/**
* Constructor that makes a ConverterASTNode from an ASTNode.
*/
ConverterASTNode::ConverterASTNode(const ASTNode &templ): ASTNode(templ.getType())
{
if (this->getType() == AST_RATIONAL)
{
this->mDenominator = templ.getDenominator();
this->mInteger = templ.getNumerator();
}
else if (this->getType() == AST_REAL || this->getType() == AST_REAL_E)
{
this->mExponent = templ.getExponent();
this->mReal = templ.getMantissa();
}
if (this->getType() == AST_PLUS || this->getType() == AST_MINUS || this->getType() == AST_TIMES || this->getType() == AST_DIVIDE || this->getType() == AST_POWER)
{
this->mChar = templ.getCharacter();
}
else if (this->getType() == AST_INTEGER)
{
this->mInteger = templ.getInteger();
}
if ((!this->isOperator()) && (!this->isNumber()))
{
this->setName(templ.getName());
}
unsigned int counter;
for (counter = 0; counter < templ.getNumChildren(); counter++)
{
this->addChild(new ConverterASTNode(*templ.getChild(counter)));
}
};
/**
* Checks that the units of the power function are consistent
*
* If inconsistent units are found, an error message is logged.
*
* The two arguments to power, which are of the form power(a, b)
* with the meaning a^b, should be as follows:
* (1) if the second argument is an integer,
* then the first argument can have any units;
* (2) if the second argument b is a rational number n/m,
* it must be possible to derive the m-th root of (a{unit})n,
* where {unit} signifies the units associated with a;
* otherwise, (3) the units of the first argument must be “dimensionless”.
* The second argument (b) should always have units of “dimensionless”.
*
*/
void
PowerUnitsCheck::checkUnitsFromPower (const Model& m,
const ASTNode& node,
const SBase & sb, bool inKL, int reactNo)
{
/* check that node has 2 children */
if (node.getNumChildren() != 2)
{
return;
}
double value;
UnitDefinition dim(m.getSBMLNamespaces());
Unit unit(m.getSBMLNamespaces());
unit.setKind(UNIT_KIND_DIMENSIONLESS);
unit.initDefaults();
dim.addUnit(&unit);
UnitFormulaFormatter *unitFormat = new UnitFormulaFormatter(&m);
UnitDefinition *tempUD = NULL;
UnitDefinition *unitsArg1, *unitsArgPower;
unitsArg1 = unitFormat->getUnitDefinition(node.getLeftChild(), inKL, reactNo);
unsigned int undeclaredUnits =
unitFormat->getContainsUndeclaredUnits();
ASTNode *child = node.getRightChild();
unitFormat->resetFlags();
unitsArgPower = unitFormat->getUnitDefinition(child, inKL, reactNo);
unsigned int undeclaredUnitsPower =
unitFormat->getContainsUndeclaredUnits();
// The second argument (b) should always have units of “dimensionless”.
// or it has undeclared units that we assume are correct
if (undeclaredUnitsPower == 0 && !UnitDefinition::areEquivalent(&dim, unitsArgPower))
{
logNonDimensionlessPowerConflict(node, sb);
}
// The first argument is dimensionless then it doesnt matter
// what the power is
if (undeclaredUnits == 0 && !UnitDefinition::areEquivalent(&dim, unitsArg1))
{
// if not argument needs to be an integer or a rational
unsigned int isInteger = 0;
unsigned int isRational = 0;
unsigned int isExpression = 0;
/* power must be an integer
* but need to check that it is not a real
* number that is integral
* i.e. mathml <cn> 2 </cn> will record a "real"
*/
if (child->isRational())
{
isRational = 1;
}
else if (child->isInteger())
{
isInteger = 1;
}
else if (child->isReal())
{
if (ceil(child->getReal()) == child->getReal())
{
isInteger = 1;
}
}
else if (child->getNumChildren() > 0)
{
// power might itself be an expression
tempUD = unitFormat->getUnitDefinition(child, inKL, reactNo);
UnitDefinition::simplify(tempUD);
if (tempUD->isVariantOfDimensionless())
{
SBMLTransforms::mapComponentValues(&m);
double value = SBMLTransforms::evaluateASTNode(child);
SBMLTransforms::clearComponentValues();
#if defined(__linux)
if (!std::isnan(value))
#else
if (!isnan(value))
#endif
{
if (floor(value) != value)
isExpression = 1;
else
isInteger = 1;
}
else
{
isExpression = 1;
}
}
else
{
/* here the child is an expression with units
* flag the expression as not checked
*/
isExpression = 1;
}
}
else
{
// power could be a parameter or a speciesReference in l3
const Parameter *param = NULL;
const SpeciesReference *sr = NULL;
if (child->isName())
{
/* Parameters may be declared in two places (the model and the
* kinetic law's local parameter list), so we have to check both.
*/
if (sb.getTypeCode() == SBML_KINETIC_LAW)
{
const KineticLaw* kl = dynamic_cast<const KineticLaw*>(&sb);
/* First try local parameters and if null is returned, try
* the global parameters */
if (kl != NULL)
{
param = kl->getParameter(child->getName());
}
}
if (param == NULL)
{
param = m.getParameter(child->getName());
}
if (param == NULL && m.getLevel() > 2)
{
// could be a species reference
sr = m.getSpeciesReference(child->getName());
}
}
if (param != NULL)
{
/* We found a parameter with this identifier. */
if (UnitDefinition::areEquivalent(&dim, unitsArgPower) || undeclaredUnitsPower)
{
value = param->getValue();
if (value != 0)
{
if (ceil(value) == value)
{
isInteger = 1;
}
}
}
else
{
/* No parameter definition found for child->getName() */
logUnitConflict(node, sb);
}
}
else if (sr != NULL)
{
// technically here there is an issue
// stoichiometry is dimensionless
SBMLTransforms::mapComponentValues(&m);
double value = SBMLTransforms::evaluateASTNode(child, &m);
SBMLTransforms::clearComponentValues();
// but it may not be an integer
#if defined(__linux)
if (!std::isnan(value))
#else
if (!isnan(value))
#endif
// we cant check
{
isExpression = 1;
}
else
{
if (ceil(value) == value)
{
isInteger = 1;
}
}
}
}
if (isRational == 1)
{
//FIX-ME will need sorting for double exponents
//* (2) if the second argument b is a rational number n/m,
//* it must be possible to derive the m-th root of (a{unit})n,
//* where {unit} signifies the units associated with a;
unsigned int impossible = 0;
for (unsigned int n = 0; impossible == 0 && n < unitsArg1->getNumUnits(); n++)
{
if ((int)(unitsArg1->getUnit(n)->getExponent()) * child->getInteger() %
child->getDenominator() != 0)
impossible = 1;
}
if (impossible)
logRationalPowerConflict(node, sb);
}
else if (isExpression == 1)
{
logExpressionPowerConflict(node, sb);
}
else if (isInteger == 0)
{
logNonIntegerPowerConflict(node, sb);
}
}
// if (!areEquivalent(dim, unitsPower))
// {
// /* 'v' does not have units of dimensionless. */
// /* If the power 'n' is a parameter, check if its units are either
// * undeclared or declared as dimensionless. If either is the case,
// * the value of 'n' must be an integer.
// */
// const Parameter *param = NULL;
// if (child->isName())
// {
// /* Parameters may be declared in two places (the model and the
// * kinetic law's local parameter list), so we have to check both.
// */
// if (sb.getTypeCode() == SBML_KINETIC_LAW)
// {
// const KineticLaw* kl = dynamic_cast<const KineticLaw*>(&sb);
// /* First try local parameters and if null is returned, try
// * the global parameters */
// if (kl != NULL)
// {
// param = kl->getParameter(child->getName());
// }
// }
// if (param == NULL)
// {
// param = m.getParameter(child->getName());
// }
//
// }
// if (param != NULL)
// {
// /* We found a parameter with this identifier. */
// if (areEquivalent(dim, unitsArgPower) || unitFormat->hasUndeclaredUnits(child))
// {
// value = param->getValue();
// if (value != 0)
// {
// if (ceil(value) != value)
// {
// logUnitConflict(node, sb);
// }
// }
// }
// else
// {
///* No parameter definition found for child->getName() */
// logUnitConflict(node, sb);
// }
// }
// else if (child->isFunction() || child->isOperator())
// {
// /* cannot test whether the value will be appropriate */
// if (!areEquivalent(dim, unitsArgPower))
// {
// logUnitConflict(node, sb);
// }
// }
// /* power must be an integer
// * but need to check that it is not a real
// * number that is integral
// * i.e. mathml <cn> 2 </cn> will record a "real"
// */
// else if (!child->isInteger())
// {
// if (!child->isReal())
// {
// logUnitConflict(node, sb);
// }
// else if (ceil(child->getReal()) != child->getReal())
// {
// logUnitConflict(node, sb);
// }
// }
// }
// else if (!areEquivalent(dim, unitsArgPower))
// {
// /* power (3, k) */
// logUnitConflict(node, sb);
// }
checkUnits(m, *node.getLeftChild(), sb, inKL, reactNo);
delete unitFormat;
delete unitsArg1;
delete unitsArgPower;
}
bool
ASTNaryFunctionNode::isSqrt() const
{
bool valid = false;
if (getType() == AST_FUNCTION_ROOT)
{
// a sqrt can have either one child that is not the degree qualifier
// or two where the first is the degree of 2
if (getNumChildren() == 1)
{
/* HACK to replicate OLD AST whic says a sqrt must have two children*/
valid = false;
//ASTBase * base1 = getChild(0);
//if (base1->isQualifier() == false)
//{
// valid = true;
//}
}
else if (getNumChildren() == 2)
{
ASTBase * base1 = ASTFunctionBase::getChild(0);
ASTFunction* fun = dynamic_cast<ASTFunction*>(base1);
if (fun != NULL)
{
if (fun->getType() == AST_QUALIFIER_DEGREE
&& fun->getNumChildren() == 1)
{
ASTBase *base2 = fun->getChild(0);
if (base2->getType() == AST_INTEGER)
{
ASTNumber *child = static_cast<ASTNumber*>(base2);
if (child->getInteger() == 2)
{
valid = true;
}
}
}
}
else
{
// here we are working the ASTNode so the casting
// is more difficult
ASTNode* newAST = dynamic_cast<ASTNode*>(base1);
if (newAST != NULL && newAST->getType() == AST_QUALIFIER_DEGREE
&& newAST->getNumChildren() == 1)
{
ASTNode* newAST1 = newAST->getChild(0);
if (newAST1->getType() == AST_INTEGER)
{
if (newAST1->getInteger() == 2)
{
valid = true;
}
}
}
else
{
if (newAST != NULL && newAST->getType() == AST_INTEGER)
{
if (newAST->getInteger() == 2)
{
valid = true;
}
}
}
}
}
}
return valid;
}
bool
ASTNaryFunctionNode::isLog10() const
{
bool valid = false;
if (getType() == AST_FUNCTION_LOG)
{
// a log can have either one child that is not the logbase qualifier
// or two where the first is the logbase of 10
if (getNumChildren() == 1)
{
ASTBase * base1 = ASTFunctionBase::getChild(0);
if (base1->isQualifier() == false)
{
valid = true;
}
}
else if (getNumChildren() == 2)
{
ASTBase * base1 = ASTFunctionBase::getChild(0);
ASTFunction* fun = dynamic_cast<ASTFunction*>(base1);
if (fun != NULL)
{
if (fun->getType() == AST_QUALIFIER_LOGBASE
&& fun->getNumChildren() == 1)
{
ASTBase *base2 = fun->getChild(0);
if (base2->getType() == AST_INTEGER)
{
ASTNumber *child = static_cast<ASTNumber*>(base2);
if (child->getInteger() == 10)
{
valid = true;
}
}
}
}
else
{
// here we are working the ASTNode so the casting
// is more difficult
ASTNode* newAST = dynamic_cast<ASTNode*>(base1);
if (newAST != NULL && newAST->getType() == AST_QUALIFIER_LOGBASE
&& newAST->getNumChildren() == 1 )
{
ASTNode* newAST1 = newAST->getChild(0);
if (newAST1->getType() == AST_INTEGER)
{
if (newAST1->getInteger() == 10)
{
valid = true;
}
}
}
else
{
if (newAST != NULL && newAST->getType() == AST_INTEGER)
{
if (newAST->getInteger() == 10)
{
valid = true;
}
}
}
}
}
}
return valid;
}
bool
ASTBinaryFunctionNode::isSqrt() const
{
bool valid = false;
ASTBase * base1 = NULL;
if (getType() == AST_FUNCTION_ROOT)
{
if (getNumChildren() == 2)
{
base1 = getChild(0);
ASTFunction* fun = dynamic_cast<ASTFunction*>(base1);
if (fun != NULL)
{
if (fun->getType() == AST_QUALIFIER_DEGREE
&& fun->getNumChildren() == 1)
{
ASTBase *base2 = fun->getChild(0);
if (base2->getType() == AST_INTEGER)
{
ASTNumber *child = static_cast<ASTNumber*>(base2);
if (child->getInteger() == 2)
{
valid = true;
}
}
}
}
else
{
// here we are working the ASTNode so the casting
// is more difficult
ASTNode* newAST = dynamic_cast<ASTNode*>(base1);
if (newAST != NULL && newAST->getType() == AST_QUALIFIER_DEGREE
&& newAST->getNumChildren() == 1)
{
ASTNode* newAST1 = newAST->getChild(0);
if (newAST1->getType() == AST_INTEGER)
{
if (newAST1->getInteger() == 2)
{
valid = true;
}
}
}
else
{
if (newAST != NULL && newAST->getType() == AST_INTEGER)
{
if (newAST->getInteger() == 2)
{
valid = true;
}
}
}
}
}
}
return valid;
}