VectorOf<Word>
PresentationParser::parseWordList( const VectorOf<Chars>& names, Chars& errMesg )
{
genNames = names;
if ( curToken == INIT ) getToken();
ListOf<Word> result;
if ( curToken == INIT ) getToken();
while ( atStartOfWord() ) {
Word w = parseWord( names, errMesg );
if ( errMesg.length() > 0 ) {
return makeVectorOf(result);
}
result.append( w );
if ( curToken == COMMA ) {
getToken();
if ( !atStartOfWord() ) {
parseError("Expected a word here");
errMesg = parseErrorMessage;
return makeVectorOf(result);
}
}
}
return makeVectorOf(result);
}
// [[Rcpp::export]]
ListOf<CharacterVector> qatd_cpp_unhash(ListOf<IntegerVector> tokens_int,
CharacterVector types){
types.push_front(""); // offset types to match index in R
List tokens_chr(tokens_int.size());
for(int i=0; i < tokens_int.size(); i++){
tokens_chr[i] = types[tokens_int[i]];
}
return tokens_chr;
}
END_TEST
START_TEST ( test_InitialAssignment_parent_create )
{
Model *m = new Model(2, 4);
InitialAssignment *ia = m->createInitialAssignment();
ListOf *lo = m->getListOfInitialAssignments();
fail_unless(lo == m->getInitialAssignment(0)->getParentSBMLObject());
fail_unless(lo == ia->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_FunctionDefinition_parent_create )
{
Model *m = new Model(2, 4);
FunctionDefinition *fd = m->createFunctionDefinition();
ListOf *lo = m->getListOfFunctionDefinitions();
fail_unless(lo == m->getFunctionDefinition(0)->getParentSBMLObject());
fail_unless(lo == fd->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_Reaction_parent_create )
{
Model *m = new Model(2, 4);
Reaction *r = m->createReaction();
ListOf *lo = m->getListOfReactions();
fail_unless(lo == m->getReaction(0)->getParentSBMLObject());
fail_unless(lo == r->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_SpeciesReference_Reactant_parent_create )
{
Reaction *r = new Reaction(2, 4);
SpeciesReference *sr = r->createReactant();
ListOf *lo = r->getListOfReactants();
fail_unless(lo == r->getReactant(0)->getParentSBMLObject());
fail_unless(lo == sr->getParentSBMLObject());
fail_unless(r == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_Event_parent_create )
{
Model *m = new Model(2, 4);
Event *e = m->createEvent();
ListOf *lo = m->getListOfEvents();
fail_unless(lo == m->getEvent(0)->getParentSBMLObject());
fail_unless(lo == e->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_CompartmentType_parent_create )
{
Model *m = new Model(2, 4);
CompartmentType *ct = m->createCompartmentType();
ListOf *lo = m->getListOfCompartmentTypes();
fail_unless(lo == m->getCompartmentType(0)->getParentSBMLObject());
fail_unless(lo == ct->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_Constraint_parent_create )
{
Model *m = new Model(2, 4);
Constraint *ct = m->createConstraint();
ListOf *lo = m->getListOfConstraints();
fail_unless(lo == m->getConstraint(0)->getParentSBMLObject());
fail_unless(lo == ct->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_SpeciesType_parent_create )
{
Model *m = new Model(2, 4);
SpeciesType *st = m->createSpeciesType();
ListOf *lo = m->getListOfSpeciesTypes();
fail_unless(lo == m->getSpeciesType(0)->getParentSBMLObject());
fail_unless(lo == st->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_SpeciesReference_Modifier_parent_create )
{
Reaction *r = new Reaction(2, 4);
ModifierSpeciesReference *sr = r->createModifier();
ListOf *lo = r->getListOfModifiers();
fail_unless(lo == sr->getParentSBMLObject());
fail_unless(lo == r->getModifier(0)->getParentSBMLObject());
fail_unless(r == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_UnitDefinition_parent_create )
{
Model *m = new Model(2, 4);
UnitDefinition *ud = m->createUnitDefinition();
ListOf *lo = m->getListOfUnitDefinitions();
fail_unless(lo == m->getUnitDefinition(0)->getParentSBMLObject());
fail_unless(lo == ud->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_RateRule_parent_create )
{
Model *m = new Model(2, 4);
RateRule *r = m->createRateRule();
ListOf *lo = m->getListOfRules();
fail_unless(lo == m->getRule(0)->getParentSBMLObject());
fail_unless(lo == r->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_Parameter_parent_create )
{
Model *m = new Model(2, 4);
Parameter *p = m->createParameter();
ListOf *lo = m->getListOfParameters();
fail_unless(lo == m->getParameter(0)->getParentSBMLObject());
fail_unless(lo == p->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_SpeciesReference_Product_parent_create_model )
{
Model *m = new Model(2, 4);
Reaction *r = m->createReaction();
SpeciesReference *sr = m->createProduct();
ListOf *lo = r->getListOfProducts();
fail_unless(lo == r->getProduct(0)->getParentSBMLObject());
fail_unless(lo == sr->getParentSBMLObject());
fail_unless(r == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_EventAssignment_parent_create )
{
Event *e = new Event(2, 4);
EventAssignment *ea = e->createEventAssignment();
ListOf *lo = e->getListOfEventAssignments();
fail_unless(lo == e->getEventAssignment(0)->getParentSBMLObject());
fail_unless(lo == ea->getParentSBMLObject());
fail_unless(e == lo->getParentSBMLObject());
}
/*
* 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;
}
// Convert a list of numeric vectors into a single numeric vector where
// each original vector is followed by an NA
// [[Rcpp::export]]
NumericVector ungroupNA(ListOf<NumericVector> x) {
int n = x.size();
// Figure out total size needed
int n_total = 0;
for (int i = 0; i < n; ++i) {
n_total += x[i].size();
}
n_total += n;
NumericVector out(n_total);
int k = 0;
for (int i = 0; i < n; ++i) {
NumericVector xi = x[i];
int ni = xi.size();
for (int j = 0; j < ni; ++j, ++k) {
out[k] = xi[j];
}
out[k++] = NA_REAL;
}
return out;
}
END_TEST
START_TEST ( test_Constraint_parent_add )
{
Constraint *ct = new Constraint(2, 4);
Model *m = new Model(2, 4);
ct->setMath(SBML_parseFormula("a-k"));
m->addConstraint(ct);
delete ct;
ListOf *lo = m->getListOfConstraints();
fail_unless(lo == m->getConstraint(0)->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_CompartmentType_parent_add )
{
CompartmentType *ct = new CompartmentType(2, 4);
Model *m = new Model(2, 4);
ct->setId("ct");
m->addCompartmentType(ct);
delete ct;
ListOf *lo = m->getListOfCompartmentTypes();
fail_unless(lo == m->getCompartmentType(0)->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_Reaction_parent_add )
{
Reaction *ia = new Reaction(2, 4);
Model *m = new Model(2, 4);
ia->setId("k");
m->addReaction(ia);
delete ia;
ListOf *lo = m->getListOfReactions();
fail_unless(lo == m->getReaction(0)->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_SpeciesReference_Reactant_parent_add )
{
SpeciesReference *sr = new SpeciesReference(2, 4);
Reaction *r = new Reaction(2, 4);
sr->setSpecies("s");
r->addReactant(sr);
delete sr;
ListOf *lo = r->getListOfReactants();
fail_unless(lo == r->getReactant(0)->getParentSBMLObject());
fail_unless(r == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_SpeciesReference_Modifier_parent_add )
{
ModifierSpeciesReference *sr = new ModifierSpeciesReference(2, 4);
sr->setSpecies("s");
Reaction *r = new Reaction(2, 4);
r->addModifier(sr);
delete sr;
ListOf *lo = r->getListOfModifiers();
fail_unless(lo == r->getModifier(0)->getParentSBMLObject());
fail_unless(r == lo->getParentSBMLObject());
}
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;
}
END_TEST
START_TEST ( test_SpeciesType_parent_add )
{
SpeciesType *ia = new SpeciesType(2, 4);
ia->setId("s");
Model *m = new Model(2, 4);
m->addSpeciesType(ia);
delete ia;
ListOf *lo = m->getListOfSpeciesTypes();
fail_unless(lo == m->getSpeciesType(0)->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_Parameter_parent_add )
{
Parameter *ia = new Parameter(2, 4);
Model *m = new Model(2, 4);
ia->setId("p");
m->addParameter(ia);
delete ia;
ListOf *lo = m->getListOfParameters();
fail_unless(lo == m->getParameter(0)->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_InitialAssignment_parent_add )
{
InitialAssignment *ia = new InitialAssignment(2, 4);
Model *m = new Model(2, 4);
ia->setSymbol("c");
ia->setMath(SBML_parseFormula("9"));
m->addInitialAssignment(ia);
delete ia;
ListOf *lo = m->getListOfInitialAssignments();
fail_unless(lo == m->getInitialAssignment(0)->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_FunctionDefinition_parent_add )
{
FunctionDefinition *fd = new FunctionDefinition(2, 4);
Model *m = new Model(2, 4);
fd->setId("fd");
fd->setMath(SBML_parseFormula("l"));
m->addFunctionDefinition(fd);
delete fd;
ListOf *lo = m->getListOfFunctionDefinitions();
fail_unless(lo == m->getFunctionDefinition(0)->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_UnitDefinition_parent_add )
{
UnitDefinition *ia = new UnitDefinition(2, 4);
Model *m = new Model(2, 4);
ia->setId("u");
ia->createUnit();
m->addUnitDefinition(ia);
delete ia;
ListOf *lo = m->getListOfUnitDefinitions();
fail_unless(lo == m->getUnitDefinition(0)->getParentSBMLObject());
fail_unless(m == lo->getParentSBMLObject());
}
END_TEST
START_TEST ( test_EventAssignment_parent_add )
{
Event *e = new Event(2, 4);
EventAssignment *ea = new EventAssignment(2, 4);
ea->setVariable("c");
ea->setMath(SBML_parseFormula("K+L"));
e->addEventAssignment(ea);
delete ea;
ListOf *lo = e->getListOfEventAssignments();
fail_unless(lo == e->getEventAssignment(0)->getParentSBMLObject());
fail_unless(e == lo->getParentSBMLObject());
}