C++ Delay::setMath方法代码示例

END_TEST

START_TEST ( test_Delay )
{
  Delay* d = new Delay(2, 4);
  
  fail_unless (!(d->hasRequiredElements()));

  d->setMath(SBML_parseFormula("a+b"));

  fail_unless (d->hasRequiredElements());

  delete d;
}

END_TEST


START_TEST ( test_Event_parent_NULL )
{
    SBMLDocument *d = new SBMLDocument(2, 4);
    Model *m = d->createModel();
    Event *c = m->createEvent();
    EventAssignment *ea = c->createEventAssignment();
    Trigger *t = new Trigger(2, 4);
    t->setMath(new ASTNode());
    Delay *dy = new Delay(2, 4);
    dy->setMath(new ASTNode());
    c->setTrigger(t);
    c->setDelay(dy);

    fail_unless(c->getAncestorOfType(SBML_MODEL) == m);
    fail_unless(c->getTrigger()->getParentSBMLObject() == c);
    fail_unless (c->getDelay()->getSBMLDocument() == d);
    fail_unless(ea->getAncestorOfType(SBML_EVENT) == c);

    Event *c1 = c->clone();
    delete d;

    fail_unless(c1->getAncestorOfType(SBML_MODEL) == NULL);
    fail_unless(c1->getParentSBMLObject() == NULL);
    fail_unless (c1->getSBMLDocument() == NULL);

    fail_unless(c1->getEventAssignment(0)->getAncestorOfType(SBML_MODEL) == NULL);
    fail_unless(c1->getEventAssignment(0)->getAncestorOfType(SBML_EVENT) == c1);
    fail_unless(c1->getEventAssignment(0)->getParentSBMLObject() != NULL);
    fail_unless(c1->getEventAssignment(0)->getSBMLDocument() == NULL);

    fail_unless(c1->getTrigger()->getAncestorOfType(SBML_MODEL) == NULL);
    fail_unless(c1->getTrigger()->getAncestorOfType(SBML_EVENT) == c1);
    fail_unless(c1->getTrigger()->getParentSBMLObject() != NULL);
    fail_unless(c1->getTrigger()->getSBMLDocument() == NULL);

    fail_unless(c1->getDelay()->getAncestorOfType(SBML_MODEL) == NULL);
    fail_unless(c1->getDelay()->getAncestorOfType(SBML_EVENT) == c1);
    fail_unless(c1->getDelay()->getParentSBMLObject() != NULL);
    fail_unless(c1->getDelay()->getSBMLDocument() == NULL);

    delete c1;
}

int Submodel::convertTimeAndExtentWith(const ASTNode* tcf, const ASTNode* xcf, const ASTNode* klmod)
{
  if (tcf==NULL && xcf==NULL) return LIBSBML_OPERATION_SUCCESS;
  Model* model = getInstantiation();
  if (model==NULL) {
    //getInstantiation sets its own error messages.
    return LIBSBML_OPERATION_FAILED;
  }
  ASTNode tcftimes(AST_TIMES);
  ASTNode tcfdiv(AST_DIVIDE);
  if (tcf != NULL) {
    tcftimes.addChild(tcf->deepCopy());
    tcfdiv.addChild(tcf->deepCopy());
  }
  ASTNode rxndivide(AST_DIVIDE);
  if (klmod != NULL) {
    ASTNode rxnref(AST_NAME);
    rxndivide.addChild(rxnref.deepCopy());
    rxndivide.addChild(klmod->deepCopy());
  }
  List* allElements = model->getAllElements();
  for (ListIterator iter = allElements->begin(); iter != allElements->end(); ++iter)
  {
    SBase* element = static_cast<SBase*>(*iter);
    assert(element != NULL);
    ASTNode* ast1 = NULL;
    ASTNode* ast2 = NULL;
    Constraint* constraint = NULL;
    Delay* delay = NULL;
    EventAssignment* ea = NULL;
    InitialAssignment* ia = NULL;
    KineticLaw* kl = NULL;
    Priority* priority = NULL;
    RateRule* rrule = NULL;
    Rule* rule = NULL;
    Submodel* submodel = NULL;
    Trigger* trigger = NULL;
    string cf = "";
    //Reaction math will be converted below, in the bits with the kinetic law.  But because of that, we need to handle references *to* the reaction:  even if it has no kinetic law, the units have changed, and this needs to be reflected by the flattening routine.
    if (rxndivide.getNumChildren() != 0 && element->getTypeCode()==SBML_REACTION && element->isSetId()) {
      rxndivide.getChild(0)->setName(element->getId().c_str());
      for (ListIterator iter = allElements->begin(); iter != allElements->end(); ++iter)
      {
        SBase* subelement = static_cast<SBase*>(*iter);
        subelement->replaceSIDWithFunction(element->getId(), &rxndivide);
      }
    }

    //Submodels need their timeConversionFactor and extentConversionFactor attributes converted.  We're moving top-down, so all we need to do here is fix the conversion factor attributes themselves, pointing them to new parameters if need be.
    if ((tcf !=NULL || xcf != NULL) && element->getTypeCode()==SBML_COMP_SUBMODEL) {
      submodel = static_cast<Submodel*>(element);
      if (tcf != NULL) {
        if (submodel->isSetTimeConversionFactor()) {
          createNewConversionFactor(cf, tcf, submodel->getTimeConversionFactor(), model);
          submodel->setTimeConversionFactor(cf);
        }
        else {
          submodel->setTimeConversionFactor(tcf->getName());
        }
      }
      if (xcf != NULL) {
        if (submodel->isSetExtentConversionFactor()) {
          createNewConversionFactor(cf, xcf, submodel->getExtentConversionFactor(), model);
          submodel->setExtentConversionFactor(cf);
        }
        else {
          submodel->setExtentConversionFactor(xcf->getName());
        }
      }
    }
    if (tcf==NULL) {
      if (klmod !=NULL && element->getTypeCode()==SBML_KINETIC_LAW) {
        kl = static_cast<KineticLaw*>(element);
        if (kl->isSetMath()) {
          ast1 = new ASTNode(AST_TIMES);
          ast1->addChild(klmod->deepCopy());
          ast1->addChild(kl->getMath()->deepCopy());
          kl->setMath(ast1);
          delete ast1;
        }
      }
    }
    else {
      // All math 'time' and 'delay' csymbols must still be converted.
      // Also, several constructs are modified directly.
      switch(element->getTypeCode()) {
        //This would be a WHOLE LOT SIMPLER if there was a 'hasMath' class in libsbml.  But even so, it would have to
        // handle the kinetic laws, rate rules, and delays separately.
      case SBML_KINETIC_LAW:
        //Kinetic laws are multiplied by 'klmod'.
        kl = static_cast<KineticLaw*>(element);
        ast1 = kl->getMath()->deepCopy();
        convertCSymbols(ast1, &tcfdiv, &tcftimes);
        if (klmod !=NULL) {
          kl = static_cast<KineticLaw*>(element);
          if (kl->isSetMath()) {
            ast2 = new ASTNode(AST_TIMES);
            ast2->addChild(klmod->deepCopy());
            ast2->addChild(ast1);
            kl->setMath(ast2);
//.........这里部分代码省略.........

void Module::CreateSBMLModel()
{
  Model* sbmlmod = m_sbml.createModel();
  sbmlmod->setId(m_modulename);
  sbmlmod->setName(m_modulename);
  sbmlmod->setNotes("<body xmlns=\"http://www.w3.org/1999/xhtml\"><p> Originally created by libAntimony " VERSION_STRING " (using libSBML " LIBSBML_DOTTED_VERSION ") </p></body>");
  char cc = g_registry.GetCC();
  //User-defined functions
  for (size_t uf=0; uf<g_registry.GetNumUserFunctions(); uf++) {
    const UserFunction* userfunction = g_registry.GetNthUserFunction(uf);
    assert(userfunction != NULL);
    FunctionDefinition* fd = sbmlmod->createFunctionDefinition();
    fd->setId(userfunction->GetModuleName());
    ASTNode* math = parseStringToASTNode(userfunction->ToSBMLString());
    fd->setMath(math);
    delete math;
  }
  //Compartments
  Compartment* defaultCompartment = sbmlmod->createCompartment();
  defaultCompartment->setId(DEFAULTCOMP);
  defaultCompartment->setConstant(true);
  defaultCompartment->setSize(1);
  defaultCompartment->setSBOTerm(410); //The 'implicit compartment'
  size_t numcomps = GetNumVariablesOfType(allCompartments);
  for (size_t comp=0; comp<numcomps; comp++) {
    const Variable* compartment = GetNthVariableOfType(allCompartments, comp);
    Compartment* sbmlcomp = sbmlmod->createCompartment();
    sbmlcomp->setId(compartment->GetNameDelimitedBy(cc));
    if (compartment->GetDisplayName() != "") {
      sbmlcomp->setName(compartment->GetDisplayName());
    }
    sbmlcomp->setConstant(compartment->GetIsConst());
    formula_type ftype = compartment->GetFormulaType();
    assert (ftype == formulaINITIAL || ftype==formulaASSIGNMENT || ftype==formulaRATE);
    if (ftype != formulaINITIAL) {
      sbmlcomp->setConstant(false);
    }
    const Formula* formula = compartment->GetFormula();
    if (formula->IsDouble()) {
      sbmlcomp->setSize(atof(formula->ToSBMLString().c_str()));
    }
    SetAssignmentFor(sbmlmod, compartment);
  }

  //Species
  size_t numspecies = GetNumVariablesOfType(allSpecies);
  for (size_t spec=0; spec < numspecies; spec++) {
    const Variable* species = GetNthVariableOfType(allSpecies, spec);
    Species* sbmlspecies = sbmlmod->createSpecies();
    sbmlspecies->setId(species->GetNameDelimitedBy(cc));
    if (species->GetDisplayName() != "") {
      sbmlspecies->setName(species->GetDisplayName());
    }
    sbmlspecies->setConstant(false); //There's no need to try to distinguish between const and var for species.
    if (species->GetIsConst()) {
      sbmlspecies->setBoundaryCondition(true);
    }
    else {
      sbmlspecies->setBoundaryCondition(false);
    }
    const Variable* compartment = species->GetCompartment();
    if (compartment == NULL) {
      sbmlspecies->setCompartment(defaultCompartment->getId());
    }
    else {
      sbmlspecies->setCompartment(compartment->GetNameDelimitedBy(cc));
    }
    const Formula* formula = species->GetFormula();
    if (formula->IsDouble()) {
      sbmlspecies->setInitialConcentration(atof(formula->ToSBMLString().c_str()));
    }
    else if (formula->IsAmountIn(species->GetCompartment())) {
      sbmlspecies->setInitialAmount(formula->ToAmount());
    }
    SetAssignmentFor(sbmlmod, species);
  }

  //Formulas
  size_t numforms = GetNumVariablesOfType(allFormulas);
  for (size_t form=0; form < numforms; form++) {
    const Variable* formvar = GetNthVariableOfType(allFormulas, form);
    const Formula*  formula = formvar->GetFormula();
    Parameter* param = sbmlmod->createParameter();
    param->setId(formvar->GetNameDelimitedBy(cc));
    if (formvar->GetDisplayName() != "") {
      param->setName(formvar->GetDisplayName());
    }
    param->setConstant(formvar->GetIsConst());
    if (formula->IsDouble()) {
      param->setValue(atof(formula->ToSBMLString().c_str()));
    }
    SetAssignmentFor(sbmlmod, formvar);
    formula_type ftype = formvar->GetFormulaType();
    assert (ftype == formulaINITIAL || ftype==formulaASSIGNMENT || ftype==formulaRATE);
    if (ftype != formulaINITIAL) {
      param->setConstant(false);
    }
  }

  //Reactions
//.........这里部分代码省略.........