int
ASTLambdaFunctionNode::removeChild(unsigned int n)
{
int removed = LIBSBML_OPERATION_FAILED;
/* need to keep track of whether we have removed a bvar */
unsigned int numBvars = getNumBvars();
if (numBvars == 0)
{
/* we are removing the body - if the index is appropriate */
return ASTFunctionBase::removeChild(n);
}
if (n < numBvars)
{
// we are removing a bvar
setNumBvars(numBvars - 1);
/* HACK TO REPLICATE OLD AST */
/* Hack to remove memory since the overall
* remove does not remove memory
* but the old api does not give access to the new
* intermediate parents so these can never
* be explicilty deleted by the user
*
* in this case the first remove is accessible
*/
ASTBase * base = ASTFunctionBase::getChild(n);
ASTNode * bvar = dynamic_cast<ASTNode*>(base);
if (bvar != NULL && bvar->getNumChildren() == 1)
{
removed = bvar->removeChild(0);
if (removed == LIBSBML_OPERATION_SUCCESS)
{
ASTBase * removedAST = NULL;
removedAST = this->ASTFunctionBase::getChild(n);
removed = ASTFunctionBase::removeChild(n);
if (removedAST != NULL) delete removedAST;
}
}
}
else
{
// we are removing the body
removed = ASTFunctionBase::removeChild(n);
}
return removed;
}
int
ASTBinaryFunctionNode::removeChild (unsigned int n)
{
int removed = LIBSBML_OPERATION_FAILED;
if (this->getType() != AST_FUNCTION_LOG)
{
removed = ASTFunctionBase::removeChild(n);
}
else
{
/* HACK TO REPLICATE OLD AST */
/* Hack to remove memory since the overall
* remove does not remove memory
* but the old api does not give access to the new
* intermediate parents so these can never
* be explicilty deleted by the user
*
* in this case the first remove is accessible
*/
if (ASTFunctionBase::getChild(n)->getType() == AST_QUALIFIER_LOGBASE)
{
ASTBase * base = ASTFunctionBase::getChild(n);
ASTNode * logbase = dynamic_cast<ASTNode*>(base);
if (logbase != NULL && logbase->getNumChildren() == 1)
{
removed = logbase->removeChild(0);
if (removed == LIBSBML_OPERATION_SUCCESS)
{
ASTBase * removedAST = NULL;
removedAST = this->ASTFunctionBase::getChild(n);
removed = ASTFunctionBase::removeChild(n);
if (removedAST != NULL) delete removedAST;
}
}
}
else
{
removed = ASTFunctionBase::removeChild(n);
}
}
return removed;
}
int
ASTNaryFunctionNode::removeChild (unsigned int n)
{
int removed = LIBSBML_OPERATION_FAILED;
if (this->getType() != AST_FUNCTION_ROOT)
{
removed = ASTFunctionBase::removeChild(n);
}
else
{
/* HACK TO REPLICATE OLD AST */
/* Hack to remove memory since the overall
* remove does not remove memory
* but the old api does not give access to the new
* intermediate parents so these can never
* be explicilty deleted by the user
*
* in this case the first remove is accessible
*/
if (ASTFunctionBase::getChild(n)->getType() == AST_QUALIFIER_DEGREE)
{
ASTBase * base = ASTFunctionBase::getChild(n);
ASTNode * degree = dynamic_cast<ASTNode*>(base);
if (degree != NULL && degree->getNumChildren() == 1)
{
removed = degree->removeChild(0);
if (removed == LIBSBML_OPERATION_SUCCESS)
{
ASTBase * removedAST = NULL;
removedAST = this->ASTFunctionBase::getChild(n);
removed = ASTFunctionBase::removeChild(n);
if (removedAST != NULL) delete removedAST;
}
}
}
else
{
removed = ASTFunctionBase::removeChild(n);
}
}
/* HACK TO REPLICATE OLD AST */
// if we now have an odd number of children the last one
// should be subject NOT the degree
if (removed == LIBSBML_OPERATION_SUCCESS)
{
unsigned int size = getNumChildren();
unsigned int numChildren = ASTFunctionBase::getNumChildren();
if ((unsigned int)(size%2) == 1)
{
ASTBase * child = ASTFunctionBase::getChild(numChildren-1);
if (child->getType() == AST_QUALIFIER_DEGREE)
{
ASTNode * degree = dynamic_cast<ASTNode *>(child);
if (degree != NULL && degree->getNumChildren() == 1)
{
ASTNode *pChild = degree->getChild(0);
degree->removeChild(0);
ASTBase * temp = this->ASTFunctionBase::getChild(numChildren-1);
this->ASTFunctionBase::removeChild(numChildren-1);
delete temp;
this->addChild(pChild);
}
}
}
}
return removed;
}
int
ASTPiecewiseFunctionNode::removeChild(unsigned int n)
{
int removed = LIBSBML_INDEX_EXCEEDS_SIZE;
/* HACK TO REPLICATE OLD AST */
/* do not return a node with teh piece or otherwise type
* return the correct child of the piece type
* or the child of the otherwise
*/
unsigned int numChildren = ASTFunctionBase::getNumChildren();
// determine index that we actually want
unsigned int childNo = (unsigned int)(n/2);
unsigned int pieceIndex = (unsigned int)(n%2);
unsigned int size = getNumChildren();
if (size == 0)
{
return LIBSBML_OPERATION_FAILED;
}
if (n < size)
{
if (getHasOtherwise() == true && childNo == numChildren - 1)
{
removed = ASTFunctionBase::removeChild(childNo);
mHasOtherwise = false;
}
else if (ASTFunctionBase::getChild(childNo)->getType()
== AST_CONSTRUCTOR_PIECE)
{
ASTBase * base = ASTFunctionBase::getChild(childNo);
ASTNode * piece = dynamic_cast<ASTNode*>(base);
if (piece != NULL)
{
if (piece->getNumChildren() > pieceIndex)
{
removed = piece->removeChild(pieceIndex);
if (removed == LIBSBML_OPERATION_SUCCESS &&
piece->getNumChildren() == 0)
{
removed = this->ASTFunctionBase::removeChild(childNo);
mNumPiece = mNumPiece - 1;
}
}
else
{
removed = LIBSBML_OPERATION_FAILED;
}
}
else
{
removed = LIBSBML_OPERATION_FAILED;
}
}
else if (n < numChildren)
{
removed = ASTFunctionBase::removeChild(n);
}
else
{
removed = LIBSBML_OPERATION_FAILED;
}
}
return removed;
}
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 = NULL;
ASTNode* tcfdiv = NULL;
if (tcf != NULL) {
tcftimes = new ASTNode(AST_TIMES);
tcftimes->addChild(tcf->deepCopy());
tcfdiv = new ASTNode(AST_DIVIDE);
tcfdiv->addChild(tcf->deepCopy());
}
ASTNode* rxndivide = NULL;
if (klmod != NULL) {
rxndivide = new ASTNode(AST_DIVIDE);
ASTNode rxnref(AST_NAME);
rxndivide->addChild(rxnref.deepCopy());
rxndivide->addChild(klmod->deepCopy());
}
List* allelements = model->getAllElements();
for (unsigned int el=0; el<allelements->getSize(); el++) {
SBase* element = static_cast<SBase*>(allelements->get(el));
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 != NULL && element->getTypeCode()==SBML_REACTION && element->isSetId()) {
rxndivide->getChild(0)->setName(element->getId().c_str());
for (unsigned int sube=0; sube<allelements->getSize(); sube++) {
SBase* subelement = static_cast<SBase*>(allelements->get(sube));
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);
}
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, rrule->getMath()->deepCopy());
rrule->setMath(tcfdiv);
tcfdiv->removeChild(0);
}
//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;
}