public PmfCompartment ToPMFCompartment()
{
string id = element.Attributes[NuMLTags.ID_ATTR].Value;
string name = element.Attributes[NuMLTags.NAME_ATTR].Value;
XmlElement annotationElement = (XmlElement)element.SelectSingleNode(NuMLTags.ANNOTATION);
if (annotationElement == null)
{
return(SBMLFactory.createPMFCompartment(id, name));
}
XmlElement metadataNode = (XmlElement)annotationElement.SelectSingleNode(SbmlTags.PMF_NS + ":" + SbmlTags.METADATA);
XmlElement pmfCodeNode = (XmlElement)metadataNode.SelectSingleNode(SbmlTags.PMF_NS + ":" + SbmlTags.SOURCE);
string pmfCode = pmfCodeNode == null ? "" : pmfCodeNode.InnerText;
XmlElement detailNode = (XmlElement)metadataNode.SelectSingleNode(SbmlTags.PMMLAB_NS + ":" + SbmlTags.DETAIL);
string detail = detailNode == null ? "" : detailNode.InnerText;
List <ModelVariable> modelVariables = null;
XmlNodeList varNodes = metadataNode.SelectNodes(SbmlTags.ENVIRONMENT);
if (varNodes.Count > 0)
{
modelVariables = new List <ModelVariable>(varNodes.Count);
for (int i = 0; i < varNodes.Count; i++)
{
XmlElement varElement = (XmlElement)varNodes.Item(i);
string varName = varElement.GetAttribute(SbmlTags.ENVIRONMENT_NAME);
double varValue;
if (varElement.HasAttribute(SbmlTags.ENVIRONMENT_VALUE))
{
varValue = double.Parse(varElement.GetAttribute(SbmlTags.ENVIRONMENT_VALUE));
}
else
{
varValue = double.NaN;
}
modelVariables.Add(new ModelVariable(varName, varValue));
}
}
return(SBMLFactory.createPMFCompartment(id, name, pmfCode, detail, modelVariables));
}
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);
}
