public ConcentrationOntology(PMFUnitDefinition unitDefinition,
PmfCompartment compartment, PmfSpecies species)
{
this.unitDefinition = unitDefinition;
this.compartment = compartment;
this.species = species;
}
public SpeciesNuMLNode(PmfSpecies species, XmlDocument doc)
{
element = doc.CreateElement(NuMLTags.SPECIES);
element.SetAttribute(NuMLTags.BOUNDARY_CONDITION_ATTR, PmfSpecies.BOUNDARY_CONDITION.ToString());
element.SetAttribute(NuMLTags.HAS_ONLY_SUBSTANCE_ATTR, PmfSpecies.ONLY_SUBSTANCE_UNITS.ToString());
element.SetAttribute(NuMLTags.COMPARTMENT_ATTR, species.getCompartment());
element.SetAttribute(NuMLTags.ID_ATTR, species.getId());
element.SetAttribute(NuMLTags.NAME_ATTR, species.getName());
element.SetAttribute(NuMLTags.SUBSTANCE_UNITS_ATTR, species.getUnits());
if (!string.IsNullOrEmpty(species.combaseCode) ||
!string.IsNullOrEmpty(species.detail) ||
!string.IsNullOrEmpty(species.description))
{
XmlElement annotation = doc.CreateElement(NuMLTags.ANNOTATION);
element.AppendChild(annotation);
XmlElement metadata = doc.CreateElement(SbmlTags.PMF_NS, SbmlTags.METADATA, "");
annotation.AppendChild(metadata);
if (!string.IsNullOrEmpty(species.combaseCode))
{
XmlElement combaseCodeNode = doc.CreateElement(SbmlTags.PMF_NS, SbmlTags.SOURCE, "");
combaseCodeNode.InnerText = species.combaseCode;
metadata.AppendChild(combaseCodeNode);
}
if (!string.IsNullOrEmpty(species.detail))
{
XmlElement detailNode = doc.CreateElement(SbmlTags.PMMLAB_NS, SbmlTags.DETAIL, "");
detailNode.InnerText = species.detail;
metadata.AppendChild(detailNode);
}
if (!string.IsNullOrEmpty(species.description))
{
XmlElement descriptionNode = doc.CreateElement(SbmlTags.PMMLAB_NS, SbmlTags.DESCRIPTION, "");
descriptionNode.InnerText = species.description;
metadata.AppendChild(descriptionNode);
}
}
}
public PmfSpecies toPMFSpecies()
{
string id = element.GetAttribute(NuMLTags.ID_ATTR);
string name = element.GetAttribute(NuMLTags.NAME_ATTR);
string compartment = element.GetAttribute(NuMLTags.COMPARTMENT_ATTR);
string substanceUnits = element.GetAttribute(NuMLTags.SUBSTANCE_UNITS_ATTR);
PmfSpecies species = SBMLFactory.createPMFSpecies(compartment, id, name, substanceUnits);
XmlElement annotationNode = (XmlElement)element.SelectSingleNode(NuMLTags.ANNOTATION);
if (annotationNode != null)
{
// metadata
XmlElement metadataNode = (XmlElement)annotationNode.SelectSingleNode(SbmlTags.PMF_NS + ":" + SbmlTags.METADATA);
// combase code
XmlElement combaseCodeNode = (XmlElement)metadataNode.SelectSingleNode(SbmlTags.PMF_NS + ":" + SbmlTags.SOURCE);
if (combaseCodeNode != null)
{
species.combaseCode = combaseCodeNode.InnerText;
}
// detail
XmlElement detailNode = (XmlElement)metadataNode.SelectSingleNode(SbmlTags.PMMLAB_NS + ":" + SbmlTags.DETAIL);
if (detailNode != null)
{
species.detail = detailNode.InnerText;
}
// description
XmlElement descriptionNode = (XmlElement)metadataNode.SelectSingleNode(SbmlTags.PMMLAB_NS + ":" + SbmlTags.DESCRIPTION);
if (descriptionNode != null)
{
species.description = descriptionNode.InnerText;
}
}
return(species);
}
public ConcentrationOntology(XmlNode node)
{
XmlNode annotationNode = node.SelectSingleNode(NuMLTags.ANNOTATION);
// retrieves unitDefinition
XmlElement unitNode = (XmlElement)annotationNode.SelectSingleNode(NuMLTags.UNIT_DEFINITION);
UnitDefinitionNuMLNode unitNuMLNode = new UnitDefinitionNuMLNode(unitNode);
unitDefinition = unitNuMLNode.ToPMFUnitDefinition();
// retrieves compartment
XmlElement compartmentNode = (XmlElement)annotationNode.SelectSingleNode(NuMLTags.COMPARTMENT);
CompartmentNuMLNode compartmentNuMLNode = new CompartmentNuMLNode(compartmentNode);
compartment = compartmentNuMLNode.ToPMFCompartment();
// retrieves species
XmlElement speciesNode = (XmlElement)annotationNode.SelectSingleNode(NuMLTags.SPECIES);
SpeciesNuMLNode speciesNuMLNode = new SpeciesNuMLNode(speciesNode);
species = speciesNuMLNode.toPMFSpecies();
}
