void myInitialAssignment_initTargetSpeciesReference(
myInitialAssignment *assign,
myReaction **reactions, unsigned int num_of_reactions) {
unsigned int i, j;
InitialAssignment_t *origin;
myReaction *re;
mySpeciesReference *product, *reactant;
const char *origin_symbol;
origin = myInitialAssignment_getOrigin(assign);
origin_symbol = InitialAssignment_getSymbol(origin);
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_symbol, SpeciesReference_getId(product->origin)) == 0) {
myInitialAssignment_setTargetSpeciesReference(assign, product);
return;
}
}
for (j = 0; j < re->num_of_reactants; j++) {
reactant = re->reactants[j];
if (SpeciesReference_isSetId(reactant->origin)
&& strcmp(origin_symbol, SpeciesReference_getId(reactant->origin)) == 0) {
myInitialAssignment_setTargetSpeciesReference(assign, reactant);
return;
}
}
}
}
END_TEST
START_TEST (test_SpeciesReference_setId)
{
const char *species = "X0";
SpeciesReference_setId(SR, species);
fail_unless( !strcmp(SpeciesReference_getId(SR), species) );
fail_unless( SpeciesReference_isSetId(SR) );
if (SpeciesReference_getId(SR) == species)
{
fail("SpeciesReference_setId(...) did not make a copy of string.");
}
/* Reflexive case (pathological) */
SpeciesReference_setId(SR, SpeciesReference_getId(SR));
fail_unless( !strcmp(SpeciesReference_getId(SR), species) );
SpeciesReference_setId(SR, NULL);
fail_unless( !SpeciesReference_isSetId(SR) );
if (SpeciesReference_getId(SR) != NULL)
{
fail("SpeciesReference_setId(SR, NULL) did not clear string.");
}
}
END_TEST
START_TEST (test_Reaction_addProductBySpecies)
{
Species_t *s = Species_create(2, 4);
Species_setId(s, "s");
Reaction_addProductBySpecies(R, s, 2.0, "sr", 0);
fail_unless( Reaction_getNumReactants(R) == 0 );
fail_unless( Reaction_getNumProducts (R) == 1 );
fail_unless( Reaction_getNumModifiers(R) == 0 );
SpeciesReference_t *sr = Reaction_getProduct(R, 0);
fail_unless(!strcmp(SpeciesReference_getSpecies(sr), "s"));
fail_unless(util_isEqual(SpeciesReference_getStoichiometry(sr), 2.0) == 1);
fail_unless(!strcmp(SpeciesReference_getId(sr), "sr"));
fail_unless(SpeciesReference_getConstant(sr) == 0);
fail_unless(Reaction_addProductBySpecies(R, s, 1.0, "sr", 0) == LIBSBML_DUPLICATE_OBJECT_ID);
fail_unless( Reaction_getNumProducts (R) == 1 );
Species_free(s);
}
END_TEST
START_TEST (test_L3_SpeciesReference_id)
{
const char *id = "mitochondria";
fail_unless( !SpeciesReference_isSetId(SR) );
SpeciesReference_setId(SR, id);
fail_unless( !strcmp(SpeciesReference_getId(SR), id) );
fail_unless( SpeciesReference_isSetId(SR) );
if (SpeciesReference_getId(SR) == id)
{
fail("SpeciesReference_setId(...) did not make a copy of string.");
}
}
END_TEST
START_TEST (test_SpeciesReference_setId4)
{
int i = SpeciesReference_setId(sr, "cell");
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( SpeciesReference_isSetId(sr) );
fail_unless( !strcmp(SpeciesReference_getId(sr), "cell" ));
i = SpeciesReference_setId(sr, NULL);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !SpeciesReference_isSetId(sr) );
}
END_TEST
START_TEST (test_L3_SpeciesReference_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
SpeciesReference_t *sr =
SpeciesReference_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) sr) == SBML_SPECIES_REFERENCE );
fail_unless( SBase_getMetaId ((SBase_t *) sr) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) sr) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) sr) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) sr) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) sr) == 1 );
fail_unless( SpeciesReference_getNamespaces (sr) != NULL );
fail_unless( XMLNamespaces_getLength(SpeciesReference_getNamespaces(sr)) == 2 );
fail_unless( SpeciesReference_getId (sr) == NULL );
fail_unless( SpeciesReference_getName (sr) == NULL );
fail_unless( SpeciesReference_getSpecies (sr) == NULL );
fail_unless( util_isNaN(SpeciesReference_getStoichiometry (sr)) );
fail_unless( SpeciesReference_getConstant(sr) == 0 );
fail_unless( !SpeciesReference_isSetId (sr) );
fail_unless( !SpeciesReference_isSetName (sr) );
fail_unless( !SpeciesReference_isSetSpecies (sr) );
fail_unless( !SpeciesReference_isSetStoichiometry (sr) );
fail_unless( !SpeciesReference_isSetConstant(sr) );
SpeciesReference_free(sr);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
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);
}
END_TEST
START_TEST (test_Reaction_addModifierBySpecies)
{
Species_t *s = Species_create(2, 4);
Species_setId(s, "s");
Reaction_addModifierBySpecies(R, s, "sr");
fail_unless( Reaction_getNumReactants(R) == 0 );
fail_unless( Reaction_getNumProducts (R) == 0 );
fail_unless( Reaction_getNumModifiers(R) == 1 );
SpeciesReference_t *sr = Reaction_getModifier(R, 0);
fail_unless(!strcmp(SpeciesReference_getSpecies(sr), "s"));
fail_unless(!strcmp(SpeciesReference_getId(sr), "sr"));
fail_unless(Reaction_addModifierBySpecies(R, s, "sr") == LIBSBML_DUPLICATE_OBJECT_ID);
fail_unless( Reaction_getNumModifiers (R) == 1 );
Species_free(s);
}
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;
}
}
}
}
