProperties(list)));
}

private static NestedDocument<QName> getSequenceV1(Sequence sequence)
{
  List<NamedProperty<QName>> list = new ArrayList<>();
  list.add(NamedProperty(Sbol1Terms.DNASequence.nucleotides, sequence.getElements()));
  return NestedDocument(Sbol1Terms.DNASequence.DNASequence, sequence.getIdentity(), NamedProperties(list));
}

private static void formatCollections (Set<Collection> collections, List<TopLevelDocument<QName>> topLevelDoc)
{
  for(Collection c : collections)
  {
    List<NamedProperty<QName>> list = new ArrayList<>();
    formatCommonTopLevelData(list, c);
    for (URI member : c.getMemberURIs())
    {
      list.add(NamedProperty(Sbol2Terms.Collection.hasMembers, member));
    }
    topLevelDoc.add(TopLevelDocument(Sbol2Terms.Collection.Collection, c.getIdentity(), NamedProperties(list)));
  }
}

private static void formatImplementation(Set<Implementation> implementations, List<TopLevelDocument<QName>> topLevelDoc) {
  for(Implementation implementation : implementations) {
    List<NamedProperty<QName>> list = new ArrayList<>();
    
    formatCommonTopLevelData(list, implementation);
          
    if (implementation.isSetBuilt()) {
      list.add(NamedProperty(Sbol2Terms.Implementation.built, implementation.getBuiltURI()));
    }
    
    topLevelDoc.add(TopLevelDocument(Sbol2Terms.Implementation.Implementation, 
        implementation.getIdentity(), NamedProperties(list)));
  }
}

private static void formatCombinatorialDerivation(Set<CombinatorialDerivation> combinatorialDerivations, List<TopLevelDocument<QName>> topLevelDoc) {
  for(CombinatorialDerivation combinatorialDerivation : combinatorialDerivations) {
    List<NamedProperty<QName>> list = new ArrayList<>();
    
    formatCommonTopLevelData(list, combinatorialDerivation);
          
    list.add(NamedProperty(Sbol2Terms.CombinatorialDerivation.template, combinatorialDerivation.getTemplateURI()));
    if (combinatorialDerivation.isSetStrategy()) {
      list.add(NamedProperty(Sbol2Terms.CombinatorialDerivation.strategy, StrategyType.convertToURI(combinatorialDerivation.getStrategy())));
    }
    formatVariableComponents(combinatorialDerivation.getVariableComponents(), list);
    
    topLevelDoc.add(TopLevelDocument(Sbol2Terms.CombinatorialDerivation.CombinatorialDerivation, 
        combinatorialDerivation.getIdentity(), NamedProperties(list)));
  }
}

public NamedProperty<To> mapVP(NamedProperty<From> f) {
 return Datatree.NamedProperty(transformName(f.getName()), mapV(f.getValue()));
}