C++ Submodel类代码示例

void checkComp(CompSBMLDocumentPlugin* compdoc, set<string>& components, set<string>& tests,  const map<string, vector<double> >& results)
{
  SBMLDocument* doc = compdoc->getSBMLDocument();
  List* allElements = doc->getAllElements();
  for (unsigned int e=0; e<allElements->getSize(); e++) {
    SBase* element = static_cast<SBase*>(allElements->get(e));
    ReplacedElement* re;
    Submodel* submod;
    switch(element->getTypeCode()) {
    case SBML_COMP_SUBMODEL:
      components.insert("comp:Submodel");
      submod = static_cast<Submodel*>(element);
      if (submod->isSetExtentConversionFactor()) {
        tests.insert("comp:ExtentConversionFactor");
      }
      if (submod->isSetTimeConversionFactor()) {
        tests.insert("comp:TimeConversionFactor");
      }
      break;
    case SBML_COMP_MODELDEFINITION:
      components.insert("comp:ModelDefinition");
      break;
    case SBML_COMP_EXTERNALMODELDEFINITION:
      components.insert("comp:ExternalModelDefinition");
      break;
    case SBML_COMP_SBASEREF:
      components.insert("comp:SBaseRef");
      break;
    case SBML_COMP_DELETION:
      components.insert("comp:Deletion");
      break;
    case SBML_COMP_REPLACEDELEMENT:
      components.insert("comp:ReplacedElement");
      re = static_cast<ReplacedElement*>(element);
      if (re->isSetConversionFactor()) {
        tests.insert("comp:ConversionFactor");
      }
      break;
    case SBML_COMP_REPLACEDBY:
      components.insert("comp:ReplacedBy");
      break;
    case SBML_COMP_PORT:
      components.insert("comp:Port");
      break;
    default:
      break;
    }
  }
  for (map<string, vector<double> >::const_iterator result=results.begin(); 
    result != results.end(); result++) {
      string id = result->first;
      if (id.find("__") != string::npos) {
        //It is probably a submodel element, renamed
        tests.insert("comp:SubmodelOutput");
      }
  }
}

int CompModelPlugin::collectDeletionsAndDeleteSome(set<SBase*>* removed, set<SBase*>* toremove)
{
  int ret = LIBSBML_OPERATION_SUCCESS;
  SBMLDocument* doc = getSBMLDocument();
  Model* model = static_cast<Model*>(getParentSBMLObject());
  if (model==NULL) {
    if (doc) {
      string error = "Unable to attempt to perform deletions in CompModelPlugin::collectDeletionsAndDeleteSome: no parent model could be found for the given 'comp' model plugin element.";
      doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error);
    }
    return LIBSBML_OPERATION_FAILED;
  }

  //Since deletions only exist in submodels, loop through the submodels.
  for (unsigned int sub=0; sub<getNumSubmodels(); sub++) {
    Submodel* submodel = getSubmodel(sub);
    //First perform any deletions
    for (unsigned int d=0; d<submodel->getNumDeletions(); d++) {
      Deletion* deletion = submodel->getDeletion(d);
      SBase* todel = deletion->getReferencedElement();
      if (todel && (todel->getTypeCode() == SBML_COMP_DELETION ||
                    todel->getTypeCode() == SBML_COMP_REPLACEDBY ||
                    todel->getTypeCode() == SBML_COMP_REPLACEDELEMENT ||
                    todel->getTypeCode() == SBML_LOCAL_PARAMETER) )
      {
        //Go ahead and delete it!
        set<SBase*> newToRemove;
        newToRemove.insert(todel);
        removeCollectedElements(removed, &newToRemove);
      }
      else {
        //Otherwise, just collect it.
        ret = deletion->collectDeletions(removed, toremove);
        if (ret!=LIBSBML_OPERATION_SUCCESS) {
          return ret;
        }
      }
    }
    //Next collect any deletions in that instantiated submodel (any that weren't just deleted)
    Model* mod = submodel->getInstantiation();
    if (mod==NULL) {
      //getInstantiation sets its own error messages.
      return LIBSBML_OPERATION_FAILED;
    }
    CompModelPlugin* modplug = static_cast<CompModelPlugin*>(mod->getPlugin(getPrefix()));
    if (modplug==NULL) {
      if (doc) {
        //Shouldn't happen:  'getInstantiation' turns on the comp plugin.
        string error = "Unable to rename elements in CompModelPlugin::collectDeletionsAndDeleteSome: no valid 'comp' plugin for the model instantiated from submodel " + submodel->getId();
        doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error);
      }
      return LIBSBML_OPERATION_FAILED;
    }
    modplug->collectDeletionsAndDeleteSome(removed, toremove);
  }
  return ret;
}

SBase* 
ReplacedElement::getReferencedElementFrom(Model* model)
{
  SBMLDocument* doc = getSBMLDocument();
  SBase* referent = Replacing::getReferencedElementFrom(model);
  if (referent != NULL) return referent;
  if (!isSetDeletion()) {
    //In this case, something else went wrong in getReferencedElementFrom, which will have set its own error message.
    return NULL;
  }
  model = getParentModel(this);
  if (model==NULL) {
    if (doc) {
      string error = "In ReplacedElement::getReferencedElementFrom, unable to find referenced deletion '" + getDeletion() + "' for <replacedElement>: no parent model could be found.";
      doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
    }
    return NULL;
  }
  CompModelPlugin* mplugin = static_cast<CompModelPlugin*>(model->getPlugin(getPrefix()));
  if (mplugin==NULL) {
    if (doc) {
      string error = "In ReplacedElement::getReferencedElementFrom, unable to find referenced deletion '" + getDeletion() + "' for <replacedElement>: no 'comp' plugin for the parent model could be found.";
      doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
    }
    return NULL;
  }
  Submodel* submod = mplugin->getSubmodel(getSubmodelRef());
  if (submod==NULL) {
    if (doc) {
      string error = "In ReplacedElement::getReferencedElementFrom, unable to find referenced deletion '" + getDeletion() + "' for <replacedElement>: no such submodel '" + getSubmodelRef() + "'.";
      doc->getErrorLog()->logPackageError("comp", CompReplacedElementSubModelRef, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
    }
    return NULL;
  }
  SBase* ret = submod->getDeletion(getDeletion());
  if (ret==NULL && doc) {
    string error = "In ReplacedElement::getReferencedElementFrom, unable to find referenced deletion '" + getDeletion() + "' for <replacedElement>: no deletion with that ID exists in the model.";
    doc->getErrorLog()->logPackageError("comp", CompDeletionMustReferenceObject, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
  }
  return ret;
}

/*
 * Loop through all Submodels in this Model, instantiate all of them, 
 * perform all deletions, and synchronize all replacements.  
 * The resulting models are stored in the Submodel objects, 
 * and available from 'Submodel::getInstantiation()'
 */
int 
CompModelPlugin::instantiateSubmodels()
{
  Model* model = static_cast<Model*>(getParentSBMLObject());
  
  if (model==NULL) 
    return LIBSBML_INVALID_OBJECT;
  
  int ret;

  // First we instantiate all the submodels.  
  // This acts recursively downward through the stack.
  for (unsigned int sub=0; sub<mListOfSubmodels.size(); sub++) 
  {
    Submodel* submodel = mListOfSubmodels.get(sub);
    // Instead of 'instantiate', since we might have already 
    // been instantiated ourselves from above.
    Model* submodinst = submodel->getInstantiation(); 
    
    if (submodinst == NULL ) {
      //'getInstantiation' already sets any errors that might have occurred.
      return LIBSBML_OPERATION_FAILED;
    }
    
    //// if we have a transformer specified, then we need to propagate it, so it can
    //// be used

    // this needs to happen in Submodel:instantiate

    //if (isSetTransformer())
    //{
    //  CompModelPlugin* other = dynamic_cast<CompModelPlugin*>(submodinst->getPlugin("comp"));
    //  if (other != NULL)
    //    other->setTransformer(getTransformer());
    //}
  }

  // Next, recursively find all the targets of SBaseRef elements 
  // and save them, since we're about to rename everything and 
  // we won't be able to find things by name any more.
  ret = saveAllReferencedElements(); 
  if (ret != LIBSBML_OPERATION_SUCCESS) {
    //saveAllReferencedElements sets any errors.
    return ret;
  }

  mRemoved.clear();
  set<SBase*> toremove;

  // Collect deletions (top-down):  
  // need to do this before renaming in case we delete a local parameter.
  ret = collectDeletionsAndDeleteSome(&mRemoved, &toremove);

  if (ret != LIBSBML_OPERATION_SUCCESS) {
    return ret;
  }

  //Next, we rename *all* the elements so everything is unique.
  ret = renameAllIDsAndPrepend("");
  if (ret != LIBSBML_OPERATION_SUCCESS) {
    return ret;
  }

  //Perform replacements and conversions (top-down) and collect them.
  ret = collectRenameAndConvertReplacements(&mRemoved, &toremove);

  if (ret != LIBSBML_OPERATION_SUCCESS) {
    return ret;
  }

  //Finally, actually remove the collected elements from the model--they are
  // all now redundant.  Have to wait until now to do this, because of the
  // possibility of nested constructs:  replacing the child of a replaced
  // element, for example, or even replacing the child of a deleted
  // element.
  removeCollectedElements(&mRemoved, &toremove);

  mRemoved.clear();

  return LIBSBML_OPERATION_SUCCESS;
}

int 
Replacing::saveReferencedElement()
{
  SBMLDocument* doc = getSBMLDocument();
  if (!isSetSubmodelRef()) {
    if (doc) {
      string error = "Unable to find referenced element in Replacing::saveReferencedElement: the given <" + getElementName() + "> element";
      if (isSetId()) {
        error += " '" + getId() + "'";
      }
      error += " has no 'submodelRef' attribute.";
      doc->getErrorLog()->logPackageError("comp", CompReplacedElementAllowedAttributes, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
    }
    return LIBSBML_INVALID_OBJECT;
  }
  Model* model = getParentModel(this);
  if (model==NULL) {
    if (doc) {
      string error = "Unable to find referenced element in Replacing::saveReferencedElement: no parent model could be found for the given <" + getElementName() + "> element";
      if (isSetId()) {
        error += " '" + getId() + "'.";
      }
      doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
    }
    return LIBSBML_OPERATION_FAILED;
  }
  CompModelPlugin* cmp = static_cast<CompModelPlugin*>(model->getPlugin(getPrefix()));
  if (cmp==NULL) {
    if (doc) {
      string error = "Unable to find referenced element in Replacing::saveReferencedElement: no 'comp' plugin for the parent model could be found for the given <" + getElementName() + "> element";
      if (isSetId()) {
        error += " '" + getId() + "'.";
      }
      doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
    }
    return LIBSBML_OPERATION_FAILED;
  }
  Submodel* submod = cmp->getSubmodel(getSubmodelRef());
  if (submod==NULL) {
    if (doc) {
      string error = "Unable to find referenced element for the given <" + getElementName() + "> element";
      if (isSetId()) {
        error += " '" + getId() + "'";
      }
      error += " in Replacing::saveReferencedElement: the submodelRef '" + getSubmodelRef() + "' could not be found in the model.";
      int errnumber = CompReplacedElementSubModelRef;
      if (getTypeCode() == SBML_COMP_REPLACEDBY) {
        errnumber = CompReplacedBySubModelRef;
      }
      doc->getErrorLog()->logPackageError("comp", errnumber, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
    }
    return LIBSBML_INVALID_ATTRIBUTE_VALUE;
  }
  Model* inst = submod->getInstantiation();
  if (inst==NULL) {
    //getInstantiation sets it own error messages.
    return LIBSBML_OPERATION_FAILED;
  }
  mReferencedElement = getReferencedElementFrom(inst);
  if (mDirectReference==NULL) {
    mDirectReference = mReferencedElement;
  }
  //getReferencedElement* set their own error messages:
  if (mReferencedElement==NULL) {
    return LIBSBML_OPERATION_FAILED;
  }
  if (mReferencedElement->getTypeCode()==SBML_COMP_PORT) {
    mReferencedElement = static_cast<Port*>(mReferencedElement)->getReferencedElement();
  }
  if (mReferencedElement==NULL) {
    return LIBSBML_OPERATION_FAILED;
  }
  return LIBSBML_OPERATION_SUCCESS;
}

int 
Submodel::instantiate()
{
  SBMLDocument* doc = getSBMLDocument();
  SBMLDocument* rootdoc = doc;
  if (doc==NULL) 
  {
    return LIBSBML_OPERATION_FAILED;
  }

  CompSBMLDocumentPlugin* docplugin = 
    static_cast<CompSBMLDocumentPlugin*>(doc->getPlugin(getPrefix()));
  if (docplugin==NULL)
  {
    return LIBSBML_OPERATION_FAILED;
  }

  SBase* parent  = getParentSBMLObject();
  string parentmodelname = "";
  string parentURI = "";
  set<string> uniqueModels;
  while (parent != NULL && parent->getTypeCode() != SBML_DOCUMENT) {
    if (parent->getTypeCode() == SBML_COMP_SUBMODEL) {
      const Submodel* parentsub = static_cast<const Submodel*>(parent);
      uniqueModels.insert(parentsub->mInstantiationOriginalURI + "::" + parentsub->getModelRef());
      if (parentURI=="") {
        parentURI=parentsub->mInstantiationOriginalURI;
      }
    }
    if (parent->getTypeCode() == SBML_MODEL ||
      parent->getTypeCode() == SBML_COMP_MODELDEFINITION)
    {
      if (parentmodelname == "") {
        parentmodelname = parent->getId();
      }
    }
    rootdoc = parent->getSBMLDocument();
    parent = parent->getParentSBMLObject();
  }

  if (mInstantiatedModel != NULL) 
  {
    delete mInstantiatedModel;
    mInstantiatedModel = NULL;
    mInstantiationOriginalURI.clear();
  }

  if (!hasRequiredAttributes()) {
    string error = "Instantiation error in Submodel::instantiate:  ";
    if (!isSetId()) {
      error += "A submodel in model '" + getParentModel(this)->getId() + "' does not have an 'id' attribute.";
    }
    else if (!isSetModelRef()) {
      error += "The submodel '" + getId() + "' does not have a 'modelRef' attribute.";
    }
    rootdoc->getErrorLog()->logPackageError("comp", CompSubmodelAllowedAttributes, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
    return LIBSBML_INVALID_OBJECT;
  }

  SBase* origmodel = docplugin->getModel(getModelRef());
  
  if (origmodel==NULL) {
    string error = "In Submodel::instantiate, unable to instantiate submodel '" + getId() + "' because the referenced model ('" + getModelRef() +"') does not exist.";
    rootdoc->getErrorLog()->logPackageError("comp", CompSubmodelMustReferenceModel, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
    return LIBSBML_INVALID_OBJECT;
  }
  ExternalModelDefinition* extmod;
  SBMLDocument* origdoc = NULL;
  string newmodel = parentURI + "::" + getModelRef();
  
  set<pair<string, string> > parents;
  switch(origmodel->getTypeCode()) 
  {
  case SBML_MODEL:
  case SBML_COMP_MODELDEFINITION:
    origdoc = origmodel->getSBMLDocument();
    mInstantiatedModel = static_cast<Model*>(origmodel)->clone();
    if (uniqueModels.insert(newmodel).second == false) {
      //Can't instantiate this model, because we are already a child of it.
      string error = "Error in Submodel::instantiate:  cannot instantiate submodel '" + getId() + "' in model '" + parentmodelname + "' because it references the model '" + getModelRef() + "', which is already an ancestor of the submodel.";
      rootdoc->getErrorLog()->logPackageError("comp", CompSubmodelCannotReferenceSelf, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
      return LIBSBML_OPERATION_FAILED;
    }
    mInstantiationOriginalURI = parentURI;
    break;
  case SBML_COMP_EXTERNALMODELDEFINITION:
    extmod = static_cast<ExternalModelDefinition*>(origmodel);
    if (extmod==NULL) 
    {
      //No error message:  it should be impossible, if origmodel has the type code 'external model definition', for it to not be castable to an external model definition.
      mInstantiatedModel = NULL;
      mInstantiationOriginalURI = "";
      return LIBSBML_OPERATION_FAILED;
    }
    mInstantiatedModel = extmod->getReferencedModel(rootdoc, parents);
    if (mInstantiatedModel == NULL) 
    {
      string error = "In Submodel::instantiate, unable to instantiate submodel '" + getId() + "' because the external model definition it referenced (model '" + getModelRef() +"') could not be resolved.";
      rootdoc->getErrorLog()->logPackageError("comp", CompSubmodelMustReferenceModel, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
      mInstantiationOriginalURI = "";
//.........这里部分代码省略.........

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
CompIdBase::checkId (const Submodel& x)
{
  if (x.isSetId()) doCheckId(x.getId(), x);
}

LIBSBML_CPP_NAMESPACE_USE

int main(int argc,char** argv)
{
  
  DynPkgNamespaces sbmlns;
  sbmlns.addPackageNamespace("comp", 1, "comp");

  // create the document

  SBMLDocument *document = new SBMLDocument(&sbmlns);
  document->setPackageRequired("dyn", true);
  document->setPackageRequired("comp", true);

  // create the Model

  Model* model=document->createModel();
  model->setId("grid2x2");

  // create the Compartment

  Compartment* compartment = model->createCompartment();
  compartment->setId("Loc1");
  compartment->setConstant(false);
  compartment->setSize(1);
  compartment->setSpatialDimensions(2.0);

  DynCompartmentPlugin* cplugin =
    static_cast<DynCompartmentPlugin*>(compartment->getPlugin("dyn"));
  
  SpatialComponent* component = cplugin->createSpatialComponent();
  component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANX);
  component->setVariable("q1_X");

  component = cplugin->createSpatialComponent();
  component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANY);
  component->setVariable("q1_Y");

  CompSBasePlugin* compPlugin = 
    static_cast<CompSBasePlugin*>(compartment->getPlugin("comp"));

  ReplacedElement* relement = compPlugin->createReplacedElement();
  relement->setIdRef("C");
  relement->setSubmodelRef("GRID_1_1_cell");

  compartment = model->createCompartment();
  compartment->setId("Loc2");
  compartment->setConstant(false);
  compartment->setSize(1);
  compartment->setSpatialDimensions(2.0);

  cplugin =
    static_cast<DynCompartmentPlugin*>(compartment->getPlugin("dyn"));

  component = cplugin->createSpatialComponent();
  component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANX);
  component->setVariable("q2_X");

  component = cplugin->createSpatialComponent();
  component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANY);
  component->setVariable("q2_Y");

  compPlugin =
    static_cast<CompSBasePlugin*>(compartment->getPlugin("comp"));

  relement = compPlugin->createReplacedElement();
  relement->setIdRef("C");
  relement->setSubmodelRef("GRID_1_2_cell");

  compartment = model->createCompartment();
  compartment->setId("Loc3");
  compartment->setConstant(false);
  compartment->setSize(1);
  compartment->setSpatialDimensions(2.0);

  cplugin =
    static_cast<DynCompartmentPlugin*>(compartment->getPlugin("dyn"));

  component = cplugin->createSpatialComponent();
  component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANX);
  component->setVariable("q3_X");

  component = cplugin->createSpatialComponent();
  component->setSpatialIndex(DYN_SPATIALKIND_CARTESIANY);
  component->setVariable("q3_Y");

  compPlugin =
    static_cast<CompSBasePlugin*>(compartment->getPlugin("comp"));

  relement = compPlugin->createReplacedElement();
  relement->setIdRef("C");
  relement->setSubmodelRef("GRID_2_1_cell");

  compartment = model->createCompartment();
  compartment->setId("Loc4");
  compartment->setConstant(false);
  compartment->setSize(1);
  compartment->setSpatialDimensions(2.0);

  cplugin =
//.........这里部分代码省略.........

//.........这里部分代码省略.........
    }
    mDirectReference = port;
    referent = port->getReferencedElementFrom(model);
  }
  else if (isSetIdRef()) {
    referent = model->getElementBySId(getIdRef());
    if (referent == NULL && doc) {
      string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element: no such SId in the model: '" + getIdRef() + "'.";
      if (doc->getErrorLog()->contains(UnrequiredPackagePresent) 
        || doc->getErrorLog()->contains(RequiredPackagePresent))
      {
        doc->getErrorLog()->logPackageError("comp", 
          CompIdRefMayReferenceUnknownPackage, getPackageVersion(), 
          getLevel(), getVersion(), error, getLine(), getColumn());
      }
      else
      {
        doc->getErrorLog()->logPackageError("comp", 
          CompIdRefMustReferenceObject, getPackageVersion(), 
          getLevel(), getVersion(), error, getLine(), getColumn());
      }
    }
  }
  else if (isSetUnitRef()) {
    referent = model->getUnitDefinition(getUnitRef());
    if (referent == NULL && doc) {
      string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element: no such Unit in the model: '" + getUnitRef() + "'.";
      doc->getErrorLog()->logPackageError("comp", CompUnitRefMustReferenceUnitDef, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
    }
  }
  else if (isSetMetaIdRef()) {
    referent = model->getElementByMetaId(getMetaIdRef());
    if (referent == NULL && doc) {
      string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element: no such metaid in the model: '" + getMetaIdRef() + "'.";
      if (doc->getErrorLog()->contains(UnrequiredPackagePresent) 
        || doc->getErrorLog()->contains(RequiredPackagePresent))
      {
        doc->getErrorLog()->logPackageError("comp", 
          CompIdRefMayReferenceUnknownPackage, getPackageVersion(), 
          getLevel(), getVersion(), error, getLine(), getColumn());
      }
      else
      {
        doc->getErrorLog()->logPackageError("comp", 
          CompMetaIdRefMustReferenceObject, getPackageVersion(), 
          getLevel(), getVersion(), error, getLine(), getColumn());
      }
    }
  }
  else {
    //This is actually possible if the subclass overrides getNumReferents() (which some do).  In that case, we just return NULL and let the overriding function find the referent instead.
    return NULL;
  }
  if (referent == NULL) {
    //No need to set an error message--one was already set above.
    return NULL;
  }
  if (isSetSBaseRef()) {
    //We're drilling into the submodels here, so our referent must be a submodel.
    if (referent->getTypeCode() != SBML_COMP_SUBMODEL) {
      if (doc) {
        string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element: the element ";
        if (referent->isSetId()) {
          error += "'" + referent->getId() + "'";
        }
        else if (referent->isSetMetaId()) {
          error += "with the metaid '" + referent->getMetaId() + "'";
        }
        error += " is not a submodel, and therefore has no subobjects for the child <sBaseRef> to refer to.";
        doc->getErrorLog()->logPackageError("comp", CompParentOfSBRefChildMustBeSubmodel, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
      }
      return NULL;
    }
    Submodel* subm = static_cast<Submodel*>(referent);
    if (subm==NULL) {
      //Note:  should be impossible.
      if (doc) {
        string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element: the element ";
        if (referent->isSetId()) {
          error += "'" + referent->getId() + "' ";
        }
        else if (referent->isSetMetaId()) {
          error += "with the metaid '" + referent->getMetaId() + "' ";
        }
        error += "claims to be a Submodel, but could not be programmatically turned into one.";
        doc->getErrorLog()->logPackageError("comp", CompParentOfSBRefChildMustBeSubmodel, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
      }
      return NULL;
    }
    Model* inst = subm->getInstantiation();
    if (inst==NULL) {
      //No need to set an additional error, as 'getInstantiation' will set one itself.
      return NULL;
    }
    //Recursive, so will set its own error messages:
    referent = getSBaseRef()->getReferencedElementFrom(inst);
    mDirectReference = getSBaseRef()->getDirectReference();
  }
  return referent;
}