public TimeOntology(XmlElement element)
{
XmlElement annotationNode = (XmlElement)element.SelectSingleNode(NuMLTags.ANNOTATION);
XmlElement unitNode = (XmlElement)annotationNode.SelectSingleNode(NuMLTags.UNIT_DEFINITION);
unitDefinition = new UnitDefinitionNuMLNode(unitNode).ToPMFUnitDefinition();
}
public ConcentrationOntology(PMFUnitDefinition unitDefinition,
PmfCompartment compartment, PmfSpecies species)
{
this.unitDefinition = unitDefinition;
this.compartment = compartment;
this.species = species;
}
public UnitDefinitionNuMLNode(PMFUnitDefinition unitDefinition, XmlDocument doc)
{
element = doc.CreateElement(NuMLTags.UNIT_DEFINITION);
element.SetAttribute(NuMLTags.ID_ATTR, unitDefinition.getId());
element.SetAttribute(NuMLTags.NAME_ATTR, unitDefinition.getName());
// Adds transformation name
if (unitDefinition.isSetTransformationName())
{
XmlElement transformationNode = doc.CreateElement(SbmlTags.PMMLAB_NS + ":" + SbmlTags.TRANSFORMATION);
transformationNode.InnerText = unitDefinition.transformationName;
element.AppendChild(transformationNode);
}
// Adds units
foreach (Unit unit in unitDefinition.getUnits())
{
element.AppendChild(new UnitNuMLNode(unit, doc).element);
}
}
public TimeOntology(PMFUnitDefinition unitDefinition)
{
this.unitDefinition = unitDefinition;
}
