CModelParameterSet * CModelParameter::getSet() const
{
if (mType == Set)
{
return static_cast< CModelParameterSet * >(const_cast< CModelParameter * >(this));
}
CModelParameterGroup * pParent = mpParent;
while (pParent != NULL)
{
if (pParent->getType() == Set)
{
return static_cast< CModelParameterSet * >(pParent);
}
pParent = pParent->getParent();
}
return NULL;
}
void CCopasiXMLParser::ModelParameterGroupElement::start(const XML_Char *pszName,
const XML_Char **papszAttrs)
{
const char * CN;
const char * pType;
CModelParameter::Type Type;
mpCurrentHandler = NULL;
mCurrentElement = mLastKnownElement;
while (mpCurrentHandler == NULL)
{
mCurrentElement++; /* We should always be on the next element */
switch (mCurrentElement)
{
case ModelParameterGroup:
if (strcmp(pszName, "ModelParameterGroup"))
CCopasiMessage(CCopasiMessage::EXCEPTION, MCXML + 10,
pszName, "ModelParameterGroup", mParser.getCurrentLineNumber());
mLastKnownElement = ModelParameterGroup;
// Element specific code.
CN = mParser.getAttributeValue("cn", papszAttrs);
pType = mParser.getAttributeValue("type", papszAttrs);
Type = toEnum(pType, CModelParameter::TypeNames, CModelParameter::Group);
{
CModelParameterGroup * pModelParameterGroup = new CModelParameterGroup(mCommon.ModelParameterGroupStack.top(), Type);
pModelParameterGroup->setCN(std::string(CN));
mCommon.ModelParameterGroupStack.push(pModelParameterGroup);
}
return;
case Content:
if (!strcmp(pszName, "ModelParameterGroup"))
{
/* If we do not have an etc element handler we create one. */
if (!mpModelParameterGroupElement)
mpModelParameterGroupElement = new ModelParameterGroupElement(mParser, mCommon);
mpCurrentHandler = mpModelParameterGroupElement;
}
else if (!strcmp(pszName, "ModelParameter"))
{
/* If we do not have an etc element handler we create one. */
if (!mpModelParameterElement)
mpModelParameterElement = new ModelParameterElement(mParser, mCommon);
mpCurrentHandler = mpModelParameterElement;
}
break;
default:
mCurrentElement = UNKNOWN_ELEMENT;
mpCurrentHandler = &mParser.mUnknownElement;
break;
}
}
mParser.pushElementHandler(mpCurrentHandler);
if (mpCurrentHandler != &mParser.mUnknownElement)
{
mLastKnownElement = mCurrentElement;
}
mParser.onStartElement(pszName, papszAttrs);
return;
}
void CModelParameterSet::createFromModel()
{
clear();
if (mpModel == NULL)
{
return;
}
CModelParameter * pParameter;
CModelParameterGroup * pGroup;
// TODO CRITICAL Create the proper structure that fits the parameter overview in the GUI
pGroup = static_cast< CModelParameterGroup *>(CModelParameterGroup::add(Group));
pGroup->setCN(CCopasiStaticString("Initial Time").getCN());
pParameter = pGroup->add(Model);
pParameter->setCN(mpModel->getCN());
pParameter->setValue(mpModel->getInitialTime(), ParticleNumbers);
pGroup = static_cast< CModelParameterGroup *>(CModelParameterGroup::add(Group));
pGroup->setCN(CCopasiStaticString("Initial Compartment Sizes").getCN());
CCopasiVector< CCompartment >::const_iterator itCompartment = mpModel->getCompartments().begin();
CCopasiVector< CCompartment >::const_iterator endCompartment = mpModel->getCompartments().end();
for (; itCompartment != endCompartment; ++itCompartment)
{
pParameter = pGroup->add(Compartment);
pParameter->setCN((*itCompartment)->getCN());
pParameter->setSimulationType((*itCompartment)->getStatus());
pParameter->setValue((*itCompartment)->getInitialValue(), ParticleNumbers);
pParameter->setInitialExpression((*itCompartment)->getInitialExpression());
}
pGroup = static_cast< CModelParameterGroup *>(CModelParameterGroup::add(Group));
pGroup->setCN(CCopasiStaticString("Initial Species Values").getCN());
CCopasiVector< CMetab >::const_iterator itSpecies = mpModel->getMetabolites().begin();
CCopasiVector< CMetab >::const_iterator endSpecies = mpModel->getMetabolites().end();
for (; itSpecies != endSpecies; ++itSpecies)
{
pParameter = pGroup->add(Species);
pParameter->setCN((*itSpecies)->getCN());
pParameter->setSimulationType((*itSpecies)->getStatus());
pParameter->setValue((*itSpecies)->getInitialValue(), ParticleNumbers);
pParameter->setInitialExpression((*itSpecies)->getInitialExpression());
}
pGroup = static_cast< CModelParameterGroup *>(CModelParameterGroup::add(Group));
pGroup->setCN(CCopasiStaticString("Initial Global Quantities").getCN());
CCopasiVector< CModelValue >::const_iterator itModelValue = mpModel->getModelValues().begin();
CCopasiVector< CModelValue >::const_iterator endModelValue = mpModel->getModelValues().end();
for (; itModelValue != endModelValue; ++itModelValue)
{
pParameter = pGroup->add(ModelValue);
pParameter->setCN((*itModelValue)->getCN());
pParameter->setSimulationType((*itModelValue)->getStatus());
pParameter->setValue((*itModelValue)->getInitialValue(), ParticleNumbers);
pParameter->setInitialExpression((*itModelValue)->getInitialExpression());
}
pGroup = static_cast< CModelParameterGroup *>(CModelParameterGroup::add(Group));
pGroup->setCN(CCopasiStaticString("Kinetic Parameters").getCN());
CCopasiVector< CReaction >::const_iterator itReaction = mpModel->getReactions().begin();
CCopasiVector< CReaction >::const_iterator endReaction = mpModel->getReactions().end();
for (; itReaction != endReaction; ++itReaction)
{
CModelParameterGroup * pReaction = static_cast< CModelParameterGroup *>(pGroup->add(Reaction));
pReaction->setCN((*itReaction)->getCN());
CCopasiParameterGroup::index_iterator itParameter = (*itReaction)->getParameters().beginIndex();
CCopasiParameterGroup::index_iterator endParameter = (*itReaction)->getParameters().endIndex();
for (; itParameter != endParameter; ++itParameter)
{
pParameter = pReaction->add(ReactionParameter);
pParameter->setCN((*itParameter)->getCN());
// Check whether this refers to a global quantity.
if ((*itReaction)->isLocalParameter((*itParameter)->getObjectName()))
{
pParameter->setSimulationType(CModelEntity::FIXED);
pParameter->setValue(*(*itParameter)->getValue().pDOUBLE, ParticleNumbers);
}
else
{
pParameter->setSimulationType(CModelEntity::ASSIGNMENT);
const std::vector<std::string> ModelValue = (*itReaction)->getParameterMapping((*itParameter)->getObjectName());
if (ModelValue.size() != 1) fatalError();
const CModelValue * pModelValue = static_cast< CModelValue * >(CCopasiRootContainer::getKeyFactory()->get(ModelValue[0]));
if (pModelValue == NULL) fatalError();
pParameter->setValue(pModelValue->getInitialValue(), ParticleNumbers);
pParameter->setInitialExpression("<" + pModelValue->getInitialValueReference()->getCN() + ">");
}
}
}
compile();
}
