/**
* Checks that the units of the arguments
* of the function are dimensionless
* and that there is only one argument
*
* If inconsistent units are found, an error message is logged.
*/
void
ArgumentsUnitsCheckWarnings::checkDimensionlessArgs (const Model& m,
const ASTNode& node,
const SBase & sb,
bool inKL, int reactNo)
{
/* check that node has children */
if (node.getNumChildren() == 0)
{
return;
}
UnitDefinition *dim = new UnitDefinition(m.getSBMLNamespaces());
Unit *unit = new Unit(m.getSBMLNamespaces());
unit->setKind(UNIT_KIND_DIMENSIONLESS);
unit->initDefaults();
UnitDefinition * tempUD;
dim->addUnit(unit);
UnitFormulaFormatter *unitFormat = new UnitFormulaFormatter(&m);
tempUD = unitFormat->getUnitDefinition(node.getChild(0), inKL, reactNo);
if (tempUD->getNumUnits() != 0 &&
!UnitDefinition::areEquivalent(dim, tempUD))
{
logInconsistentDimensionless(node, sb);
}
delete tempUD;
delete dim;
delete unit;
delete unitFormat;
}
/*
* Checks that the units of the delay function are consistent
*
* If inconsistent units are found, an error message is logged.
*/
void
ArgumentsUnitsCheck::checkUnitsFromDelay (const Model& m,
const ASTNode& node,
const SBase & sb, bool inKL, int reactNo)
{
/* check that node has two children */
if (node.getNumChildren() != 2)
{
return;
}
if (!m.getSBMLNamespaces()->getNamespaces())
{
#if 0
cout << "[DEBUG] XMLNS IS NULL" << endl;
#endif
}
/* delay(x, t)
* no restrictions on units of x
* but t must have units of time
*/
UnitDefinition *time = new UnitDefinition(m.getSBMLNamespaces());
Unit *unit = new Unit(m.getSBMLNamespaces());
unit->setKind(UNIT_KIND_SECOND);
unit->initDefaults();
UnitDefinition * tempUD;
time->addUnit(unit);
UnitFormulaFormatter *unitFormat = new UnitFormulaFormatter(&m);
tempUD = unitFormat->getUnitDefinition(node.getRightChild(), inKL, reactNo);
if (!unitFormat->getContainsUndeclaredUnits())
{
if (!UnitDefinition::areEquivalent(time, tempUD))
{
logInconsistentDelay(node, sb);
}
}
delete time;
delete tempUD;
delete unit;
delete unitFormat;
checkUnits(m, *node.getLeftChild(), sb, inKL, reactNo);
}
/*
* Checks that the units of the function are consistent
* for a function returning value with same units as argument(s)
*
* If inconsistent units are found, an error message is logged.
*/
void
ArgumentsUnitsCheck::checkSameUnitsAsArgs (const Model& m,
const ASTNode& node,
const SBase & sb, bool inKL,
int reactNo)
{
/* check that node has children */
if (node.getNumChildren() == 0)
{
return;
}
UnitDefinition * ud;
UnitDefinition * tempUD = NULL;
unsigned int n;
unsigned int i = 0;
UnitFormulaFormatter *unitFormat = new UnitFormulaFormatter(&m);
ud = unitFormat->getUnitDefinition(node.getChild(i), inKL, reactNo);
/* get the first child that is not a parameter with undeclared units */
while (unitFormat->getContainsUndeclaredUnits() &&
i < node.getNumChildren()-1)
{
delete ud;
i++;
unitFormat->resetFlags();
ud = unitFormat->getUnitDefinition(node.getChild(i), inKL, reactNo);
}
/* check that all children have the same units
* unless one of the children is a parameter with undeclared units
* which is not tested */
for (n = i+1; n < node.getNumChildren(); n++)
{
unitFormat->resetFlags();
tempUD = unitFormat->getUnitDefinition(node.getChild(n), inKL, reactNo);
if (!unitFormat->getContainsUndeclaredUnits())
{
if (!UnitDefinition::areIdenticalSIUnits(ud, tempUD))
{
logInconsistentSameUnits(node, sb);
}
}
delete tempUD;
}
delete unitFormat;
delete ud;
for (n = 0; n < node.getNumChildren(); n++)
{
checkUnits(m, *node.getChild(n), sb, inKL, reactNo);
}
}
/**
* 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;
}
/*
* Checks that the units of the piecewise function are consistent
*
* If inconsistent units are found, an error message is logged.
*/
void
ArgumentsUnitsCheck::checkUnitsFromPiecewise (const Model& m,
const ASTNode& node,
const SBase & sb, bool inKL, int reactNo)
{
/* check that node has children */
if (node.getNumChildren() == 0)
{
return;
}
/* piecewise(a0, a1, a2, a3, ...)
* a0 and a2, a(n_even) must have same units
* a1, a3, a(n_odd) must be dimensionless
*/
unsigned int n;
UnitDefinition *dim = new UnitDefinition(m.getSBMLNamespaces());
Unit *unit = new Unit(m.getSBMLNamespaces());
unit->setKind(UNIT_KIND_DIMENSIONLESS);
unit->initDefaults();
UnitDefinition * tempUD;
UnitDefinition * tempUD1 = NULL;
dim->addUnit(unit);
UnitFormulaFormatter *unitFormat = new UnitFormulaFormatter(&m);
tempUD = unitFormat->getUnitDefinition(node.getChild(0), inKL, reactNo);
for(n = 2; n < node.getNumChildren(); n+=2)
{
tempUD1 = unitFormat->getUnitDefinition(node.getChild(n), inKL, reactNo);
if (!unitFormat->getContainsUndeclaredUnits())
{
if (!UnitDefinition::areEquivalent(tempUD, tempUD1))
{
logInconsistentPiecewise(node, sb);
}
}
delete tempUD1;
}
delete tempUD;
for(n = 1; n < node.getNumChildren(); n+=2)
{
tempUD = unitFormat->getUnitDefinition(node.getChild(n), inKL, reactNo);
if (!UnitDefinition::areEquivalent(tempUD, dim))
{
logInconsistentPiecewiseCondition(node, sb);
}
delete tempUD;
}
delete dim;
delete unit;
delete unitFormat;
for(n = 0; n < node.getNumChildren(); n++)
{
checkUnits(m, *node.getChild(n), sb, inKL, reactNo);
}
}
