C++ CCopasiDataModel::getCurrentSBMLDocument方法代码示例

void test000061::test_bug_1044()
{
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  std::istringstream iss(test000061::MODEL_STRING1);
  CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
  CModel* pModel = pDataModel->getModel();
  CPPUNIT_ASSERT(pModel != NULL);
  // check if the model has been loaded correctly
  CPPUNIT_ASSERT(pModel->getModelValues().size() == 1);
  const CModelValue* pModelValue = pModel->getModelValues()[0];
  CPPUNIT_ASSERT(pModelValue != NULL);
  CPPUNIT_ASSERT(pModelValue->getObjectName() == "A");
  CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::ASSIGNMENT);
  CPPUNIT_ASSERT(pModelValue->getExpressionPtr() != NULL);
  const CEvaluationNode* pRoot = pModelValue->getExpressionPtr()->getRoot();
  CPPUNIT_ASSERT(pRoot != NULL);
  CPPUNIT_ASSERT(CEvaluationNode::type(pRoot->getType()) == CEvaluationNode::INVALID);
  const SBMLDocument* pDocument = pDataModel->getCurrentSBMLDocument();
  CPPUNIT_ASSERT(pDocument == NULL);
  // export the model to SBML
  bool exception = false;

  try
    {
      CPPUNIT_ASSERT(pDataModel->exportSBMLToString(NULL, 2, 1).empty() == true);
    }
  catch (...)
    {
      exception = true;
    }

  CPPUNIT_ASSERT(exception == true);
  CPPUNIT_ASSERT(pDataModel->getCurrentSBMLDocument() == NULL);
  // check if the correct error message has been created.
  const CCopasiMessage& message = CCopasiMessage::getLastMessage();
  CPPUNIT_ASSERT(message.getNumber() == MCSBML + 70);
  CPPUNIT_ASSERT(message.getType() == CCopasiMessage::EXCEPTION);
  CPPUNIT_ASSERT(CCopasiMessage::size() == 0);
}

/**
 * This method tries to import CellDesigner annotations.
 */
void DataModelGUI::importCellDesigner()
{
  // add code to check for CellDesigner annotations
  // ask the user if the annotations should be imported
  CCopasiDataModel* pDataModel = (*CCopasiRootContainer::getDatamodelList())[0];
  assert(pDataModel != NULL);

  if (pDataModel != NULL)
    {
      SBMLDocument* pSBMLDocument = pDataModel->getCurrentSBMLDocument();

      if (pSBMLDocument != NULL &&
          pSBMLDocument->getModel() != NULL &&
          pSBMLDocument->getModel()->getAnnotation() != NULL)
        {
          // check for the CellDesigner namespace
          std::pair<bool, std::string> foundNamespace = CCellDesignerImporter::findCellDesignerNamespace(pSBMLDocument);

          if (foundNamespace.first == true)
            {
              const XMLNode* pAnno = CCellDesignerImporter::findCellDesignerAnnotation(pSBMLDocument, pSBMLDocument->getModel()->getAnnotation());

              // first we check if there are supported cell designer annotations
              if (pAnno != NULL)
                {
                  // check if the file contains the correct version
                  double version = CCellDesignerImporter::determineVersion(pAnno);

                  if (version < 4.0)
                    {
                      CCopasiMessage(CCopasiMessage::RAW, "CellDesigner annotation was found in the file, but the version is not supported.\nPlease open the file in the latest version of CellDesigner and save it again.");
                    }
                  else
                    {
                      bool importCD = false;
#if LIBSBML_VERSION >= 50400
                      // if we don't have a layout import it!
                      LayoutModelPlugin* mplugin = (LayoutModelPlugin*)pSBMLDocument->getModel()->getPlugin("layout");

                      if (mplugin == NULL || (mplugin != NULL && mplugin->getNumLayouts() == 0))
                        importCD = true;

#endif

                      // ask the user if the CellDesigner annotation should be imported
                      if (importCD || CQMessageBox::question(NULL, "CellDesigner import", "A CellDesigner diagram was found in this file.\nDo you want to import the diagram?" , QMessageBox::Yes | QMessageBox::No , QMessageBox::No) == QMessageBox::Yes)
                        {
                          // do the import
                          CCellDesignerImporter cd_importer(pSBMLDocument);

                          if (cd_importer.getLayout() == NULL)
                            {
                              CCopasiMessage(CCopasiMessage::WARNING, "Sorry, CellDesigner annotations could not be importet.");
                            }
                          else
                            {
                              // now we have to import the created layout
                              // create the model map
                              std::string s1, s2;
                              std::map<std::string, std::string> modelmap;
                              std::map<CCopasiObject*, SBase*>::const_iterator it;
                              std::map<CCopasiObject*, SBase*>::const_iterator itEnd = pDataModel->getCopasi2SBMLMap().end();

                              for (it = pDataModel->getCopasi2SBMLMap().begin(); it != itEnd; ++it)
                                {
                                  s1 = SBMLUtils::getIdFromSBase(it->second);

                                  if (it->first)
                                    {
                                      s2 = it->first->getKey();
                                    }
                                  else
                                    {
                                      s2 = "";
                                    }

                                  if ((s1 != "") && (s2 != ""))
                                    {
                                      modelmap[s1] = s2;
                                    }
                                }

                              // the layout map and the id to key map can be empty
                              std::map<std::string, std::string> layoutmap;
                              std::map<std::string, std::string> idToKeyMap;
#ifdef USE_CRENDER_EXTENSION
                              CLayout* pLayout = SBMLDocumentLoader::createLayout(*cd_importer.getLayout(), modelmap, layoutmap, idToKeyMap);
#else
                              CLayout* pLayout = SBMLDocumentLoader::createLayout(*cd_importer.getLayout(), modelmap, layoutmap);
#endif /* USE_CRENDER_EXTENSION */

                              // add the layout to the DataModel
                              if (pLayout != NULL && pDataModel->getListOfLayouts() != NULL)
                                {
                                  // the addLayout methods expects a map as the second argument which currently is
                                  // ignored, so we just pass an empty one
                                  // TODO maybe the methods actually expects one of the maps above (layoutmap or idToKeyMap), but
//.........这里部分代码省略.........

void test000009::test_references_to_species()
{
  // load the CPS file
  // export to SBML
  // check the resulting SBML model
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  std::istringstream iss(test000009::MODEL_STRING);
  CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
  CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
  CPPUNIT_ASSERT(pDataModel->exportSBMLToString(NULL, 2, 3).empty() == false);
  SBMLDocument* pDocument = pDataModel->getCurrentSBMLDocument();
  CPPUNIT_ASSERT(pDocument != NULL);
  Model* pModel = pDocument->getModel();
  CPPUNIT_ASSERT(pModel != NULL);
  // assert that there is only one compartment and
  // assert the compartment is constant
  CPPUNIT_ASSERT(pModel->getNumCompartments() == 1);
  Compartment* pCompartment = pModel->getCompartment(0);
  CPPUNIT_ASSERT(pCompartment->getConstant() == false);
  CPPUNIT_ASSERT(pModel->getNumSpecies() == 2);
  Species* pSpecies = pModel->getSpecies(1);
  CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() == true);
  pSpecies = pModel->getSpecies(0);
  std::string idSpeciesA = pSpecies->getId();
  CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() == true);
  CPPUNIT_ASSERT(pModel->getNumRules() == 2);
  // there are two rules, one is the rule for the compartment
  AssignmentRule* pRule = dynamic_cast<AssignmentRule*>(pModel->getRule(0));
  CPPUNIT_ASSERT(pRule != NULL);
  CPPUNIT_ASSERT(pModel->getNumParameters() == 1);
  Parameter* pParameter = pModel->getParameter(0);
  CPPUNIT_ASSERT(pParameter != NULL);

  if (pRule->getVariable() != pParameter->getId())
    {
      pRule = dynamic_cast<AssignmentRule*>(pModel->getRule(1));
    }

  CPPUNIT_ASSERT(pRule->getVariable() == pParameter->getId());
  const ASTNode* pMath = pRule->getMath();
  CPPUNIT_ASSERT(pMath != NULL);
  // the expression should be the species divided by the volume
  CPPUNIT_ASSERT(pMath->getType() == AST_DIVIDE);
  CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
  CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
  CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pSpecies->getId());
  CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
  CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
  CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pCompartment->getId());
  CPPUNIT_ASSERT(pModel->getNumReactions() == 2);
  Reaction* pReaction = pModel->getReaction(0);
  // make sure this is reaction A ->
  CPPUNIT_ASSERT(pReaction != NULL);
  CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
  CPPUNIT_ASSERT(pReaction->getNumProducts() == 0);
  // check if all references in the kinetic law are unmodified
  // math element must be a multiplication of the mass action term by
  // the compartment volume
  // the mass action term is a multiplication of the parameter node by
  // the species node
  // the code that multiplies the reaction by the compartments volume
  // recognizes the division of the species by the compartment and cancels
  // those two
  CPPUNIT_ASSERT(pReaction->isSetKineticLaw() == true);
  KineticLaw* pLaw = pReaction->getKineticLaw();
  CPPUNIT_ASSERT(pLaw != NULL);
  CPPUNIT_ASSERT(pLaw->isSetMath() == true);
  pMath = pLaw->getMath();
  CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
  CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
  CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
  CPPUNIT_ASSERT(pMath->getChild(0)->getName() == std::string("k1"));
  CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
  CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
  CPPUNIT_ASSERT(pMath->getChild(1)->getName() == idSpeciesA);

  pReaction = pModel->getReaction(1);
  // make sure this is reaction A -> S
  CPPUNIT_ASSERT(pReaction != NULL);
  CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
  CPPUNIT_ASSERT(pReaction->getNumProducts() == 1);
  // check if all references in the kinetic law are unmodified
  // math element must be a multiplication of the compartments volume with
  // a function call with three arguments
  // the first argument is the reference to the species
  CPPUNIT_ASSERT(pReaction->isSetKineticLaw() == true);
  pLaw = pReaction->getKineticLaw();
  CPPUNIT_ASSERT(pLaw != NULL);
  CPPUNIT_ASSERT(pLaw->isSetMath() == true);
  pMath = pLaw->getMath();
  CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
  CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
  CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
  CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pCompartment->getId());
  pMath = pMath->getChild(1);
  CPPUNIT_ASSERT(pMath != NULL);
  CPPUNIT_ASSERT(pMath->getType() == AST_FUNCTION);
  CPPUNIT_ASSERT(pMath->getNumChildren() == 3);
  pMath = pMath->getChild(0);
  CPPUNIT_ASSERT(pMath != NULL);
//.........这里部分代码省略.........

void test000054::test_bug1002()
{
  // load the CPS file
  // export to SBML
  // check the resulting SBML model
  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
  std::istringstream iss(test000054::MODEL_STRING);
  CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
  CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
  CPPUNIT_ASSERT(pDataModel->exportSBMLToString(NULL, 2, 3).empty() == false);
  SBMLDocument* pDocument = pDataModel->getCurrentSBMLDocument();
  CPPUNIT_ASSERT(pDocument != NULL);
  Model* pSBMLModel = pDocument->getModel();
  CPPUNIT_ASSERT(pSBMLModel != NULL);
  CPPUNIT_ASSERT(pSBMLModel->getNumCompartments() == 0);
  CPPUNIT_ASSERT(pSBMLModel->getNumSpecies() == 0);
  CPPUNIT_ASSERT(pSBMLModel->getNumReactions() == 0);
  CPPUNIT_ASSERT(pSBMLModel->getNumInitialAssignments() == 0);
  CPPUNIT_ASSERT(pSBMLModel->getNumParameters() == 5);
  const Parameter* pParameter1 = pSBMLModel->getParameter(0);
  CPPUNIT_ASSERT(pParameter1 != NULL);
  CPPUNIT_ASSERT(pParameter1->getConstant() == false);
  const Parameter* pParameter2 = pSBMLModel->getParameter(1);
  CPPUNIT_ASSERT(pParameter2 != NULL);
  CPPUNIT_ASSERT(pParameter2->getConstant() == false);
  const Parameter* pParameter3 = pSBMLModel->getParameter(2);
  CPPUNIT_ASSERT(pParameter3 != NULL);
  CPPUNIT_ASSERT(pParameter3->getConstant() == false);
  const Parameter* pParameter4 = pSBMLModel->getParameter(3);
  CPPUNIT_ASSERT(pParameter4 != NULL);
  CPPUNIT_ASSERT(pParameter4->getConstant() == false);
  const Parameter* pParameter5 = pSBMLModel->getParameter(4);
  CPPUNIT_ASSERT(pParameter5 != NULL);
  CPPUNIT_ASSERT(pParameter5->getConstant() == false);
  CPPUNIT_ASSERT(pSBMLModel->getNumRules() == 5);

  const Rule* pRule = pSBMLModel->getRule(0);
  CPPUNIT_ASSERT(pRule != NULL);
  CPPUNIT_ASSERT(pRule->getTypeCode() == SBML_ASSIGNMENT_RULE);
  const AssignmentRule* pARule = dynamic_cast<const AssignmentRule*>(pRule);
  CPPUNIT_ASSERT(pARule != NULL);
  CPPUNIT_ASSERT(pARule->getVariable() == pParameter4->getId());
  CPPUNIT_ASSERT(pARule->isSetMath() == true);
  const ASTNode* pMath = pARule->getMath();
  CPPUNIT_ASSERT(pMath != NULL);
  CPPUNIT_ASSERT(pMath->getType() == AST_PLUS);
  CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
  const ASTNode* pChild1 = pMath->getChild(0);
  CPPUNIT_ASSERT(pChild1 != NULL);
  CPPUNIT_ASSERT(pChild1->getType() == AST_REAL);
  CPPUNIT_ASSERT(fabs((pChild1->getReal() - 2.0) / 2.0) < 1e-15);
  const ASTNode* pChild2 = pMath->getChild(1);
  CPPUNIT_ASSERT(pChild2 != NULL);
  CPPUNIT_ASSERT(pChild2->getType() == AST_REAL);
  CPPUNIT_ASSERT(fabs((pChild2->getReal() - 4.0) / 4.0) < 1e-15);

  pRule = pSBMLModel->getRule(1);
  CPPUNIT_ASSERT(pRule != NULL);
  CPPUNIT_ASSERT(pRule->getTypeCode() == SBML_ASSIGNMENT_RULE);
  pARule = dynamic_cast<const AssignmentRule*>(pRule);
  CPPUNIT_ASSERT(pARule != NULL);
  CPPUNIT_ASSERT(pARule->getVariable() == pParameter1->getId());
  CPPUNIT_ASSERT(pARule->isSetMath() == true);
  pMath = pARule->getMath();
  CPPUNIT_ASSERT(pMath != NULL);
  CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
  CPPUNIT_ASSERT(pMath->getName() == pParameter4->getId());
  CPPUNIT_ASSERT(pMath->getNumChildren() == 0);

  pRule = pSBMLModel->getRule(2);
  CPPUNIT_ASSERT(pRule != NULL);
  CPPUNIT_ASSERT(pRule->getTypeCode() == SBML_ASSIGNMENT_RULE);
  pARule = dynamic_cast<const AssignmentRule*>(pRule);
  CPPUNIT_ASSERT(pARule != NULL);
  CPPUNIT_ASSERT(pARule->getVariable() == pParameter3->getId());
  CPPUNIT_ASSERT(pARule->isSetMath() == true);
  pMath = pARule->getMath();
  CPPUNIT_ASSERT(pMath != NULL);
  CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
  CPPUNIT_ASSERT(pMath->getName() == pParameter1->getId());
  CPPUNIT_ASSERT(pMath->getNumChildren() == 0);

  pRule = pSBMLModel->getRule(3);
  CPPUNIT_ASSERT(pRule != NULL);
  CPPUNIT_ASSERT(pRule->getTypeCode() == SBML_ASSIGNMENT_RULE);
  pARule = dynamic_cast<const AssignmentRule*>(pRule);
  CPPUNIT_ASSERT(pARule != NULL);
  CPPUNIT_ASSERT(pARule->getVariable() == pParameter5->getId());
  CPPUNIT_ASSERT(pARule->isSetMath() == true);
  pMath = pARule->getMath();
  CPPUNIT_ASSERT(pMath != NULL);
  CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
  CPPUNIT_ASSERT(pMath->getName() == pParameter3->getId());
  CPPUNIT_ASSERT(pMath->getNumChildren() == 0);

  pRule = pSBMLModel->getRule(4);
  CPPUNIT_ASSERT(pRule != NULL);
  CPPUNIT_ASSERT(pRule->getTypeCode() == SBML_ASSIGNMENT_RULE);
  pARule = dynamic_cast<const AssignmentRule*>(pRule);
  CPPUNIT_ASSERT(pARule != NULL);
//.........这里部分代码省略.........