//Deprecated function
int Replacing::performReplacement()
{
set<SBase*> toremove;
set<SBase*>* removed = NULL;
CompModelPlugin* cmp = NULL;
SBase* parent = getParentSBMLObject();
while (parent != NULL && parent->getTypeCode() != SBML_DOCUMENT) {
if (parent->getTypeCode() == SBML_COMP_MODELDEFINITION ||
parent->getTypeCode() == SBML_MODEL) {
cmp = static_cast<CompModelPlugin*>(parent->getPlugin("comp"));
if (cmp != NULL) {
removed = cmp->getRemovedSet();
}
}
parent = parent->getParentSBMLObject();
}
int ret = performReplacementAndCollect(removed, &toremove);
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
if (cmp == NULL) {
return LIBSBML_INVALID_OBJECT;
}
return cmp->removeCollectedElements(removed, &toremove);
}
/** @cond doxygenLibsbmlInternal */
int
Replacing::replaceWithAndMaybeDelete(SBase* replacement, bool deleteme, ASTNode* conversionFactor)
{
//All of the following function calls that could result in errors set their own error messages.
SBase* replaced = getReferencedElement();
if (replaced==NULL) return LIBSBML_INVALID_OBJECT;
//Rename things
int ret = updateIDs(replaced, replacement);
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
//Perform any conversions on references in the submodel.
ret = performConversions(replacement, &conversionFactor);
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
//Finally, recurse down if there are things the replaced element itself replaced (or used to be replaced by)
CompSBasePlugin* replacedplug = static_cast<CompSBasePlugin*>(replaced->getPlugin(getPrefix()));
if (replacedplug==NULL) {
//assert(false); //Not sure when this situation would come up, so I would like to see an example.
//(sadly, I cannot set an assert in production code.)
return LIBSBML_OPERATION_SUCCESS; //I guess? LS DEBUG
}
for (unsigned int re=0; re<replacedplug->getNumReplacedElements(); re++) {
ret = replacedplug->getReplacedElement(re)->replaceWithAndMaybeDelete(replacement, true, conversionFactor);
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
}
if (replacedplug->isSetReplacedBy()) {
ret = replacedplug->getReplacedBy()->replaceWithAndMaybeDelete(replacement, deleteme, conversionFactor);
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
}
return LIBSBML_OPERATION_SUCCESS;
}
int SBaseRef::collectDeletions(set<SBase*>* removed, set<SBase*>* toremove)
{
SBase* todelete = getReferencedElement();
if (todelete==NULL) {
return LIBSBML_INVALID_OBJECT;
}
if (removed) {
if (removed->find(todelete) != removed->end()) {
//Already deleted or replaced.
return LIBSBML_OPERATION_SUCCESS;
}
}
if (toremove) {
toremove->insert(todelete);
}
CompSBasePlugin* todplug = static_cast<CompSBasePlugin*>(todelete->getPlugin(getPrefix()));
if (todplug != NULL) {
for (unsigned long re=0; re<todplug->getNumReplacedElements(); re++) {
todplug->getReplacedElement(re)->collectDeletions(removed, toremove);
}
if (todplug->isSetReplacedBy()) {
todplug->getReplacedBy()->collectDeletions(removed, toremove);
}
}
return LIBSBML_OPERATION_SUCCESS;
}
/*
* Checks that all ids on the following Model objects are unique:
* FunctionDefinitions, Species, Compartments, global Parameters,
* Reactions, and Events.
*/
void
PackageIdReplacementCheck::check_ (const Model& m, const Model& object)
{
unsigned int n, size;
const CompSBasePlugin * plug;
ReplacedFilter filter;
ReplacedByFilter repByFilter;
/* get all elements that have replaced elements */
List* allElements = const_cast<Model *>(&m)->getAllElements(&filter);
size = allElements->getSize();
for (n = 0; n < size; ++n)
{
SBase *sb = static_cast<SBase*>(allElements->get(n));
plug = static_cast<const CompSBasePlugin*>(sb->getPlugin("comp"));
for (unsigned int i = 0; i < plug->getNumReplacedElements(); i++)
{
checkReferencedElement(*(const_cast<ReplacedElement*>
(plug->getReplacedElement(i))));
}
}
delete allElements;
/* get all elements that have replaced elements */
allElements = const_cast<Model *>(&m)->getAllElements(&repByFilter);
size = allElements->getSize();
for (n = 0; n < size; ++n)
{
SBase *sb = static_cast<SBase*>(allElements->get(n));
plug = static_cast<const CompSBasePlugin*>(sb->getPlugin("comp"));
checkReferencedElement(*(const_cast<ReplacedBy*>
(plug->getReplacedBy())));
}
delete allElements;
}
/** @cond doxygenLibsbmlInternal */
void CompModelPlugin::findUniqueSubmodPrefixes(vector<string>& submodids, List* allElements)
{
vector<int> suffixes(submodids.size(), 0);
bool done=false;
while (!done) {
done = true;
for (size_t str=0; str<submodids.size(); str++) {
stringstream fullprefix;
fullprefix << submodids[str];
if (suffixes[str] > 0) {
fullprefix << suffixes[str];
}
fullprefix << getDivider();
for (unsigned long el=0; el<allElements->getSize(); ++el) {
SBase* element = static_cast<SBase*>(allElements->get((unsigned int)el));
if (element==NULL) {
assert(false);
continue;
}
if (element->isSetId() && element->getId().find(fullprefix.str())==0) {
done = false;
continue;
}
else if (element->isSetMetaId() && element->getMetaId().find(fullprefix.str())==0) {
done = false;
continue;
}
else if (element->hasNonstandardIdentifierBeginningWith(fullprefix.str())) {
done = false;
continue;
}
else {
for (unsigned int p=0; p<element->getNumPlugins(); p++) {
if (element->getPlugin(p)->hasIdentifierBeginningWith(fullprefix.str())) {
done = false;
continue;
}
}
}
}
if (!done) {
suffixes[str]++;
continue; //Start over from the first ID; otherwise we end up checking a lot of things twice.
}
}
}
//Now change the submodid's:
for (size_t str=0; str<submodids.size(); str++) {
stringstream fullprefix;
fullprefix << submodids[str];
if (suffixes[str] > 0) {
fullprefix << suffixes[str];
}
fullprefix << getDivider();
submodids[str] = fullprefix.str();
}
}
int
ReplacedBy::removeFromParentAndDelete()
{
SBase* parent = getParentSBMLObject();
if (parent==NULL) return LIBSBML_OPERATION_FAILED;
CompSBasePlugin* comp_parent = static_cast<CompSBasePlugin*>(parent->getPlugin(getPrefix()));
if (comp_parent==NULL) return LIBSBML_OPERATION_FAILED;
return comp_parent->unsetReplacedBy();
}
Model* CompModelPlugin::flattenModel() const
{
//First make a copy of our parent (the model to be flattened):
const Model* parent = static_cast<const Model*>(getParentSBMLObject());
if (parent==NULL) {
return NULL;
}
//doc needs to be non-const so that the error messages can be updated. Otherwise, nothing changes.
SBMLDocument* doc = const_cast<SBMLDocument*>(getSBMLDocument());
if (doc==NULL) {
return NULL;
}
//Set the original document so that it can find the model definitions
//and external model definitions while we flatten.
Model* flat = parent->clone();
flat->setSBMLDocument(doc);
CompModelPlugin* flatplug =
static_cast<CompModelPlugin*>(flat->getPlugin(getPrefix()));
// Now instantiate its submodels and
// follow all renaming/deletion/replacement rules.
vector<const Model*> submods;
int success = flatplug->instantiateSubmodels();
if (success != LIBSBML_OPERATION_SUCCESS) {
//instantiateSubmodels sets its own error messages.
delete flat;
return NULL;
}
//Now start the aggregation process.
//This goes from the bottom up, calling 'appendFrom' iteratively
//(from the plugin).
for (unsigned int sm=0; sm<flatplug->getNumSubmodels(); sm++)
{
Model* submodel = flatplug->getSubmodel(sm)->getInstantiation();
if (submodel==NULL) {
//getInstantiation should be calling a cached value by now, but if not, it will set its own error messages.
delete flat;
return NULL;
}
CompModelPlugin* submodplug =
static_cast<CompModelPlugin*>(submodel->getPlugin(getPrefix()));
if (submodplug != NULL) {
//Strip the ports from the submodel, as we no longer need them.
while (submodplug->getNumPorts() > 0)
{
delete submodplug->removePort(0);
}
}
success = flat->appendFrom(submodel);
if (success != LIBSBML_OPERATION_SUCCESS) {
string error = "Unable to flatten model in CompModelPlugin::flattenModel: appending elements from the submodel '" + submodel->getId() + "' to the elements of the parent model failed.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error);
delete flat;
return NULL;
}
}
// Now we clear the saved referenced elements in the local Port objects,
// but point them to the new object if necessary.
flatplug->resetPorts();
// Next, strip the package info from 'flat'.
// We're going to remove everything but the Ports:
flatplug->mListOfSubmodels.clear();
flatplug->clearReplacedElements();
flatplug->unsetReplacedBy();
List* allelements = flat->getAllElements();
vector<SBase*> nonReplacedElements;
for (unsigned int el=0; el<allelements->getSize(); el++)
{
SBase* element = static_cast<SBase*>(allelements->get(el));
int type = element->getTypeCode();
if (!(type==SBML_COMP_REPLACEDBY ||
type==SBML_COMP_REPLACEDELEMENT ||
type==SBML_COMP_SBASEREF))
{
nonReplacedElements.push_back(element);
}
}
// delete the list
delete allelements;
for (unsigned int el=0; el<nonReplacedElements.size(); el++)
{
SBase* element = nonReplacedElements[el];
CompSBasePlugin* elplug =
static_cast<CompSBasePlugin*>(element->getPlugin(getPrefix()));
if (elplug != NULL)
{
elplug->clearReplacedElements();
elplug->unsetReplacedBy();
}
}
//Finally, unset the document again.
flat->setSBMLDocument(NULL);
return flat;
}
int ReplacedElement::performReplacementAndCollect(set<SBase*>* removed, set<SBase*>* toremove)
{
SBMLDocument* doc = getSBMLDocument();
if (isSetDeletion()) {
//Deletions don't need to be replaced.
return LIBSBML_OPERATION_SUCCESS;
}
//Find the various objects and plugin objects we need for this to work.
SBase* lore = getParentSBMLObject();
ListOf* lorelist = static_cast<ListOf*>(lore);
if (lore == NULL) {
if (doc) {
string error = "Cannot carry out replacement in ReplacedElement::performReplacement: no parent <listOfReplacedElements> could be found for the given replacement element.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
if (lore->getTypeCode() != SBML_LIST_OF || lorelist->getItemTypeCode() != SBML_COMP_REPLACEDELEMENT) {
if (doc) {
string error = "Cannot carry out replacement in ReplacedElement::performReplacement: no parent <listOfReplacedElements> could be found for the given replacement element.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
SBase* parent = lore->getParentSBMLObject();
if (parent==NULL) {
if (doc) {
string error = "Cannot carry out replacement in ReplacedElement::performReplacement: no parent could be found for the parent <listOfReplacedElements> object.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
SBase* ref = getReferencedElement();
if (ref==NULL) {
//getReferencedElement sets its own error messages.
return LIBSBML_INVALID_OBJECT;
}
if (removed && removed->find(ref)!=removed->end()) {
//Already deleted: can't get the deleted element's ID to
if (doc) {
string error = "Cannot carry out replacement in ReplacedElement::performReplacement: a <" + parent->getElementName() + ">";
if (parent->isSetId()) {
error += " with the ID '" + parent->getId() + "'";
}
error += " has a child <replacedElement> that points to something that has already been deleted, probably because its parent was deleted.";
doc->getErrorLog()->logPackageError("comp", CompDeletedReplacement, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return LIBSBML_INVALID_OBJECT;
}
//Update the IDs.
int ret = updateIDs(ref, parent);
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
//Perform any conversions on references in the submodel.
ASTNode* blank = NULL;
ret = performConversions(parent, &blank);
if (ret != LIBSBML_OPERATION_SUCCESS)
{
if (blank != NULL)
{
delete blank;
}
return ret;
}
CompSBasePlugin* refplug = static_cast<CompSBasePlugin*>(ref->getPlugin(getPrefix()));
if (refplug != NULL) {
//Now recurse down the 'replace*' tree, renaming IDs and deleting things as we go.
for (unsigned int re=0; re<refplug->getNumReplacedElements(); re++) {
refplug->getReplacedElement(re)->replaceWithAndMaybeDelete(parent, true, blank);
if (toremove) {
toremove->insert(refplug->getReplacedElement(re)->getReferencedElement());
}
}
if (refplug->isSetReplacedBy()) {
//Even if the subelement used to be replaced by something further down, it is now being replaced by the parent. It just can't catch a break, it seems.
refplug->getReplacedBy()->replaceWithAndMaybeDelete(parent, true, blank);
if (toremove) {
toremove->insert(refplug->getReplacedBy()->getReferencedElement());
}
}
}
if (toremove) {
toremove->insert(ref);
}
if (blank != NULL)
{
delete blank;
}
return LIBSBML_OPERATION_SUCCESS;
}