Beispiel #1
0
int main()
{
  // initialize the backend library
  // since we are not interested in the arguments
  // that are passed to main, we pass 0 and NULL to
  // init
  CCopasiRootContainer::init(0, NULL);
  assert(CCopasiRootContainer::getRoot() != NULL);
  // create a new datamodel
  CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();
  assert(CCopasiRootContainer::getDatamodelList()->size() == 1);
  // get the model from the datamodel
  CModel* pModel = pDataModel->getModel();
  assert(pModel != NULL);
  // set the units for the model
  // we want seconds as the time unit
  // microliter as the volume units
  // and nanomole as the substance units
  pModel->setTimeUnit(CModel::s);
  pModel->setVolumeUnit(CModel::microl);
  pModel->setQuantityUnit(CModel::nMol);

  // we have to keep a set of all the initial values that are changed during
  // the model building process
  // They are needed after the model has been built to make sure all initial
  // values are set to the correct initial value
  std::set<const CCopasiObject*> changedObjects;

  // create a compartment with the name cell and an initial volume of 5.0
  // microliter
  CCompartment* pCompartment = pModel->createCompartment("cell", 5.0);
  const CCopasiObject* pObject = pCompartment->getValueReference();
  assert(pObject != NULL);
  changedObjects.insert(pObject);
  assert(pCompartment != NULL);
  assert(pModel->getCompartments().size() == 1);
  // create a new metabolite with the name S and an inital
  // concentration of 10 nanomol
  // the metabolite belongs to the compartment we created and is is to be
  // fixed
  CMetab* pS = pModel->createMetabolite("S", pCompartment->getObjectName(), 10.0, CMetab::FIXED);
  pObject = pS->getInitialConcentrationReference();
  assert(pObject != NULL);
  changedObjects.insert(pObject);
  assert(pCompartment != NULL);
  assert(pS != NULL);
  assert(pModel->getMetabolites().size() == 1);
  // create a second metabolite called P with an initial
  // concentration of 0. This metabolite is to be changed by reactions
  CMetab* pP = pModel->createMetabolite("P", pCompartment->getObjectName(), 0.0, CMetab::REACTIONS);
  assert(pP != NULL);
  pObject = pP->getInitialConcentrationReference();
  assert(pObject != NULL);
  changedObjects.insert(pObject);
  assert(pModel->getMetabolites().size() == 2);
  // now we create a reaction
  CReaction* pReaction = pModel->createReaction("reaction");
  assert(pReaction != NULL);
  assert(pModel->getReactions().size() == 1);
  // reaction converts S to P
  // we can set these on the chemical equation of the reaction
  CChemEq* pChemEq = &pReaction->getChemEq();
  // S is a substrate with stoichiometry 1
  pChemEq->addMetabolite(pS->getKey(), 1.0, CChemEq::SUBSTRATE);
  // P is a product with stoichiometry 1
  pChemEq->addMetabolite(pP->getKey(), 1.0, CChemEq::PRODUCT);
  assert(pChemEq->getSubstrates().size() == 1);
  assert(pChemEq->getProducts().size() == 1);
  // this reaction is to be irreversible
  pReaction->setReversible(false);
  assert(pReaction->isReversible() == false);

  CModelValue* pMV = pModel->createModelValue("K", 42.0);
  // set the status to FIXED
  pMV->setStatus(CModelValue::FIXED);
  assert(pMV != NULL);
  pObject = pMV->getInitialValueReference();
  assert(pObject != NULL);
  changedObjects.insert(pObject);
  assert(pModel->getModelValues().size() == 1);

  // now we ned to set a kinetic law on the reaction
  // for this we create a user defined function
  CFunctionDB* pFunDB = CCopasiRootContainer::getFunctionList();
  assert(pFunDB != NULL);

  CKinFunction* pFunction = new CKinFunction("My Rate Law");

  pFunDB->add(pFunction, true);
  CFunction* pRateLaw = dynamic_cast<CFunction*>(pFunDB->findFunction("My Rate Law"));

  assert(pRateLaw != NULL);

  // now we create the formula for the function and set it on the function
  std::string formula = "(1-0.4/(EXPONENTIALE^(temp-37)))*0.00001448471257*1.4^(temp-37)*substrate";

  bool result = pFunction->setInfix(formula);
  assert(result == true);
  // make the function irreversible
  pFunction->setReversible(TriFalse);
  // the formula string should have been parsed now
  // and COPASI should have determined that the formula string contained 2 parameters (temp and substrate)
  CFunctionParameters& variables = pFunction->getVariables();
  // per default the usage of those parameters will be set to VARIABLE
  size_t index = pFunction->getVariableIndex("temp");
  assert(index != C_INVALID_INDEX);
  CFunctionParameter* pParam = variables[index];
  assert(pParam->getUsage() == CFunctionParameter::VARIABLE);
  // This is correct for temp, but substrate should get the usage SUBSTRATE in order
  // for us to use the function with the reaction created above
  // So we need to set the usage for "substrate" manually
  index = pFunction->getVariableIndex("substrate");
  assert(index != C_INVALID_INDEX);
  pParam = variables[index];
  pParam->setUsage(CFunctionParameter::SUBSTRATE);

  // set the rate law for the reaction
  pReaction->setFunction(pFunction);
  assert(pReaction->getFunction() != NULL);

  // COPASI also needs to know what object it has to assocuiate with the individual function parameters
  // In our case we need to tell COPASI that substrate is to be replaced by the substrate of the reaction
  // and temp is to be replaced by the global parameter K
  pReaction->setParameterMapping("substrate", pS->getKey());
  pReaction->setParameterMapping("temp", pMV->getKey());

  // finally compile the model
  // compile needs to be done before updating all initial values for
  // the model with the refresh sequence
  pModel->compileIfNecessary(NULL);

  // now that we are done building the model, we have to make sure all
  // initial values are updated according to their dependencies
  std::vector<Refresh*> refreshes = pModel->buildInitialRefreshSequence(changedObjects);
  std::vector<Refresh*>::iterator it2 = refreshes.begin(), endit2 = refreshes.end();

  while (it2 != endit2)
    {
      // call each refresh
      (**it2)();
      ++it2;
    }

  // save the model to a COPASI file
  // we save to a file named example1.cps, we don't want a progress report
  // and we want to overwrite any existing file with the same name
  // Default tasks are automatically generated and will always appear in cps
  // file unless they are explicitley deleted before saving.
  pDataModel->saveModel("example7.cps", NULL, true);

  // export the model to an SBML file
  // we save to a file named example1.xml, we want to overwrite any
  // existing file with the same name and we want SBML L2V3
  pDataModel->exportSBML("example7.xml", true, 2, 3);

  // destroy the root container once we are done
  CCopasiRootContainer::destroy();
}
Beispiel #2
0
void test_compare_utilities::test_copasi_function_expansion()
{
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;;
  std::istringstream iss(test_compare_utilities::MODEL_STRING1);
  CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
  CFunctionDB* pFunctionDB = CCopasiRootContainer::getFunctionList();
  // function_5
  CEvaluationTree* pTree = pFunctionDB->findFunction("function_4");
  CPPUNIT_ASSERT(pTree != NULL);
  // generate a call node
  CFunction* pFunction = dynamic_cast<CFunction*>(pTree);
  CPPUNIT_ASSERT(pFunction != NULL);
  CEvaluationNodeCall* pCallNode = new CEvaluationNodeCall(CEvaluationNode::S_FUNCTION, pFunction->getObjectName());
  CPPUNIT_ASSERT(pCallNode != NULL);
  CFunctionParameters* pFunctionParameters = &pFunction->getVariables();
  unsigned int i = 0, iMax = pFunctionParameters->size();

  while (i < iMax)
    {
      CFunctionParameter* pParameter = (*pFunctionParameters)[i];
      CPPUNIT_ASSERT(pParameter != NULL);
      CEvaluationNodeVariable* pVariableNode = new CEvaluationNodeVariable(CEvaluationNode::S_DEFAULT, pParameter->getObjectName());
      pCallNode->addChild(pVariableNode);
      ++i;
    }

  CEvaluationNode* pExpanded = expand_function_calls(pCallNode, pFunctionDB);
  delete pCallNode;
  CPPUNIT_ASSERT(pExpanded != NULL);
  CPPUNIT_ASSERT(pExpanded->mainType() == CEvaluationNode::T_OPERATOR);
  CPPUNIT_ASSERT(pExpanded->subType() == CEvaluationNode::S_DIVIDE);
  CEvaluationNode* pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_PLUS);
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
  CPPUNIT_ASSERT(pChild->getData() == std::string("y"));
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
  CPPUNIT_ASSERT(pChild->getData() == std::string("x"));
  CPPUNIT_ASSERT(pChild->getSibling() == NULL);
  pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild()->getSibling());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
  CPPUNIT_ASSERT((fabs(pChild->getValue() - 2.0) / 2.0) < 1e-6);
  CPPUNIT_ASSERT(pChild->getSibling() == NULL);
  delete pExpanded;

  // function_5
  pTree = pFunctionDB->findFunction("function_5");
  CPPUNIT_ASSERT(pTree != NULL);
  // generate a call node
  pFunction = dynamic_cast<CFunction*>(pTree);
  CPPUNIT_ASSERT(pFunction != NULL);
  pCallNode = new CEvaluationNodeCall(CEvaluationNode::S_FUNCTION, pFunction->getObjectName());
  CPPUNIT_ASSERT(pCallNode != NULL);
  pFunctionParameters = &pFunction->getVariables();
  i = 0, iMax = pFunctionParameters->size();

  while (i < iMax)
    {
      CFunctionParameter* pParameter = (*pFunctionParameters)[i];
      CPPUNIT_ASSERT(pParameter != NULL);
      CEvaluationNodeVariable* pVariableNode = new CEvaluationNodeVariable(CEvaluationNode::S_DEFAULT, pParameter->getObjectName());
      pCallNode->addChild(pVariableNode);
      ++i;
    }

  pExpanded = expand_function_calls(pCallNode, pFunctionDB);
  delete pCallNode;
  CPPUNIT_ASSERT(pExpanded != NULL);
  CPPUNIT_ASSERT(pExpanded->mainType() == CEvaluationNode::T_OPERATOR);
  CPPUNIT_ASSERT(pExpanded->subType() == CEvaluationNode::S_PLUS);
  pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MINUS);
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
  CPPUNIT_ASSERT(pChild->getData() == std::string("a"));
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MULTIPLY);
  CPPUNIT_ASSERT(pChild->getSibling() == NULL);
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
  CPPUNIT_ASSERT(pChild->getData() == std::string("c"));
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
  CPPUNIT_ASSERT((fabs(pChild->getValue() - 1.3) / 1.3) < 1e-6);
  CPPUNIT_ASSERT(pChild->getSibling() == NULL);

  // (3*b)-5.23
  pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild()->getSibling());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MINUS);
  // 3*b
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MULTIPLY);
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
  CPPUNIT_ASSERT((fabs(pChild->getValue() - 3.0) / 3.0) < 1e-6);
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
  CPPUNIT_ASSERT(pChild->getData() == std::string("b"));
  CPPUNIT_ASSERT(pChild->getSibling() == NULL);
  // 5.23
  pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild()->getSibling()->getChild()->getSibling());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
  CPPUNIT_ASSERT((fabs(pChild->getValue() - 5.23) / 5.23) < 1e-6);
  CPPUNIT_ASSERT(pChild->getSibling() == NULL);

  delete pExpanded;

  // function_6
  pTree = pFunctionDB->findFunction("function_6");
  CPPUNIT_ASSERT(pTree != NULL);
  // generate a call node
  pFunction = dynamic_cast<CFunction*>(pTree);
  CPPUNIT_ASSERT(pFunction != NULL);
  pCallNode = new CEvaluationNodeCall(CEvaluationNode::S_FUNCTION, pFunction->getObjectName());
  CPPUNIT_ASSERT(pCallNode != NULL);
  pFunctionParameters = &pFunction->getVariables();
  i = 0, iMax = pFunctionParameters->size();

  while (i < iMax)
    {
      CFunctionParameter* pParameter = (*pFunctionParameters)[i];
      CPPUNIT_ASSERT(pParameter != NULL);
      CEvaluationNodeVariable* pVariableNode = new CEvaluationNodeVariable(CEvaluationNode::S_DEFAULT, pParameter->getObjectName());
      pCallNode->addChild(pVariableNode);
      ++i;
    }

  pExpanded = expand_function_calls(pCallNode, pFunctionDB);
  delete pCallNode;
  CPPUNIT_ASSERT(pExpanded != NULL);
  // (k1-k3*1.3)+((3*k2)-5.23)
  CPPUNIT_ASSERT(pExpanded->mainType() == CEvaluationNode::T_OPERATOR);
  CPPUNIT_ASSERT(pExpanded->subType() == CEvaluationNode::S_PLUS);
  pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MINUS);
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
  CPPUNIT_ASSERT(pChild->getData() == std::string("k1"));
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MULTIPLY);
  CPPUNIT_ASSERT(pChild->getSibling() == NULL);
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
  CPPUNIT_ASSERT(pChild->getData() == std::string("k3"));
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
  CPPUNIT_ASSERT((fabs(pChild->getValue() - 1.3) / 1.3) < 1e-6);
  CPPUNIT_ASSERT(pChild->getSibling() == NULL);

  // (3*b)-5.23
  pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild()->getSibling());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MINUS);
  // 3*b
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_OPERATOR);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_MULTIPLY);
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getChild());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
  CPPUNIT_ASSERT((fabs(pChild->getValue() - 3.0) / 3.0) < 1e-6);
  pChild = dynamic_cast<CEvaluationNode*>(pChild->getSibling());
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_VARIABLE);
  CPPUNIT_ASSERT(pChild->getData() == std::string("k2"));
  CPPUNIT_ASSERT(pChild->getSibling() == NULL);
  // 5.23
  pChild = dynamic_cast<CEvaluationNode*>(pExpanded->getChild()->getSibling()->getChild()->getSibling());
  CPPUNIT_ASSERT(pChild != NULL);
  CPPUNIT_ASSERT(pChild->mainType() == CEvaluationNode::T_NUMBER);
  CPPUNIT_ASSERT(pChild->subType() == CEvaluationNode::S_DOUBLE);
  CPPUNIT_ASSERT((fabs(pChild->getValue() - 5.23) / 5.23) < 1e-6);
  CPPUNIT_ASSERT(pChild->getSibling() == NULL);

  delete pExpanded;
}
Beispiel #3
0
// This is only used when reading Gepasi Files
void CKinFunction::createParameters()
{
  CCopasiVectorN < CFunctionParameter > Substrates;
  CCopasiVectorN < CFunctionParameter > Products;
  CCopasiVectorN < CFunctionParameter > Modifiers;
  CCopasiVectorN < CFunctionParameter > Parameters;
  CCopasiVectorN < CFunctionParameter > Volumes;

  size_t i, imax = mNodes.size();

  CFunctionParameter *pParameter;

  for (i = 0; i < imax; i++)
    {
      if (mNodes[i]->getType() == N_IDENTIFIER)
        {
          // We need to check that we have no reserved name.
          const char *Reserved[] =
            {"pi", "exponentiale", "true", "false", "infinity", "nan",
             "PI", "EXPONENTIALE", "TRUE", "FALSE", "INFINITY", "NAN"
            };

          std::string Name = mNodes[i]->getName();
          size_t j, jmax = 12;

          for (j = 0; j < jmax; j++)
            if (Name == Reserved[j]) break;

          if (j != jmax)
            {
              // It is save to prepend the identifyer with '_' since this is not allowed in
              // Gepasi but within COPASI.
              std::string OldName = Name;
              Name = "_" + Name;

              // We have to replace the corresponding CEvaluationNodes to reflect the change.
              std::vector< CEvaluationNode * >::iterator it = mpNodeList->begin();
              std::vector< CEvaluationNode * >::iterator end = mpNodeList->end();

              for (; it != end; ++it)
                if (((*it)->getType() & 0xFF000000) == CEvaluationNode::CONSTANT &&
                    (*it)->getData() == OldName)
                  (*it)->setData(Name);

              // The Infix has changed we need to update it.
              setInfix(mpRoot->buildInfix());
            }

          pParameter = new CFunctionParameter(Name);
          pParameter->setType(CFunctionParameter::FLOAT64);

          switch (mNodes[i]->getSubtype())
            {
              case N_SUBSTRATE:
                pParameter->setUsage(CFunctionParameter::SUBSTRATE);

                if (Substrates.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
                  Substrates.add(pParameter, false);
                else
                  pdelete(pParameter);

                break;

              case N_PRODUCT:
                pParameter->setUsage(CFunctionParameter::PRODUCT);

                if (Products.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
                  Products.add(pParameter, false);
                else
                  pdelete(pParameter);

                break;

              case N_MODIFIER:
                pParameter->setUsage(CFunctionParameter::MODIFIER);

                if (Modifiers.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
                  Modifiers.add(pParameter, false);
                else
                  pdelete(pParameter);

                break;

              case N_KCONSTANT:
              case N_NOP:
                pParameter->setUsage(CFunctionParameter::PARAMETER);

                if (Parameters.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
                  Parameters.add(pParameter, false);
                else
                  pdelete(pParameter);

                break;

              case N_VOLUME:
                pParameter->setUsage(CFunctionParameter::VOLUME);

                if (Volumes.getIndex(pParameter->getObjectName()) == C_INVALID_INDEX)
                  Volumes.add(pParameter, false);
                else
                  pdelete(pParameter);

                break;

              default:
                pdelete(pParameter);
                fatalError();
            }
        }
    }

  getVariables().cleanup();

  imax = Substrates.size();

  for (i = 0; i < imax; i++)
    getVariables().add(Substrates[i], true);

  Substrates.cleanup();

  imax = Products.size();

  for (i = 0; i < imax; i++)
    getVariables().add(Products[i], true);

  Products.cleanup();

  imax = Modifiers.size();

  for (i = 0; i < imax; i++)
    getVariables().add(Modifiers[i], true);

  Modifiers.cleanup();

  imax = Parameters.size();

  for (i = 0; i < imax; i++)
    getVariables().add(Parameters[i], true);

  Parameters.cleanup();

  imax = Volumes.size();

  for (i = 0; i < imax; i++)
    getVariables().add(Volumes[i], true);

  Volumes.cleanup();
}