/** @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;
}
CompSBasePlugin::CompSBasePlugin(const CompSBasePlugin& orig)
: SBasePlugin(orig)
, mListOfReplacedElements(NULL)
, mReplacedBy(NULL)
{
if (orig.isSetReplacedBy()) {
mReplacedBy = orig.mReplacedBy->clone();
mReplacedBy->connectToParent(getParentSBMLObject());
}
if (orig.getNumReplacedElements() > 0) {
createListOfReplacedElements();
for (unsigned int re=0; re<orig.getNumReplacedElements(); re++) {
mListOfReplacedElements->append(orig.getReplacedElement(re));
}
}
connectToChild();
}
END_TEST
START_TEST (test_comp_sbase)
{
SBMLNamespaces sbmlns(3,1,"comp",1);
Parameter param(&sbmlns);
CompSBasePlugin* pplugin = static_cast<CompSBasePlugin*>(param.getPlugin("comp"));
fail_unless(pplugin->getNumReplacedElements()==0);
ReplacedElement* re = pplugin->createReplacedElement();
re->setMetaId("re1");
fail_unless(pplugin->getNumReplacedElements()==1);
fail_unless(pplugin->addReplacedElement(NULL)==LIBSBML_INVALID_OBJECT);
ReplacedElement re2(3, 1);
re2.setMetaId("re2");
fail_unless(pplugin->addReplacedElement(&re2)==LIBSBML_INVALID_OBJECT);
re2.setDeletion("ID1");
fail_unless(pplugin->addReplacedElement(&re2)==LIBSBML_INVALID_OBJECT);
re2.setSubmodelRef("mod1");
fail_unless(pplugin->addReplacedElement(&re2)==LIBSBML_OPERATION_SUCCESS);
ReplacedElement* reref = pplugin->getReplacedElement(1);
fail_unless(reref != NULL);
fail_unless(reref->getMetaId()=="re2");
reref = pplugin->getReplacedElement(0);
fail_unless(reref != NULL);
fail_unless(reref->getMetaId()=="re1");
re->setDeletion("ID1");
fail_unless(reref->getDeletion()=="ID1");
fail_unless(pplugin->removeReplacedElement(3)==NULL);
fail_unless(pplugin->removeReplacedElement(0)==re);
fail_unless(pplugin->getReplacedElement(1)==NULL);
fail_unless(pplugin->isSetReplacedBy()==false);
ReplacedBy* rb = pplugin->createReplacedBy();
fail_unless(rb != NULL);
fail_unless(pplugin->isSetReplacedBy()==true);
fail_unless(pplugin->setReplacedBy(NULL)==LIBSBML_OPERATION_SUCCESS);
fail_unless(pplugin->isSetReplacedBy()==false);
ReplacedBy rb2(3,1);
fail_unless(pplugin->setReplacedBy(&rb2)==LIBSBML_INVALID_OBJECT);
rb2.setIdRef("ID1");
fail_unless(pplugin->setReplacedBy(&rb2)==LIBSBML_INVALID_OBJECT);
rb2.setSubmodelRef("mod1");
fail_unless(pplugin->setReplacedBy(&rb2)==LIBSBML_OPERATION_SUCCESS);
fail_unless(pplugin->unsetReplacedBy()==LIBSBML_OPERATION_SUCCESS);
}
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;
}