END_TEST
START_TEST (test_AssignmentRule_setVariable)
{
const char *variable = "x";
Rule_setVariable(AR, variable);
fail_unless( !strcmp(Rule_getVariable(AR), variable) );
fail_unless( Rule_isSetVariable(AR) );
if (Rule_getVariable(AR) == variable)
{
fail("Rule_setVariable(...) did not make a copy of string.");
}
/* Reflexive case (pathological) */
Rule_setVariable(AR, Rule_getVariable(AR));
fail_unless( !strcmp(Rule_getVariable(AR), variable) );
Rule_setVariable(AR, NULL);
fail_unless( !Rule_isSetVariable(AR) );
if (Rule_getVariable(AR) != NULL)
{
fail("Rule_setVariable(AR, NULL) did not clear string.");
}
}
END_TEST
START_TEST (test_ParameterRule_setName)
{
const char *name = "cell";
const char *c;
Rule_setVariable(PR, name);
fail_unless( !strcmp(Rule_getVariable(PR), name));
fail_unless( Rule_isSetVariable(PR) );
if (Rule_getVariable(PR) == name)
{
fail( "ParameterRule_setName(...) did not make a copy of string." );
}
/* Reflexive case (pathological) */
c = Rule_getVariable(PR);
Rule_setVariable(PR, c);
fail_unless( !strcmp(Rule_getVariable(PR), name),
NULL );
Rule_setVariable(PR, NULL);
fail_unless( !Rule_isSetVariable(PR) );
if (Rule_getVariable(PR) != NULL)
{
fail( "Rule_setVariable(PR, NULL)"
" did not clear string." );
}
}
END_TEST
START_TEST (test_AssignmentRule_createWithFormula)
{
const ASTNode_t *math;
char *formula;
Rule_t *ar = Rule_createAssignment(2, 4);
Rule_setVariable(ar, "s");
Rule_setFormula(ar, "1 + 1");
fail_unless( SBase_getTypeCode ((SBase_t *) ar) == SBML_ASSIGNMENT_RULE );
fail_unless( SBase_getMetaId ((SBase_t *) ar) == NULL );
fail_unless( !strcmp(Rule_getVariable(ar), "s") );
math = Rule_getMath((Rule_t *) ar);
fail_unless(math != NULL);
formula = SBML_formulaToString(math);
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "1 + 1") );
fail_unless( !strcmp(Rule_getFormula((Rule_t *) ar), formula) );
Rule_free(ar);
safe_free(formula);
}
END_TEST
START_TEST (test_SpeciesConcentrationRule_setSpecies)
{
const char *species = "s2";
const char *s;
Rule_setVariable(SCR, species);
fail_unless( !strcmp(Rule_getVariable(SCR), species),
NULL );
fail_unless( Rule_isSetVariable(SCR) );
if (Rule_getVariable(SCR) == species)
{
fail( "SpeciesConcentrationRule_setSpecies(...)"
" did not make a copy of string." );
}
/* Reflexive case (pathological) */
s = Rule_getVariable(SCR);
Rule_setVariable(SCR, s);
fail_unless( !strcmp(Rule_getVariable(SCR), species),
NULL );
Rule_setVariable(SCR, NULL);
fail_unless( !Rule_isSetVariable(SCR) );
if (Rule_getVariable(SCR) != NULL)
{
fail( "SpeciesConcentrationRule_setSpecies(SCR, NULL)"
" did not clear string." );
}
}
END_TEST
START_TEST (test_CompartmentVolumeRule_setCompartment)
{
const char *c;
const char *compartment = "cell";
Rule_setVariable(CVR, compartment);
fail_unless( !strcmp(Rule_getVariable(CVR), compartment),
NULL );
fail_unless( Rule_isSetVariable(CVR) );
if (Rule_getVariable(CVR) == compartment)
{
fail( "Rule_setVariable(...)"
" did not make a copy of string." );
}
/* Reflexive case (pathological) */
c = Rule_getVariable(CVR);
Rule_setVariable(CVR, c);
fail_unless( !strcmp(Rule_getVariable(CVR), compartment),
NULL );
Rule_setVariable(CVR, NULL);
fail_unless( !Rule_isSetVariable(CVR) );
if (Rule_getVariable(CVR) != NULL)
{
fail( "Rule_setVariable(CVR, NULL)"
" did not clear string." );
}
}
END_TEST
START_TEST (test_AssignmentRule_createWithMath)
{
ASTNode_t *math = SBML_parseFormula("1 + 1");
Rule_t *ar = Rule_createAssignment(2, 4);
Rule_setVariable(ar, "s");
Rule_setMath(ar, math);
fail_unless( SBase_getTypeCode ((SBase_t *) ar) == SBML_ASSIGNMENT_RULE );
fail_unless( SBase_getMetaId ((SBase_t *) ar) == NULL );
fail_unless( !strcmp(Rule_getVariable(ar), "s") );
fail_unless( !strcmp(Rule_getFormula((Rule_t *) ar), "1 + 1") );
fail_unless( Rule_getMath((Rule_t *) ar) != math );
Rule_free(ar);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_stoichiometryMath)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
Model_t *m = SBMLDocument_createModel(d);
Compartment_t *c = Model_createCompartment(m);
Compartment_setId ( c, "c" );
Species_t *s = Model_createSpecies(m);
Species_setId(s, "s");
Species_setCompartment(s, "c");
Reaction_t * r = Model_createReaction(m);
SpeciesReference_t *sr = Reaction_createReactant(r);
SpeciesReference_setSpecies(sr, "s");
StoichiometryMath_t *sm = SpeciesReference_createStoichiometryMath(sr);
ASTNode_t * ast = SBML_parseFormula("c*2");
StoichiometryMath_setMath(sm, ast);
fail_unless(Model_getNumRules(m) == 0);
fail_unless(SpeciesReference_isSetId(sr) == 0);
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1);
m = SBMLDocument_getModel(d);
r = Model_getReaction(m, 0);
sr = Reaction_getReactant(r, 0);
fail_unless(Model_getNumRules(m) == 1);
fail_unless(SpeciesReference_isSetId(sr) == 1);
Rule_t *rule = Model_getRule(m, 0);
fail_unless( strcmp(SpeciesReference_getId(sr), Rule_getVariable(rule)) == 0 );
SBMLDocument_free(d);
}
void myRule_initTarget(
myRule *rule,
mySpecies **species, unsigned int num_of_species,
myParameter **parameters, unsigned int num_of_parameters,
myCompartment **compartments, unsigned int num_of_compartments,
myReaction **reactions, unsigned int num_of_reactions) {
unsigned int i, j;
Rule_t *origin;
const char *origin_var;
mySpecies *sp;
myParameter *param;
myCompartment *comp;
myReaction *re;
mySpeciesReference *product, *reactant;
origin = myRule_getOrigin(rule);
origin_var = Rule_getVariable(origin);
for (i = 0; i < num_of_species; i++) {
sp = species[i];
if (strcmp(origin_var, Species_getId(sp->origin)) == 0) {
myRule_setTargetSpecies(rule, sp);
mySpecies_setDependingRule(sp, rule);
return;
}
}
for (i = 0; i < num_of_parameters; i++) {
param = parameters[i];
if (strcmp(origin_var, Parameter_getId(param->origin)) == 0) {
myRule_setTargetParameter(rule, param);
myParameter_setDependingRule(param, rule);
return;
}
}
for (i = 0; i < num_of_compartments; i++) {
comp = compartments[i];
if (strcmp(origin_var, Compartment_getId(comp->origin)) == 0) {
myRule_setTargetCompartment(rule, comp);
myCompartment_setDependingRule(comp, rule);
return;
}
}
for (i=0; i < num_of_reactions; i++) {
re = reactions[i];
for (j = 0; j < re->num_of_products; j++) {
product = re->products[j];
if (SpeciesReference_isSetId(product->origin)
&& strcmp(origin_var, SpeciesReference_getId(product->origin)) == 0) {
myRule_setTargetSpeciesReference(rule, product);
mySpeciesReference_setDependingRule(product, rule);
return;
}
}
for (j = 0; j < re->num_of_reactants; j++) {
reactant = re->reactants[j];
if (SpeciesReference_isSetId(reactant->origin)
&& strcmp(origin_var, SpeciesReference_getId(reactant->origin)) == 0) {
myRule_setTargetSpeciesReference(rule, reactant);
mySpeciesReference_setDependingRule(reactant, rule);
return;
}
}
}
}