void
PackageIdReplacementCheck::checkReferencedElement(ReplacedElement& repE)
{
// if the deletion attribute is set then it does not point
// to another package element
if (repE.isSetDeletion() == true)
{
return;
}
unsigned int numErrsB4 = repE.getSBMLDocument()->getNumErrors();
SBase* refElem = repE.getReferencedElement();
// if there is an issue with references the getReferencedElement
// will log errors and possibly fail
// we dont want to try any further
unsigned int numErrsAfter = repE.getSBMLDocument()->getNumErrors();
if (numErrsB4 != numErrsAfter || refElem == NULL)
{
return;
}
SBase * parent = repE.getParentSBMLObject()->getParentSBMLObject();
if (refElem->isSetId() == true && parent->isSetId() == false)
{
logMissingIdAttribute(repE, refElem, parent);
}
}
void
PackageIdReplacementCheck::checkReferencedElement(ReplacedBy& repBy)
{
unsigned int numErrsB4 = repBy.getSBMLDocument()->getNumErrors();
SBase* refElem = repBy.getReferencedElement();
// if there is an issue with references the getReferencedElement
// will log errors and possibly fail
// we dont want to try any further
unsigned int numErrsAfter = repBy.getSBMLDocument()->getNumErrors();
if (numErrsB4 != numErrsAfter || refElem == NULL)
{
return;
}
SBase * parent = repBy.getParentSBMLObject();
if (parent->isSetId() == true && refElem->isSetId() == false)
{
logMissingIdAttribute(repBy, refElem, parent);
}
}
/*
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given @p id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
NumericArgsMathCheck::getMessage (const ASTNode& node, const SBase& object)
{
ostringstream msg;
//msg << getPreamble();
char * formula = SBML_formulaToString(&node);
msg << "The formula '" << formula;
msg << "' in the " << getFieldname() << " element of the <" << object.getElementName();
msg << "> ";
switch(object.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (object.isSetId()) {
msg << "with id '" << object.getId() << "' ";
}
break;
}
msg << "uses an argument to a operator that expects a numeric value.";
safe_free(formula);
return msg.str();
}
/*
* Logs a message about the conditional part of a piecewise function
* that should have dimensionless units
*/
void
ArgumentsUnitsCheck::logInconsistentPiecewiseCondition (const ASTNode & node,
const SBase & sb)
{
char * formula = SBML_formulaToString(&node);
msg = "The formula '";
msg += formula;
msg += "' in the math element of the <";
msg += sb.getElementName();
msg += "> ";
switch(sb.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (sb.isSetId()) {
msg += "with id '";
msg += sb.getId() + "' ";
}
break;
}
msg += "uses a piecewise function";
msg += " where the conditional statement is not dimensionless.";
safe_free(formula);
logFailure(sb, msg);
}
/*
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given @p id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
PieceBooleanMathCheck::getMessage (const ASTNode& node, const SBase& object)
{
ostringstream oss_msg;
//oss_msg << getPreamble();
char * formula = SBML_formulaToString(&node);
oss_msg << "The formula '" << formula;
oss_msg << "' in the " << getFieldname() << " element of the <" << object.getElementName();
oss_msg << "> ";
switch(object.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (object.isSetId()) {
oss_msg << "with id '" << object.getId() << "' ";
}
break;
}
oss_msg << "uses a piecewise function that does not return a Boolean.";
safe_free(formula);
return oss_msg.str();
}
/*
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given @p id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
FunctionApplyMathCheck::getMessage (const ASTNode& node, const SBase& object)
{
ostringstream msg;
//msg << getPreamble();
char * formula = SBML_formulaToString(&node);
msg << "The formula '" << formula;
msg << "' in the " << getFieldname() << " element of the <" << object.getElementName();
msg << "> ";
switch(object.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (object.isSetId()) {
msg << "with id '" << object.getId() << "' ";
}
break;
}
msg << "uses '" << node.getName() << "' which is not a function definition id.";
safe_free(formula);
return msg.str();
}
/*
* Subclasses should override this method to read values from the given
* XMLAttributes set into their specific fields. Be sure to call your
* parents implementation of this method as well.
*/
void
SpeciesReference::readL3Attributes (const XMLAttributes& attributes)
{
const unsigned int level = 3;
const unsigned int version = getVersion();
//
// stoichiometry: double { use="optional" default="1" } (L2v1->)
//
mIsSetStoichiometry = attributes.readInto("stoichiometry", mStoichiometry, getErrorLog(), false, getLine(), getColumn());
string elplusid = "<" + getElementName() + ">";
if (!mId.empty()) {
elplusid += " with the id '" + mId + "'";
}
SBase* rxn = getAncestorOfType(SBML_REACTION);
if (rxn && rxn->isSetId())
{
elplusid += " from the <reaction> with the id '" + rxn->getId() + "'";
}
//
// constant: bool { use="required" } (L3v1 -> )
//
mIsSetConstant = attributes.readInto("constant", mConstant, getErrorLog(), false, getLine(), getColumn());
if (!mIsSetConstant && !isModifier())
{
logError(AllowedAttributesOnSpeciesReference, level, version,
"The required attribute 'constant' is missing from the "
+ elplusid + ".");
}
}
/*
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given @p id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
CiElementMathCheck::getMessage (const ASTNode& node, const SBase& object)
{
ostringstream msg;
//msg << getPreamble();
char * formula = SBML_formulaToString(&node);
msg << "The formula '" << formula;
msg << "' in the " << getFieldname() << " element of the <" << object.getElementName();
msg << "> ";
switch(object.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (object.isSetId()) {
msg << "with id '" << object.getId() << "' ";
}
break;
}
if (object.getLevel() == 2 && object.getVersion() == 1)
msg << "uses '" << node.getName() << "' that is not the id of a species/compartment/parameter.";
else if (object.getLevel() < 3)
msg << "uses '" << node.getName() << "' that is not the id of a species/compartment/parameter/reaction.";
else
msg << "uses '" << node.getName() << "' that is not the id of a species/compartment/parameter/reaction/speciesReference.";
safe_free(formula);
return msg.str();
}
/*
* Logs a message about a function that should return same units
* as the arguments
*/
void
ArgumentsUnitsCheck::logInconsistentSameUnits (const ASTNode & node,
const SBase & sb)
{
char * formula = SBML_formulaToString(&node);
msg = "The formula '" ;
msg += formula;
msg += "' in the math element of the <";
msg += sb.getElementName();
msg += "> ";
switch(sb.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (sb.isSetId()) {
msg += "with id '";
msg += sb.getId() + "' ";
}
break;
}
msg += "can only act on variables with the same units.";
safe_free(formula);
logFailure(sb, msg);
}
/*
* @return the error message to use when logging constraint violations.
* This method is called by logFailure.
*
* Returns a message that the given @p id and its corresponding object are
* in conflict with an object previously defined.
*/
const string
ArgumentsUnitsCheck::getMessage (const ASTNode& node, const SBase& object)
{
ostringstream msg;
//msg << getPreamble();
char * formula = SBML_formulaToString(&node);
msg << "The formula '" << formula;
msg << "' in the " << getFieldname() << " element of the <" << object.getElementName();
msg << "> ";
switch(object.getTypeCode()) {
case SBML_INITIAL_ASSIGNMENT:
case SBML_EVENT_ASSIGNMENT:
case SBML_ASSIGNMENT_RULE:
case SBML_RATE_RULE:
//LS DEBUG: could use other attribute values, or 'isSetActualId'.
break;
default:
if (object.isSetId()) {
msg << "with id '" << object.getId() << "' ";
}
break;
}
msg << "produces an exponent that is not an integer and thus may produce ";
msg << "invalid units.";
safe_free(formula);
return msg.str();
}
/** @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();
}
}
void
GroupsUniqueModelWideIds::logId (const SBase& object)
{
if (object.isSetId())
{
const string& id = object.getId();
mIdMap.insert( make_pair(id, &object) );
}
}
/*
* Checks that the id associated with the given object is unique. If it
* is not, logIdConflict is called.
*/
void
GroupsUniqueModelWideIds::doCheckId (const SBase& object)
{
if (object.isSetId())
{
const string& id = object.getId();
if (mIdMap.insert( make_pair(id, &object) ).second == false)
{
logIdConflict(id, object);
}
}
}
SBase*
ListOf::getElementBySId(const std::string& id)
{
if (id.empty()) return NULL;
for (unsigned int i = 0; i < size(); i++)
{
SBase* obj = get(i);
if (obj->isSetId() && obj->getId() == id)
{
return obj;
}
obj = obj->getElementBySId(id);
if (obj != NULL) return obj;
}
return getElementFromPluginsBySId(id);
}
/** @cond doxygenLibsbmlInternal */
void CompModelPlugin::resetPorts()
{
for (unsigned int p=0; p<getNumPorts(); p++) {
Port* port = getPort(p);
SBase* referenced = port->getReferencedElement();
if (port->isSetSBaseRef()) {
port->unsetSBaseRef();
port->unsetIdRef();
port->unsetMetaIdRef();
port->unsetUnitRef();
int type = referenced->getTypeCode();
if (referenced->isSetId() &&
type != SBML_INITIAL_ASSIGNMENT &&
type != SBML_ASSIGNMENT_RULE &&
type != SBML_RATE_RULE &&
type != SBML_EVENT_ASSIGNMENT) {
if (type==SBML_UNIT_DEFINITION) {
port->setUnitRef(referenced->getId());
}
else {
port->setIdRef(referenced->getId());
}
}
else if (referenced->isSetMetaId()) {
port->setMetaIdRef(referenced->getMetaId());
}
else {
stringstream newname;
newname << "auto_port_" << p;
referenced->setMetaId(newname.str());
port->setMetaIdRef(newname.str());
}
}
port->clearReferencedElement();
}
}
int ReplacedBy::performReplacementAndCollect(set<SBase*>* removed, set<SBase*>* toremove)
{
SBMLDocument* doc = getSBMLDocument();
//Find the various objects and plugin objects we need for this to work.
SBase* parent = getParentSBMLObject();
if (parent==NULL) {
if (doc) {
string error = "Unable to perform replacement in ReplacedBy::performReplacement: no parent object for this <replacedBy> could be found.";
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;
}
//Update the IDs. (Will set its own error messages.)
int ret = updateIDs(ref, parent);
//ReplacedBy elements do get the name of the top-level element, assuming it has one:
if (parent->isSetId()) {
ref->setId(parent->getId());
}
if (parent->isSetMetaId()) {
ref->setMetaId(parent->getMetaId());
}
if (ret != LIBSBML_OPERATION_SUCCESS) return ret;
//And finally, get ready to delete the parent object.
if (toremove) {
toremove->insert(parent);
}
return LIBSBML_OPERATION_SUCCESS;
}
SBase*
SBaseRef::getReferencedElementFrom(Model* model)
{
SBMLDocument* doc = getSBMLDocument();
if (!hasRequiredAttributes()) {
if (doc) {
string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element from <" + getElementName() + "> ";
if (isSetId()) {
error += "with ID '" + getId() + "' ";
}
error += "as it does not have the required attributes.";
int en = CompSBaseRefMustReferenceObject;
switch(getTypeCode()) {
case SBML_COMP_REPLACEDBY:
en = CompReplacedByAllowedAttributes;
break;
case SBML_COMP_REPLACEDELEMENT:
en = CompReplacedElementAllowedAttributes;
break;
case SBML_COMP_PORT:
en = CompPortAllowedAttributes;
break;
case SBML_COMP_DELETION:
en = CompDeletionAllowedAttributes;
}
doc->getErrorLog()->logPackageError("comp", en, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return NULL;
}
SBase* referent = NULL;
if (isSetPortRef()) {
CompModelPlugin* mplugin = static_cast<CompModelPlugin*>(model->getPlugin(getPrefix()));
Port* port = mplugin->getPort(getPortRef());
if (port==NULL) {
if (doc) {
string error = "In SBaseRef::getReferencedElementFrom, unable to find referenced element from SBase reference ";
if (isSetId()) {
error += "'" + getId() + "' ";
}
error += "as the port it references ('" + getPortRef() +"') could not be found.";
doc->getErrorLog()->logPackageError("comp", CompPortRefMustReferencePort, getPackageVersion(), getLevel(), getVersion(), error, getLine(), getColumn());
}
return NULL;
}
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;
}
//static
void SBMLUtils::collectIds(Model* pModel, std::map<std::string, const SBase*>& ids, std::map<std::string, const SBase*>& metaIds)
{
if (pModel != NULL)
{
// the model itself
SBase* pSBase = NULL;
std::string id;
if (pModel->isSetId())
{
id = pModel->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pModel->isSetMetaId())
{
id = pModel->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// ListOfFunctionDefinitions
pSBase = pModel->getListOfFunctionDefinitions();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// all FunctionDefinitions
unsigned int i, iMax = pModel->getListOfFunctionDefinitions()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getListOfFunctionDefinitions()->get(i);
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfUnitDefinition
pSBase = pModel->getListOfUnitDefinitions();
if (pSBase != NULL)
{
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// all UnitDefinitions
// for each UnitDefinition: ListOfUnits, each Unit in ListOfUnits
unsigned int i, iMax = pModel->getListOfUnitDefinitions()->size();
for (i = 0; i < iMax; ++i)
{
/* UnitDefinitions have their ids in a different namespace
so we only consider meta ids.
*/
UnitDefinition* pUDef = pModel->getUnitDefinition(i);
assert(pUDef != NULL);
if (pUDef->isSetMetaId())
{
id = pUDef->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pUDef));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
ListOf* pList = pUDef->getListOfUnits();
if (pList != NULL)
{
if (pList->isSetMetaId())
{
id = pList->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pList));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
unsigned j, jMax = pList->size();
for (j = 0; j < jMax; ++j)
{
pSBase = pList->get(j);
assert(pSBase != NULL);
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
}
}
// ListOfCompartmentTypes
pSBase = pModel->getListOfCompartmentTypes();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each compartment type
unsigned int i, iMax = pModel->getListOfCompartmentTypes()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getCompartmentType(i);
assert(pSBase != NULL);
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfSpeciesTypes
pSBase = pModel->getListOfSpeciesTypes();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each species type
unsigned int i, iMax = pModel->getListOfSpeciesTypes()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getSpeciesType(i);
assert(pSBase != NULL);
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfCompartments
pSBase = pModel->getListOfCompartments();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// all compartments
unsigned int i, iMax = pModel->getListOfCompartments()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getCompartment(i);
assert(pSBase != NULL);
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfSpecies
pSBase = pModel->getListOfSpecies();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// all species
unsigned int i, iMax = pModel->getListOfSpecies()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getSpecies(i);
assert(pSBase != NULL);
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfParameters
pSBase = pModel->getListOfParameters();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each parameter
unsigned int i, iMax = pModel->getListOfParameters()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getParameter(i);
assert(pSBase != NULL);
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfInitialAssignments
pSBase = pModel->getListOfInitialAssignments();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each initial assignment
unsigned int i, iMax = pModel->getListOfInitialAssignments()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getInitialAssignment(i);
assert(pSBase != NULL);
// initial assignments have no ids
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfRules
pSBase = pModel->getListOfRules();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each rule
unsigned int i, iMax = pModel->getListOfRules()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getRule(i);
assert(pSBase != NULL);
// rules don't have ids
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfConstraints
pSBase = pModel->getListOfConstraints();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each constraint
unsigned int i, iMax = pModel->getListOfConstraints()->size();
for (i = 0; i < iMax; ++i)
{
pSBase = pModel->getConstraint(i);
assert(pSBase != NULL);
// constraints don't have ids
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
// ListOfReactions
pSBase = pModel->getListOfReactions();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// all reactions
unsigned int i, iMax = pModel->getListOfReactions()->size();
for (i = 0; i < iMax; ++i)
{
Reaction* pReaction = pModel->getReaction(i);
assert(pReaction != NULL);
if (pReaction->isSetId())
{
id = pReaction->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pReaction));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pReaction->isSetMetaId())
{
id = pReaction->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pReaction));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// for each reaction: ListOfSubstrates, each substrate, ListOfProducts, each
// Product, ListOfModifieres, each modifier, KineticLaw, ListOfparameters,
// each parameter
if (pReaction->getListOfReactants() != NULL)
{
pSBase = pReaction->getListOfReactants();
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
unsigned int j, jMax = pReaction->getListOfReactants()->size();
for (j = 0; j < jMax; ++j)
{
pSBase = pReaction->getReactant(j);
assert(pSBase != NULL);
// since L2V2 species references can have ids
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
if (pReaction->getListOfProducts() != NULL)
{
pSBase = pReaction->getListOfProducts();
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
unsigned int j, jMax = pReaction->getListOfProducts()->size();
for (j = 0; j < jMax; ++j)
{
pSBase = pReaction->getProduct(j);
assert(pSBase != NULL);
// since L2V2 species references can have ids
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
if (pReaction->getListOfModifiers() != NULL)
{
pSBase = pReaction->getListOfModifiers();
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
unsigned int j, jMax = pReaction->getListOfModifiers()->size();
for (j = 0; j < jMax; ++j)
{
pSBase = pReaction->getModifier(j);
assert(pSBase != NULL);
// since L2V2 species references can have ids
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
KineticLaw* pKLaw = pReaction->getKineticLaw();
if (pKLaw != NULL)
{
if (pKLaw->isSetMetaId())
{
id = pKLaw->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pKLaw));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
pSBase = pKLaw->getListOfParameters();
if (pSBase != NULL)
{
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
unsigned int j, jMax = pKLaw->getListOfParameters()->size();
for (j = 0; j < jMax; ++j)
{
pSBase = pKLaw->getParameter(j);
assert(pSBase != NULL);
// local parameters have their ids in a
// different namespace
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
}
}
}
// ListOfEvents
pSBase = pModel->getListOfEvents();
if (pSBase != NULL)
{
if (pSBase->isSetId())
{
id = pSBase->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pModel));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// each event
unsigned int i, iMax = pModel->getListOfEvents()->size();
for (i = 0; i < iMax; ++i)
{
Event* pEvent = pModel->getEvent(i);
assert(pEvent != NULL);
if (pEvent->isSetId())
{
id = pEvent->getId();
if (ids.find(id) == ids.end())
{
ids.insert(std::pair<const std::string, const SBase*>(id, pEvent));
}
else
{
CCopasiMessage(CCopasiMessage::EXCEPTION, MCSBML + 68, id.c_str());
}
}
if (pEvent->isSetMetaId())
{
id = pEvent->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pEvent));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
// in each event Trigger,Delay,ListOfEventAssignments, each event assignment
if (pEvent->isSetTrigger())
{
pSBase = pEvent->getTrigger();
assert(pSBase != NULL);
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
if (pEvent->isSetDelay())
{
pSBase = pEvent->getDelay();
assert(pSBase != NULL);
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
if (pEvent->getListOfEventAssignments() != NULL)
{
pSBase = pEvent->getListOfEventAssignments();
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
unsigned int j, jMax = pEvent->getListOfEventAssignments()->size();
for (j = 0; j < jMax; ++j)
{
pSBase = pEvent->getEventAssignment(j);
assert(pSBase != NULL);
if (pSBase->isSetMetaId())
{
id = pSBase->getMetaId();
if (metaIds.find(id) == metaIds.end())
{
metaIds.insert(std::pair<const std::string, const SBase*>(id, pSBase));
}
else
{
CCopasiMessage(CCopasiMessage::WARNING, MCSBML + 67, id.c_str());
}
}
}
}
}
}
}
}
int CompModelPlugin::saveAllReferencedElements(set<SBase*> uniqueRefs, set<SBase*> replacedBys)
{
SBMLDocument* doc = getSBMLDocument();
Model* model = static_cast<Model*>(getParentSBMLObject());
if (model==NULL) {
if (doc) {
string error = "Unable to discover any referenced elements in CompModelPlugin::saveAllReferencedElements: no Model parent of the 'comp' model plugin.";
doc->getErrorLog()->logPackageError("comp", CompModelFlatteningFailed, getPackageVersion(), getLevel(), getVersion(), error);
}
return LIBSBML_OPERATION_FAILED;
}
int ret = LIBSBML_OPERATION_SUCCESS;
//Get a list of everything, pull out anything that's a deletion, replacement, or port, and save what they're pointing to.
//At the same time, make sure that no two things point to the same thing.
set<SBase*> RE_deletions = set<SBase*>(); //Deletions only point to things in the same model.
List* allElements = model->getAllElements();
string modname = "the main model in the document";
if (model->isSetId()) {
modname = "the model '" + model->getId() + "'";
}
set<SBase*> todelete;
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_DELETION ||
type==SBML_COMP_REPLACEDBY ||
type==SBML_COMP_REPLACEDELEMENT ||
type==SBML_COMP_PORT) {
//Don't worry about SBML_COMP_SBASEREF because they're all children of one of the above types.
SBaseRef* reference = static_cast<SBaseRef*>(element);
ReplacedElement* re = static_cast<ReplacedElement*>(element);
ret = reference->saveReferencedElement();
if (ret != LIBSBML_OPERATION_SUCCESS)
{
if (type != SBML_COMP_REPLACEDBY && doc)
{
SBMLErrorLog* errlog = doc->getErrorLog();
SBMLError* lasterr = const_cast<SBMLError*>
(doc->getErrorLog()->getError(doc->getNumErrors()-1));
if ( (errlog->contains(UnrequiredPackagePresent) ||
errlog->contains(RequiredPackagePresent)))
{
if ( lasterr->getErrorId() == CompIdRefMustReferenceObject)
{
//Change the error into a warning
string fullmsg = lasterr->getMessage()
+ " However, this may be because of the unrecognized "
+ "package present in this document: ignoring this "
+ "element and flattening anyway.";
errlog->remove(lasterr->getErrorId());
errlog->logPackageError("comp",
CompIdRefMayReferenceUnknownPackage, getPackageVersion(),
getLevel(), getVersion(), fullmsg, element->getLine(),
element->getColumn(), LIBSBML_SEV_WARNING);
}
else if ( lasterr->getErrorId() == CompMetaIdRefMustReferenceObject)
{
//Change the error into a warning
string fullmsg = lasterr->getMessage()
+ " However, this may be because of the unrecognized "
+ "package present in this document: ignoring this "
+ "element and flattening anyway.";
errlog->remove(lasterr->getErrorId());
errlog->logPackageError("comp",
CompMetaIdRefMayReferenceUnknownPkg, getPackageVersion(),
getLevel(), getVersion(), fullmsg, element->getLine(),
element->getColumn(), LIBSBML_SEV_WARNING);
}
}
//Whether or not we could figure out the error, we can always still continue flattening.
todelete.insert(element);
continue;
}
else {
delete allElements;
return ret;
}
}
SBase* direct = reference->getDirectReference();
bool adddirect = true;
if (type == SBML_COMP_REPLACEDBY) {
SBase* rbParent = reference->getParentSBMLObject();
if (uniqueRefs.insert(rbParent).second == false) {
if (doc) {
string error = "Error discovered in CompModelPlugin::saveAllReferencedElements when checking " + modname + ": a <" + rbParent->getElementName() + "> ";
if (direct->isSetId()) {
error += "with the id '" + rbParent->getId() + "'";
if (rbParent->isSetMetaId()) {
error += ", and the metaid '" + rbParent->getMetaId() + "'";
}
}
else if (rbParent->isSetMetaId()) {
error += "with the metaId '" + rbParent->getMetaId() + "'";
}
error += " has a <replacedBy> child and is also pointed to by a <port>, <deletion>, <replacedElement>, or one or more <replacedBy> objects.";
doc->getErrorLog()->logPackageError("comp", CompNoMultipleReferences, getPackageVersion(), getLevel(), getVersion(), error);
}
delete allElements;
return LIBSBML_OPERATION_FAILED;
}
adddirect = replacedBys.insert(direct).second;
}
if (type==SBML_COMP_REPLACEDELEMENT && re->isSetDeletion()) {
adddirect = RE_deletions.insert(direct).second;
}
if (adddirect) {
if (uniqueRefs.insert(direct).second == false) {
if (doc) {
string error = "Error discovered in CompModelPlugin::saveAllReferencedElements when checking " + modname + ": ";
if (replacedBys.find(direct) != replacedBys.end()) {
error += "one or more <replacedBy> elements, plus a <deletion>, <replacedElement>, or <port> element";
}
else if (RE_deletions.find(direct) != RE_deletions.end()) {
error += "one or more <replacedElement> elements using a 'deletion' attribute, plus a <deletion>, <replacedElement>, or <port> element";
}
else {
error += "multiple <deletion>, <replacedElement>, and/or <port> elements";
}
error += " point directly to the <" + direct->getElementName() + "> ";
if (direct->isSetId()) {
error += "with the id '" + direct->getId() + "'";
if (direct->isSetMetaId()) {
error += ", and the metaid '" + direct->getMetaId() + "'";
}
error += ".";
}
else if (direct->isSetMetaId()) {
error += "with the metaId '" + direct->getMetaId() + "'.";
}
doc->getErrorLog()->logPackageError("comp", CompNoMultipleReferences, getPackageVersion(), getLevel(), getVersion(), error);
}
delete allElements;
return LIBSBML_OPERATION_FAILED;
}
}
}
}
for(set<SBase*>::iterator el=todelete.begin(); el != todelete.end(); el++) {
(*el)->removeFromParentAndDelete();
}
delete allElements;
//Now call saveAllReferencedElements for all instantiated submodels.
for (unsigned long sm=0; sm<getNumSubmodels(); ++sm) {
Model* sub = getSubmodel((unsigned int)sm)->getInstantiation();
if (sub==NULL) {
return LIBSBML_OPERATION_FAILED;
}
CompModelPlugin* subplug = static_cast<CompModelPlugin*>(sub->getPlugin(getPrefix()));
if (subplug==NULL) {
return LIBSBML_OPERATION_FAILED;
}
ret = subplug->saveAllReferencedElements(uniqueRefs, replacedBys);
if (ret != LIBSBML_OPERATION_SUCCESS) {
return ret;
}
}
return LIBSBML_OPERATION_SUCCESS;
}
int
SBMLIdConverter::convert()
{
if (mDocument == NULL) return LIBSBML_INVALID_OBJECT;
Model* mModel = mDocument->getModel();
if (mModel == NULL) return LIBSBML_INVALID_OBJECT;
// nothing to do
if (!mProps->hasOption("currentIds") || !mProps->hasOption("newIds"))
return LIBSBML_OPERATION_SUCCESS;
bool success = true;
IdList currentIds(mProps->getOption("currentIds")->getValue());
IdList newIds(mProps->getOption("newIds")->getValue());
// if the size does not match something is wrong.
if (newIds.size() != currentIds.size())
return LIBSBML_UNEXPECTED_ATTRIBUTE;
List* allElements = mDocument->getAllElements();
std::map<std::string, std::string> renamed;
// rename ids
for (unsigned int i = 0; i < allElements->getSize(); ++i)
{
SBase* current = static_cast<SBase*>(allElements->get(i));
if (current == NULL || !current->isSetId()
|| current->getTypeCode() == SBML_LOCAL_PARAMETER)
continue;
for (unsigned int j = 0; j < currentIds.size(); ++j)
{
if (current->getId() != currentIds.at((int)j))
continue;
// return error code in case new id is invalid
if (!SyntaxChecker::isValidSBMLSId(newIds.at((int)j)))
{
delete allElements;
return LIBSBML_INVALID_ATTRIBUTE_VALUE;
}
current->setId(newIds.at((int)j));
renamed[currentIds.at((int)j)] = newIds.at((int)j);
break;
}
}
// update all references that we changed
std::map<std::string, std::string>::const_iterator it;
for (unsigned int i = 0; i < allElements->getSize(); ++i)
{
SBase* current = static_cast<SBase*>(allElements->get(i));
for (it = renamed.begin(); it != renamed.end(); ++it)
{
current->renameSIdRefs(it->first, it->second);
}
}
delete allElements;
if (success) return LIBSBML_OPERATION_SUCCESS;
return LIBSBML_OPERATION_FAILED;
}
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);
delete ast2;
}
}
else {
kl->setMath(ast1);
delete ast1;
}
break;
case SBML_DELAY:
//Delays are multiplied by the time conversion factor.
delay = static_cast<Delay*>(element);
if (delay->isSetMath()) {
ast1 = delay->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
tcftimes.addChild(ast1);
delay->setMath(&tcftimes);
tcftimes.removeChild(1);
delete ast1;
}
break;
case SBML_RATE_RULE:
//Rate rules are divided by the time conversion factor.
rrule = static_cast<RateRule*>(element);
if (rrule->isSetMath()) {
ast1 = rrule->getMath()->deepCopy();
tcfdiv.insertChild(0, ast1);
rrule->setMath(&tcfdiv);
tcfdiv.removeChild(0);
delete ast1;
}
//Fall through to:
case SBML_ASSIGNMENT_RULE:
case SBML_ALGEBRAIC_RULE:
//Rules in general need csymbols converted.
rule = static_cast<Rule*>(element);
if (rule->isSetMath()) {
ast1 = rule->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
rule->setMath(ast1);
delete ast1;
}
break;
case SBML_EVENT_ASSIGNMENT:
//Event assignments need csymbols converted.
ea = static_cast<EventAssignment*>(element);
if (ea->isSetMath()) {
ast1 = ea->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
ea->setMath(ast1);
delete ast1;
}
break;
case SBML_INITIAL_ASSIGNMENT:
//Initial assignments need csymbols converted.
ia = static_cast<InitialAssignment*>(element);
if (ia->isSetMath()) {
ast1 = ia->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
ia->setMath(ast1);
delete ast1;
}
break;
case SBML_CONSTRAINT:
//Constraints need csymbols converted.
constraint = static_cast<Constraint*>(element);
if (constraint->isSetMath()) {
ast1 = constraint->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
constraint->setMath(ast1);
delete ast1;
}
break;
case SBML_PRIORITY:
//Priorities need csymbols converted.
priority = static_cast<Priority*>(element);
if (priority->isSetMath()) {
ast1 = priority->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
priority->setMath(ast1);
delete ast1;
}
break;
case SBML_TRIGGER:
//Triggers need csymbols converted.
trigger = static_cast<Trigger*>(element);
if (trigger->isSetMath()) {
ast1 = trigger->getMath()->deepCopy();
convertCSymbols(ast1, &tcfdiv, &tcftimes);
trigger->setMath(ast1);
delete ast1;
}
break;
default:
//Do nothing! If we wanted to call a plugin routine, this would be the place. The only other alternative is to #ifdef some code in here that deals with the math-containing package objects explicitly. Which might be the best option, all told.
break;
}
}
}
delete allElements;
return 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;
}