C++ Submodel::getInstantiation方法代码示例

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;
}

/*
 * 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 CompModelPlugin::collectRenameAndConvertReplacements(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 perform replacements in CompModelPlugin::collectRenameAndConvertReplacements: 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;
  }
  List* allElements = model->getAllElements();
  vector<ReplacedElement*> res;
  vector<ReplacedBy*> rbs;
  //Collect replaced elements and replaced by's.
  for (unsigned int e=0; e<allElements->getSize(); e++) {
    SBase* element = static_cast<SBase*>(allElements->get(e));
    int type = element->getTypeCode();
    if (type==SBML_COMP_REPLACEDELEMENT) {
      ReplacedElement* reference = static_cast<ReplacedElement*>(element);
      res.push_back(reference);
    }
    if (type==SBML_COMP_REPLACEDBY) {
      ReplacedBy* reference = static_cast<ReplacedBy*>(element);
      rbs.push_back(reference);
    }
  }
  delete allElements;

  //ReplacedElement replacements
  for (size_t re=0; re<res.size(); re++) {
    ret = res[re]->performReplacementAndCollect(removed, toremove);
    if (ret != LIBSBML_OPERATION_SUCCESS) {
      return ret;
    }
  }

  //Now do the same thing for anything left over in the submodels
  for (unsigned int sub=0; sub<getNumSubmodels(); sub++) {
    Submodel* submodel = getSubmodel(sub);
    Model* mod = submodel->getInstantiation();
    if (mod==NULL) return LIBSBML_OPERATION_FAILED;
    CompModelPlugin* modplug = static_cast<CompModelPlugin*>(mod->getPlugin(getPrefix()));
    if (modplug==NULL) return LIBSBML_OPERATION_FAILED;
    //'left behind' converions (not LaHaye-style)
    ret = submodel->convertTimeAndExtent();
    if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
    ret = modplug->collectRenameAndConvertReplacements(removed, toremove);
    if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
  }

  //Perform ReplacedBy replacements *after* the submodels are done, so that the topmost-level names take precedence.
  for (size_t rb=0; rb<rbs.size(); rb++) {
    ret = rbs[rb]->performReplacementAndCollect(removed, toremove);
    if (ret != LIBSBML_OPERATION_SUCCESS) {
      return ret;
    }
  }

  return ret;
}

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;
}

//.........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;
}