END_TEST
START_TEST (test_getUnitDefinition_power_one_child)
{
ASTNode * node = new ASTNode(AST_POWER);
ASTNode * c = new ASTNode(AST_NAME);
c->setName("k");
node->addChild(c);
UnitDefinition * ud = NULL;
ud = uff->getUnitDefinition(node);
fail_unless(uff->getContainsUndeclaredUnits() == true);
fail_unless(uff->canIgnoreUndeclaredUnits() == false);
fail_unless(ud != NULL);
fail_unless(ud->getNumUnits() == 1);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);
fail_unless(util_isEqual(ud->getUnit(0)->getExponent(), 1));
delete node;
delete ud;
}
END_TEST
START_TEST (test_CalcUnitDefinition_assignmentRule1)
{
UnitDefinition *fud = m->getParameter("e")->getDerivedUnitDefinition();
fail_unless(fud->getNumUnits() == 0);
m->getParameter("e")->setCalculatingUnits(true);
fud = m->getParameter("e")->getDerivedUnitDefinition();
m->getParameter("e")->setCalculatingUnits(false);
fail_unless(fud->getNumUnits() == 2);
fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);
fail_unless(fud->getUnit(0)->getMultiplier() == 1);
fail_unless(fud->getUnit(0)->getScale() == 0);
fail_unless(fud->getUnit(0)->getExponent() == 1);
fail_unless(fud->getUnit(0)->getOffset() == 0.0);
fail_unless(fud->getUnit(0)->getKind() == UNIT_KIND_METRE);
fail_unless(fud->getUnit(1)->getMultiplier() == 1);
fail_unless(fud->getUnit(1)->getScale() == 0);
fail_unless(fud->getUnit(1)->getExponent() == -1);
fail_unless(fud->getUnit(1)->getOffset() == 0.0);
fail_unless(fud->getUnit(1)->getKind() == UNIT_KIND_SECOND);
delete fud;
}
END_TEST
START_TEST (test_DerivedUnitDefinition_event)
{
UnitDefinition *fud = m->getEvent(0)->getEventAssignment(0)->getDerivedUnitDefinition();
bool undecl = m->getEvent(0)->getEventAssignment(0)->containsUndeclaredUnits();
fail_unless(undecl == 1);
fail_unless(fud->getNumUnits() == 2);
fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);
fail_unless(fud->getUnit(0)->getMultiplier() == 1);
fail_unless(fud->getUnit(0)->getScale() == 0);
fail_unless(fud->getUnit(0)->getExponent() == 1);
fail_unless(fud->getUnit(0)->getOffset() == 0.0);
fail_unless(fud->getUnit(0)->getKind() == UNIT_KIND_METRE);
fail_unless(fud->getUnit(1)->getMultiplier() == 1);
fail_unless(fud->getUnit(1)->getScale() == 0);
fail_unless(fud->getUnit(1)->getExponent() == -1);
fail_unless(fud->getUnit(1)->getOffset() == 0.0);
fail_unless(fud->getUnit(1)->getKind() == UNIT_KIND_SECOND);
}
END_TEST
START_TEST (test_DerivedUnitDefinition_parameter)
{
UnitDefinition *fud = m->getParameter(0)->getDerivedUnitDefinition();
fail_unless(fud->getNumUnits() == 2);
fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);
fail_unless(fud->getUnit(0)->getMultiplier() == 1);
fail_unless(fud->getUnit(0)->getScale() == 0);
fail_unless(fud->getUnit(0)->getExponent() == 1);
fail_unless(fud->getUnit(0)->getOffset() == 0.0);
fail_unless(fud->getUnit(0)->getKind() == UNIT_KIND_METRE);
fail_unless(fud->getUnit(1)->getMultiplier() == 1);
fail_unless(fud->getUnit(1)->getScale() == 0);
fail_unless(fud->getUnit(1)->getExponent() == -1);
fail_unless(fud->getUnit(1)->getOffset() == 0.0);
fail_unless(fud->getUnit(1)->getKind() == UNIT_KIND_SECOND);
fud = m->getParameter(1)->getDerivedUnitDefinition();
fail_unless(fud->getNumUnits() == 0);
fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);
}
END_TEST
#if (0)
START_TEST (test_getUnitDefinition_power_minus_double_exponent)
{
ASTNode * node = new ASTNode(AST_POWER);
ASTNode * c = new ASTNode(AST_NAME);
c->setName("k");
ASTNode * c1 = new ASTNode(AST_REAL);
c1->setValue(0.3);
ASTNode * c2 = new ASTNode(AST_MINUS);
c2->addChild(c1);
node->addChild(c);
node->addChild(c2);
UnitDefinition * ud = NULL;
ud = uff->getUnitDefinition(node);
fail_unless(uff->getContainsUndeclaredUnits() == false);
fail_unless(uff->canIgnoreUndeclaredUnits() == false);
fail_unless(ud != NULL);
fail_unless(ud->getNumUnits() == 1);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);
fail_unless(util_isEqual(ud->getUnit(0)->getExponentAsDouble(), -0.3));
delete node;
delete ud;
}
END_TEST
#endif
START_TEST (test_getUnitDefinition_power_dim_param_exponent)
{
ASTNode * node = new ASTNode(AST_POWER);
ASTNode * c = new ASTNode(AST_NAME);
c->setName("k");
ASTNode * c1 = new ASTNode(AST_NAME);
c1->setName("a");
node->addChild(c);
node->addChild(c1);
UnitDefinition * ud = NULL;
ud = uff->getUnitDefinition(node);
fail_unless(uff->getContainsUndeclaredUnits() == false);
fail_unless(uff->canIgnoreUndeclaredUnits() == false);
fail_unless(ud != NULL);
fail_unless(ud->getNumUnits() == 1);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);
fail_unless(util_isEqual(ud->getUnit(0)->getExponentAsDouble(), 3.5));
delete node;
delete ud;
}
END_TEST
START_TEST(test_unitdefinition_divide2)
{
UnitDefinition* ud = new UnitDefinition(2, 2);
UnitDefinition* ud1 = new UnitDefinition(2, 2);
UnitDefinition* udTemp;
Unit* u = ud->createUnit();
u->setKind(UNIT_KIND_METRE);
Unit* u1 = ud1->createUnit();
u1->setKind(UNIT_KIND_MOLE);
udTemp = UnitDefinition::divide(ud, ud1);
fail_unless(udTemp->getNumUnits() == 2);
fail_unless(udTemp->getUnit(0)->getKind() == UNIT_KIND_METRE);
fail_unless(udTemp->getUnit(1)->getKind() == UNIT_KIND_MOLE);
fail_unless(udTemp->getUnit(1)->getExponent() == -1);
fail_unless(udTemp->getLevel() == 2);
fail_unless(udTemp->getVersion() == 2);
delete ud1;
delete ud;
delete udTemp;
}
END_TEST
START_TEST (test_CalcUnitDefinition_local1)
{
UnitDefinition *fud = m->getReaction("R5")->getKineticLaw()
->getLocalParameter(0)->getDerivedUnitDefinition();
fail_unless(fud->getNumUnits() == 0);
m->getReaction("R5")->getKineticLaw()
->getLocalParameter(0)->setCalculatingUnits(true);
fud = m->getReaction("R5")->getKineticLaw()
->getLocalParameter(0)->getDerivedUnitDefinition();
m->getReaction("R5")->getKineticLaw()
->getLocalParameter(0)->setCalculatingUnits(false);
fail_unless(fud->getNumUnits() == 1);
fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);
fail_unless(fud->getUnit(0)->getMultiplier() == 1);
fail_unless(fud->getUnit(0)->getScale() == 0);
fail_unless(fud->getUnit(0)->getExponent() == 1);
fail_unless(fud->getUnit(0)->getOffset() == 0.0);
fail_unless(fud->getUnit(0)->getKind() == UNIT_KIND_SECOND);
}
END_TEST
START_TEST (test_UnitFormulaFormatter2_getUnitDefinition_model_extent)
{
UnitDefinition * ud = NULL;
/* model extent units */
ud = uff->getExtentUnitDefinition();
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_MOLE);
/* check deals with invalid nodes */
delete ud;
UnitDefinition * ud1 = NULL;
m->unsetExtentUnits();
ud1 = uff->getExtentUnitDefinition();
fail_unless (ud1->getNumUnits() == 0);
delete ud1;
}
END_TEST
START_TEST (test_UnitFormulaFormatter_getUnitDefinition_plus)
{
UnitDefinition * ud = new UnitDefinition(2, 4);
ud = uff->getUnitDefinition(m->getRule(3)->getMath());
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);
/* check an invalid node */
delete ud;
UnitDefinition * ud1 = new UnitDefinition(m->getLevel(), m->getVersion());
ASTNode *node = new ASTNode(AST_PLUS);
ud1 = uff->getUnitDefinition(node);
fail_unless (ud1->getNumUnits() == 0);
delete ud1;
delete node;
}
std::string Expression2PresentationMMLUnits::getMathML(const UnitDefinition & ud) const
{
std::string tmp;
/*tmp += "<mrow>";
unsigned int i, imax = ud.getNumUnits();
for (i=0; i<imax; ++i)
{
if (i) tmp += "<mo>·</mo>";
tmp += getMathML(ud.getUnit(i), false);
}
tmp += "</mrow>";*/
tmp += "<mrow>";
bool isFirst = true;
unsigned int i, imax = ud.getNumUnits();
for (i = 0; i < imax; ++i)
{
if (ud.getUnit(i)->getExponent() >= 0)
{
if (!isFirst) tmp += "<mo>·</mo>";
tmp += getMathML(ud.getUnit(i), true);
isFirst = false;
}
}
if (isFirst) tmp += "<mn>1</mn>"; //there are no units with pos. exponent
std::string tmp2;
isFirst = true;
for (i = 0; i < imax; ++i)
{
if (ud.getUnit(i)->getExponent() < 0)
{
if (!isFirst) tmp2 += "<mo>·</mo>";
tmp2 += getMathML(ud.getUnit(i), true);
isFirst = false;
}
}
if (!isFirst) tmp += "<mo>/</mo>" + tmp2; //only create fraction when there is a denominator
tmp += "</mrow>";
return tmp;
}
END_TEST
START_TEST (test_infer_localParam_fromReaction)
{
string filename(TestDataDirectory);
filename += "inferUnits-3.xml";
SBMLDocument* d = readSBMLFromFile(filename.c_str());
fail_unless(d != NULL);
LocalParameter * p = d->getModel()->getReaction(1)->
getKineticLaw()->getLocalParameter("k2");
fail_unless(p->isSetUnits() == false);
p->setCalculatingUnits(true);
UnitDefinition *ud = p->getDerivedUnitDefinition();
fail_unless(ud->getNumUnits() == 1);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == -1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_SECOND);
delete ud;
// TO DO make the units converter do local parameters;
//fail_unless(d->getModel()->getNumUnitDefinitions() == 3);
//
//SBMLInferUnitsConverter * units = new SBMLInferUnitsConverter();
//units->setDocument(d);
//fail_unless (units->convert() == LIBSBML_OPERATION_SUCCESS);
//kl = d->getModel()->getReaction(1)->getKineticLaw();
//fail_unless(kl->getLocalParameter("k2")->isSetUnits() == true);
//fail_unless(kl->getLocalParameter("k2")->getUnits() == "per_time");
//delete units;
delete d;
}
END_TEST
START_TEST (test_infer_newUD)
{
string filename(TestDataDirectory);
filename += "inferUnits.xml";
SBMLDocument* d = readSBMLFromFile(filename.c_str());
fail_unless(d != NULL);
fail_unless(d->getModel()->getParameter("b")->isSetUnits() == false);
fail_unless(d->getModel()->getNumUnitDefinitions() == 1);
SBMLInferUnitsConverter * units = new SBMLInferUnitsConverter();
units->setDocument(d);
fail_unless (units->convert() == LIBSBML_OPERATION_SUCCESS);
fail_unless(d->getModel()->getParameter("b")->isSetUnits() == true);
fail_unless(d->getModel()->getParameter("b")->getUnits() == "unitSid_0");
fail_unless(d->getModel()->getNumUnitDefinitions() == 2);
UnitDefinition *ud = d->getModel()->getUnitDefinition(1);
fail_unless(ud->getId() == "unitSid_0");
fail_unless(ud->getNumUnits() == 2);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_LITRE);
fail_unless(ud->getUnit(1)->getMultiplier() == 1);
fail_unless(ud->getUnit(1)->getScale() == 0);
fail_unless(ud->getUnit(1)->getExponent() == 1);
fail_unless(ud->getUnit(1)->getOffset() == 0.0);
fail_unless(ud->getUnit(1)->getKind() == UNIT_KIND_METRE);
delete units;
delete d;
}
END_TEST
START_TEST (test_UnitFormulaFormatter_getUnitDefinition_root)
{
UnitDefinition * ud = new UnitDefinition(2, 4);
ud = uff->getUnitDefinition(m->getRule(8)->getMath());
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_VOLT);
delete ud;
}
/*
* Eliminate all dimensionless units from the given UnitDefinition.
* A new UnitDefinition without the dimensionless units is returned.
* The scale and multiplier are preserved. If the UnitDefinition has only
* one unit the is a dimensionless, it is not deleted.
* @param UnitDefinition* pUdef
* @return UnitDefinition* result
*/
LIBSBML_EXTERN
UnitDefinition* UnitConversionFactory::eliminateDimensionless(UnitDefinition* pUdef)
{
unsigned int maxUnits = pUdef->getNumUnits();
UnitDefinition* pTmpUdef = NULL;
Unit* pU = NULL;
if (maxUnits > 1)
{
int scale = 0;
double multiplier = 1.0;
unsigned int i = 0;
pTmpUdef = new UnitDefinition(UnitConversionFactory::SBML_LEVEL, UnitConversionFactory::SBML_VERSION);
while (i < maxUnits)
{
pU = new Unit(*(pUdef->getUnit(i)));
if (pU->getKind() != UNIT_KIND_DIMENSIONLESS)
{
pTmpUdef->addUnit(pU);
}
else
{
// conserve scale and multiplier
scale = scale + pU->getScale();
multiplier = multiplier * pU->getMultiplier();
}
delete pU;
++i;
}
i = pTmpUdef->getNumUnits();
if (i > 0 && i < maxUnits)
{
pTmpUdef->setName(pUdef->getName());
pTmpUdef->setId(pUdef->getId());
pU = pTmpUdef->getUnit(0);
pU->setScale(pU->getScale() + scale);
pU->setMultiplier(pU->getMultiplier()*multiplier);
}
else
{
delete pTmpUdef;
pTmpUdef = NULL;
}
}
return pTmpUdef;
}
END_TEST
START_TEST (test_CalcUnitDefinition_global_with_local_known)
{
UnitDefinition *fud = m->getParameter("q")->getDerivedUnitDefinition();
fail_unless(fud->getNumUnits() == 0);
m->getParameter("q")->setCalculatingUnits(true);
fud = m->getParameter("q")->getDerivedUnitDefinition();
m->getParameter("q")->setCalculatingUnits(false);
fail_unless(fud->getNumUnits() == 1);
fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);
fail_unless(fud->getUnit(0)->getMultiplier() == 1);
fail_unless(fud->getUnit(0)->getScale() == 0);
fail_unless(fud->getUnit(0)->getExponent() == 1);
fail_unless(fud->getUnit(0)->getOffset() == 0.0);
fail_unless(fud->getUnit(0)->getKind() == UNIT_KIND_LITRE);
}
/*
* Returns a string representation of the given Unit. THis function is
* only for debugging purposes.
* @param const UnitDefinition& uDef
* @return std::string unitDefinitionRepresentation
*/
LIBSBML_EXTERN
std::string UnitConversionFactory::toString(const UnitDefinition& uDef)
{
unsigned int maxUnits = uDef.getNumUnits();
unsigned int i;
std::stringstream ss;
for (i = 0; i < maxUnits; ++i)
{
ss << "(" << UnitConversionFactory::toString(*(uDef.getUnit(i))) << ") ";
}
return ss.str();
}
END_TEST
START_TEST (test_UnitFormulaFormatter2_getUnitDefinition_event)
{
UnitDefinition * ud = NULL;
/* event with no time units */
ud = uff->getUnitDefinitionFromEventTime(m->getEvent(0));
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 60);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_SECOND);
/* check deals with invalid nodes */
delete ud;
UnitDefinition * ud1 = NULL;
Event *e = new Event(m->getLevel(), m->getVersion());
e->setId("p");
m->unsetTimeUnits();
ud1 = uff->getUnitDefinitionFromEventTime(e);
fail_unless (ud1->getNumUnits() == 0);
delete e;
delete ud1;
}
END_TEST
START_TEST(test_unitdefinition_order)
{
UnitDefinition* ud = new UnitDefinition(2, 4);
Unit* u = new Unit(2, 4);
u->setKind(UNIT_KIND_METRE);
Unit* u1 = new Unit(2, 4);
u1->setKind(UNIT_KIND_AMPERE);
Unit* u2 = new Unit(2, 4);
u2->setKind(UNIT_KIND_HERTZ);
ud->addUnit(u);
ud->addUnit(u1);
ud->addUnit(u2);
UnitDefinition::reorder(ud);
fail_unless(ud->getNumUnits() == 3);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_AMPERE);
fail_unless(ud->getUnit(1)->getKind() == UNIT_KIND_HERTZ);
fail_unless(ud->getUnit(2)->getKind() == UNIT_KIND_METRE);
/* NULL case*/
ud = NULL;
UnitDefinition::reorder(ud);
fail_unless(ud == NULL);
delete u;
delete u1;
delete u2;
delete ud;
}
END_TEST
START_TEST (test_UnitFormulaFormatter_getUnitDefinition_piecewise)
{
UnitDefinition * ud = new UnitDefinition(2, 4);
ud = uff->getUnitDefinition(m->getRule(7)->getMath());
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);
/* check deals with invalid nodes */
delete ud;
UnitDefinition * ud1 = new UnitDefinition(m->getLevel(), m->getVersion());
ASTNode *node = new ASTNode(AST_FUNCTION_PIECEWISE);
ud1 == uff->getUnitDefinition(node);
fail_unless (ud1->getNumUnits() == 0);
ASTNode *c = new ASTNode(AST_UNKNOWN);
node->addChild(c);
ud1 == uff->getUnitDefinition(node);
fail_unless (ud1->getNumUnits() == 0);
delete ud1;
delete node;
}
END_TEST
START_TEST (test_DerivedUnitDefinition_reaction)
{
UnitDefinition *fud = m->getReaction(0)->getKineticLaw()->getDerivedUnitDefinition();
bool undecl = m->getReaction(0)->getKineticLaw()->containsUndeclaredUnits();
fail_unless(undecl == 0);
fail_unless(fud->getNumUnits() == 2);
fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);
fail_unless(fud->getUnit(0)->getMultiplier() == 1);
fail_unless(fud->getUnit(0)->getScale() == 0);
fail_unless(fud->getUnit(0)->getExponent() == 1);
fail_unless(fud->getUnit(0)->getOffset() == 0.0);
fail_unless(fud->getUnit(0)->getKind() == UNIT_KIND_MOLE);
fail_unless(fud->getUnit(1)->getMultiplier() == 1);
fail_unless(fud->getUnit(1)->getScale() == 0);
fail_unless(fud->getUnit(1)->getExponent() == -1);
fail_unless(fud->getUnit(1)->getOffset() == 0.0);
fail_unless(fud->getUnit(1)->getKind() == UNIT_KIND_SECOND);
fud = m->getReaction(0)->getReactant(0)->getStoichiometryMath()->getDerivedUnitDefinition();
undecl = m->getReaction(0)->getReactant(0)->getStoichiometryMath()->containsUndeclaredUnits();
fail_unless(undecl == 1);
fail_unless(fud->getNumUnits() == 0);
fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);
}
END_TEST
START_TEST (test_CalcUnitDefinition_priority)
{
UnitDefinition *fud = m->getParameter("m")->getDerivedUnitDefinition();
fail_unless(fud->getNumUnits() == 0);
m->getParameter("m")->setCalculatingUnits(true);
fud = m->getParameter("m")->getDerivedUnitDefinition();
m->getParameter("m")->setCalculatingUnits(false);
fail_unless(fud->getNumUnits() == 1);
fail_unless(!strcmp(fud->getId().c_str(), ""), NULL);
fail_unless(fud->getUnit(0)->getMultiplier() == 1);
fail_unless(fud->getUnit(0)->getScale() == 0);
fail_unless(fud->getUnit(0)->getExponent() == 1);
fail_unless(fud->getUnit(0)->getOffset() == 0.0);
fail_unless(fud->getUnit(0)->getKind() == UNIT_KIND_DIMENSIONLESS);
delete fud;
}
/*
* The functions determins wether the given UnitDefinition contains only
* units from the list given as the second argument.
* @param const UnitDefinition& uDef
* @param const ListOf& unitList
* @return bool containsOnlyGivenUnits
*/
LIBSBML_EXTERN
bool UnitConversionFactory::containsOnlyGivenUnits(const UnitDefinition& uDef, const ListOf& unitList)
{
bool result = true;
UnitDefinition* pTmpUdef = UnitConversionFactory::convertToSI(uDef);
if (pTmpUdef)
{
unsigned int i;
unsigned int maxUnits = pTmpUdef->getNumUnits();
for (i = 0; i < maxUnits; ++i)
{
Unit* pU = pTmpUdef->getUnit(i);
UnitKind_t kind = pU->getKind();
unsigned int j;
unsigned int maxUnits2 = unitList.size();
bool found = false;
for (j = 0; j < maxUnits2; ++j)
{
const Unit* pU2 = dynamic_cast<const Unit*>(unitList.get(j));
if (!pU2) break;
if (pU2->getKind() == kind)
{
found = true;
break;
}
}
if (!found)
{
result = false;
break;
}
}
delete pTmpUdef;
}
else
{
result = false;
}
return result;
}
END_TEST
START_TEST ( test_Unit_parent_create )
{
UnitDefinition* ud = new UnitDefinition(2, 4);
Unit * u = ud->createUnit();
fail_unless(ud->getNumUnits() == 1);
ListOf *lo = ud->getListOfUnits();
fail_unless(lo == ud->getUnit(0)->getParentSBMLObject());
fail_unless(lo == u->getParentSBMLObject());
fail_unless(ud == lo->getParentSBMLObject());
delete ud;
}
double SbmlReader::unitsforRates() {
double lvalue =1;
for (unsigned int n=0; n < model_->getNumUnitDefinitions(); n++) {
UnitDefinition * ud = model_->getUnitDefinition(n);
for (unsigned int ut=0; ut <ud->getNumUnits(); ut++) {
Unit * unit = ud->getUnit(ut);
if (ud->getId() == "substance") {
if ( unit->isMole() ) {
double exponent = unit->getExponent();
double multiplier = unit->getMultiplier();
int scale = unit->getScale();
double offset = unit->getOffset();
lvalue *= pow( multiplier * pow(10.0,scale), exponent ) + offset;
return lvalue;
}
}
}
}
return lvalue;
}//unitforRates
END_TEST
START_TEST (test_unitdefinition_simplify1)
{
UnitDefinition *ud = new UnitDefinition(2, 1);
Unit * u = ud->createUnit();
u->setKind(UNIT_KIND_MOLE);
Unit * u1 = ud->createUnit();
u1->setKind(UNIT_KIND_MOLE);
u1->setExponent(-1);
UnitDefinition::simplify(ud);
fail_unless( ud->getNumUnits() == 1);
fail_unless( ud->getUnit(0)->getKind() == UNIT_KIND_DIMENSIONLESS );
delete ud;
}
END_TEST
START_TEST (test_UnitFormulaFormatter2_getUnitDefinition_species_extent)
{
UnitDefinition * ud = NULL;
/* model extent units + conversion on species*/
ud = uff->getSpeciesExtentUnitDefinition(m->getSpecies(0));
fail_unless(ud->getNumUnits() == 2);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_MOLE);
fail_unless(ud->getUnit(1)->getMultiplier() == 1);
fail_unless(ud->getUnit(1)->getScale() == 0);
fail_unless(ud->getUnit(1)->getExponent() == 1);
fail_unless(ud->getUnit(1)->getOffset() == 0.0);
fail_unless(ud->getUnit(1)->getKind() == UNIT_KIND_SECOND);
delete ud;
/* model extent units + conversion on model*/
ud = uff->getSpeciesExtentUnitDefinition(m->getSpecies(1));
fail_unless(ud->getNumUnits() == 2);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_MOLE);
fail_unless(ud->getUnit(1)->getMultiplier() == 1);
fail_unless(ud->getUnit(1)->getScale() == 0);
fail_unless(ud->getUnit(1)->getExponent() == 1);
fail_unless(ud->getUnit(1)->getOffset() == 0.0);
fail_unless(ud->getUnit(1)->getKind() == UNIT_KIND_SECOND);
/* check deals with invalid nodes */
delete ud;
UnitDefinition * ud1 = NULL;
m->unsetConversionFactor();
ud1 = uff->getSpeciesExtentUnitDefinition(m->getSpecies(1));
fail_unless (ud1->getNumUnits() == 0);
m->getSpecies(0)->unsetConversionFactor();
delete ud1;
ud1 = uff->getSpeciesExtentUnitDefinition(m->getSpecies(0));
fail_unless (ud1->getNumUnits() == 0);
m->getSpecies(0)->setConversionFactor("cf");
m->unsetExtentUnits();
delete ud1;
ud1 = uff->getSpeciesExtentUnitDefinition(m->getSpecies(0));
fail_unless (ud1->getNumUnits() == 0);
delete ud1;
}
END_TEST
START_TEST (test_UnitFormulaFormatter2_getUnitDefinition_function)
{
UnitDefinition * ud;
/* function applied to numbers only */
ud = uff->getUnitDefinition(m->getRule(0)->getMath());
fail_unless(ud->getNumUnits() == 0);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
delete ud;
/* function applied to components */
uff->resetFlags();
ud = uff->getUnitDefinition(m->getRule(1)->getMath());
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);
delete ud;
/* function with two arguments but only one bvar */
uff->resetFlags();
ud = uff->getUnitDefinition(m->getRule(2)->getMath());
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 3);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);
delete ud;
///* function with two arguments but only one bvar */
uff->resetFlags();
ud = uff->getUnitDefinition(m->getRule(3)->getMath());
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == -1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_SECOND);
delete ud;
}
END_TEST
START_TEST (test_UnitFormulaFormatter2_getUnitDefinition_parameter)
{
UnitDefinition * ud = NULL;
/* parameter with declared standard units */
ud = uff->getUnitDefinitionFromParameter(m->getParameter(0));
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);
delete ud;
/* parameter with declared units from unit definition */
ud = uff->getUnitDefinitionFromParameter(m->getParameter(1));
fail_unless(ud->getNumUnits() == 2);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_METRE);
fail_unless(ud->getUnit(1)->getMultiplier() == 1);
fail_unless(ud->getUnit(1)->getScale() == 0);
fail_unless(ud->getUnit(1)->getExponent() == -1);
fail_unless(ud->getUnit(1)->getOffset() == 0.0);
fail_unless(ud->getUnit(1)->getKind() == UNIT_KIND_SECOND);
delete ud;
/* parameter with no declared units */
ud = uff->getUnitDefinitionFromParameter(m->getParameter(2));
fail_unless(ud->getNumUnits() == 0);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
/* check deals with invalid nodes */
delete ud;
UnitDefinition * ud1 = NULL;
Parameter *p = new Parameter(m->getLevel(), m->getVersion());
p->setId("p");
p->setUnits("undefined");
ud1 = uff->getUnitDefinitionFromParameter(p);
fail_unless (ud1->getNumUnits() == 0);
delete p;
delete ud1;
}
END_TEST
START_TEST (test_UnitFormulaFormatter2_getUnitDefinition_species)
{
UnitDefinition * ud = NULL;
/* species with declared standard units for substance and comp with units*/
ud = uff->getUnitDefinitionFromSpecies(m->getSpecies(0));
fail_unless(ud->getNumUnits() == 2);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_MOLE);
fail_unless(ud->getUnit(1)->getMultiplier() == 1);
fail_unless(ud->getUnit(1)->getScale() == 0);
fail_unless(ud->getUnit(1)->getExponent() == -1);
fail_unless(ud->getUnit(1)->getOffset() == 0.0);
fail_unless(ud->getUnit(1)->getKind() == UNIT_KIND_LITRE);
delete ud;
ud = uff->getSpeciesSubstanceUnitDefinition(m->getSpecies(0));
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_MOLE);
delete ud;
/* species with declared standard units for substance
and hasOnlySubstanceUnits = 1*/
ud = uff->getUnitDefinitionFromSpecies(m->getSpecies(1));
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == -2);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_MOLE);
delete ud;
ud = uff->getSpeciesSubstanceUnitDefinition(m->getSpecies(1));
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == -2);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_MOLE);
delete ud;
/* species with units from model substance*/
ud = uff->getUnitDefinitionFromSpecies(m->getSpecies(2));
fail_unless(ud->getNumUnits() == 2);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_MOLE);
fail_unless(ud->getUnit(1)->getMultiplier() == 1);
fail_unless(ud->getUnit(1)->getScale() == 0);
fail_unless(ud->getUnit(1)->getExponent() == -1);
fail_unless(ud->getUnit(1)->getOffset() == 0.0);
fail_unless(ud->getUnit(1)->getKind() == UNIT_KIND_LITRE);
delete ud;
ud = uff->getSpeciesSubstanceUnitDefinition(m->getSpecies(2));
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_MOLE);
delete ud;
/* species with declared standard units for substance and no spatialSizeUnits*/
ud = uff->getUnitDefinitionFromSpecies(m->getSpecies(3));
fail_unless(ud->getNumUnits() == 0);
delete ud;
ud = uff->getSpeciesSubstanceUnitDefinition(m->getSpecies(3));
fail_unless(ud->getNumUnits() == 1);
fail_unless(!strcmp(ud->getId().c_str(), ""), NULL);
fail_unless(ud->getUnit(0)->getMultiplier() == 1);
fail_unless(ud->getUnit(0)->getScale() == 0);
fail_unless(ud->getUnit(0)->getExponent() == 1);
fail_unless(ud->getUnit(0)->getOffset() == 0.0);
fail_unless(ud->getUnit(0)->getKind() == UNIT_KIND_MOLE);
///* check deals with invalid nodes */
delete ud;
UnitDefinition * ud1 = NULL;
Species *s = new Species(m->getLevel(), m->getVersion());
s->setId("s");
s->setUnits("undefined");
ud1 = uff->getUnitDefinitionFromSpecies(s);
fail_unless (ud1->getNumUnits() == 0);
delete ud1;
ud1 = uff->getSpeciesSubstanceUnitDefinition(s);
fail_unless (ud1->getNumUnits() == 0);
s->setUnits("mole"); // here the compartment size will be NULL
delete ud1;
ud1 = uff->getUnitDefinitionFromSpecies(s);
fail_unless (ud1->getNumUnits() == 1);
delete ud1;
ud1 = uff->getSpeciesSubstanceUnitDefinition(s);
fail_unless (ud1->getNumUnits() == 1);
delete s;
delete ud1;
}
