END_TEST
START_TEST (test_L3_Species_initDefaults)
{
Species_t *s = Species_create(3,1);
fail_unless( Species_getId (s) == NULL );
fail_unless( Species_getName (s) == NULL );
fail_unless( Species_getCompartment (s) == NULL );
fail_unless( util_isNaN(Species_getInitialAmount (s)) );
fail_unless( util_isNaN(Species_getInitialConcentration (s)) );
fail_unless( Species_getSubstanceUnits (s) == NULL );
fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 );
fail_unless( Species_getBoundaryCondition(s) == 0 );
fail_unless( Species_getConstant(s) == 0 );
fail_unless( Species_getConversionFactor (s) == NULL );
fail_unless( !Species_isSetId (s) );
fail_unless( !Species_isSetName (s) );
fail_unless( !Species_isSetCompartment (s) );
fail_unless( !Species_isSetInitialAmount (s) );
fail_unless( !Species_isSetInitialConcentration (s) );
fail_unless( !Species_isSetSubstanceUnits (s) );
fail_unless( !Species_isSetHasOnlySubstanceUnits(s) );
fail_unless( !Species_isSetBoundaryCondition(s) );
fail_unless( !Species_isSetConstant(s) );
fail_unless( !Species_isSetConversionFactor (s) );
Species_initDefaults(s);
fail_unless( Species_getId (s) == NULL );
fail_unless( Species_getName (s) == NULL );
fail_unless( Species_getCompartment (s) == NULL );
fail_unless( util_isNaN(Species_getInitialAmount (s)) );
fail_unless( util_isNaN(Species_getInitialConcentration (s)) );
fail_unless( !strcmp(Species_getSubstanceUnits (s),"mole" ));
fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 );
fail_unless( Species_getBoundaryCondition(s) == 0 );
fail_unless( Species_getConstant(s) == 0 );
fail_unless( Species_getConversionFactor (s) == NULL );
fail_unless( !Species_isSetId (s) );
fail_unless( !Species_isSetName (s) );
fail_unless( !Species_isSetCompartment (s) );
fail_unless( !Species_isSetInitialAmount (s) );
fail_unless( !Species_isSetInitialConcentration (s) );
fail_unless( Species_isSetSubstanceUnits (s) );
fail_unless( Species_isSetHasOnlySubstanceUnits(s) );
fail_unless( Species_isSetBoundaryCondition(s) );
fail_unless( Species_isSetConstant(s) );
fail_unless( !Species_isSetConversionFactor (s) );
Species_free(s);
}
END_TEST
START_TEST (test_Species_setInitialConcentration)
{
fail_unless( !Species_isSetInitialAmount (S) );
fail_unless( !Species_isSetInitialConcentration(S) );
Species_setInitialConcentration(S, 3.4);
fail_unless( !Species_isSetInitialAmount (S) );
fail_unless( Species_isSetInitialConcentration(S) );
fail_unless( Species_getInitialConcentration(S) == 3.4 );
}
END_TEST
START_TEST (test_Species_setInitialAmount1)
{
int i = Species_setInitialAmount(C, 2.0);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getInitialAmount(C) == 2.0 );
fail_unless( Species_isSetInitialAmount(C));
i = Species_unsetInitialAmount(C);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Species_isSetInitialAmount(C));
}
void printSpecies(Model_t *m, FILE *f)
{
int i, j;
Species_t *s;
Compartment_t *c;
fprintf(f, "\n");
fprintf(f, "# Initial Conditions for Species and Compartments:\n");
for ( i=0; i<Model_getNumCompartments(m); i++ ) {
if ( i== 0 ) fprintf(f, "# Compartments:\n");
c = Model_getCompartment(m,i);
if(Compartment_isSetId(c))
fprintf(f, "%s ", Compartment_getId(c));
if(Compartment_isSetName(c))
fprintf(f, "(%s) ", Compartment_getName(c));
if ( Compartment_isSetVolume(c) )
fprintf(f, "= %g; ", Compartment_getSize(c));
fprintf(f, "%s", Compartment_getConstant(c) ? "" : "variable; ");
if(Compartment_isSetOutside(c))
fprintf(f, "outside %s; ", Compartment_getOutside(c));
/* fprintf(f, "\n"); */
fprintf(f, "dimensions %d; ", Compartment_getSpatialDimensions(c));
if(Compartment_isSetUnits(c))
fprintf(f, "[%s]; ", Compartment_getUnits(c));
fprintf(f, "\n");
fprintf(f, "# Species concentrations in `compartment' %s\n",
Compartment_getId(c));
for(j=0;j<Model_getNumSpecies(m);j++){
s = Model_getSpecies(m,j);
if(strcmp(Species_getCompartment(s), Compartment_getId(c))==0){
fprintf(f, "%s ", Species_getId(s));
if(Species_isSetName(s))
fprintf(f, "(%s) ", Species_getName(s));
if ( Species_isSetInitialAmount(s) )
fprintf(f, "= %g/%g; ",
Species_getInitialAmount(s),
Compartment_getSize(c));
else if ( Species_isSetInitialConcentration(s) )
fprintf(f, "= %g; ", Species_getInitialConcentration(s));
else
fprintf(f, "# no initial value;");
fprintf(f, "%s", Species_getBoundaryCondition(s) ? "boundary;" : "");
fprintf(f, "%s", Species_getConstant(s) ? "constant;" : "");
if(Species_isSetCharge(s))
fprintf(f, "charge = %d; ", Species_getCharge(s));
fprintf(f, "\n");
}
}
fprintf(f, "\n");
}
}
END_TEST
START_TEST (test_L3_Species_initialAmount)
{
double initialAmount = 0.2;
fail_unless( !Species_isSetInitialAmount(S));
fail_unless( util_isNaN(Species_getInitialAmount(S)));
Species_setInitialAmount(S, initialAmount);
fail_unless( Species_getInitialAmount(S) == initialAmount );
fail_unless( Species_isSetInitialAmount(S) );
Species_unsetInitialAmount(S);
fail_unless( !Species_isSetInitialAmount(S) );
fail_unless( util_isNaN(Species_getInitialAmount(S)));
}
END_TEST
START_TEST (test_Species_setInitialAmount2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setInitialAmount(c, 4);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getInitialAmount(c) == 4.0 );
fail_unless( Species_isSetInitialAmount(c));
i = Species_unsetInitialAmount(c);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Species_isSetInitialAmount(c));
Species_free(c);
}
END_TEST
START_TEST (test_L3_Species_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);
Species_t *s =
Species_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) s) == SBML_SPECIES );
fail_unless( SBase_getMetaId ((SBase_t *) s) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) s) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) s) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) s) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) s) == 1 );
fail_unless( Species_getNamespaces (s) != NULL );
fail_unless( XMLNamespaces_getLength(Species_getNamespaces(s)) == 2 );
fail_unless( Species_getId (s) == NULL );
fail_unless( Species_getName (s) == NULL );
fail_unless( Species_getCompartment (s) == NULL );
fail_unless( util_isNaN(Species_getInitialAmount (s)) );
fail_unless( util_isNaN(Species_getInitialConcentration (s)) );
fail_unless( Species_getSubstanceUnits (s) == NULL );
fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 );
fail_unless( Species_getBoundaryCondition(s) == 0 );
fail_unless( Species_getConstant(s) == 0 );
fail_unless( Species_getConversionFactor (s) == NULL );
fail_unless( !Species_isSetId (s) );
fail_unless( !Species_isSetName (s) );
fail_unless( !Species_isSetCompartment (s) );
fail_unless( !Species_isSetInitialAmount (s) );
fail_unless( !Species_isSetInitialConcentration (s) );
fail_unless( !Species_isSetSubstanceUnits (s) );
fail_unless( !Species_isSetHasOnlySubstanceUnits(s) );
fail_unless( !Species_isSetBoundaryCondition(s) );
fail_unless( !Species_isSetConstant(s) );
fail_unless( !Species_isSetConversionFactor (s) );
Species_free(s);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
/*
setValues: the user can enter a species name and
change its initial condition (amount or concentration)
*/
static void setValues(Model_t *m) {
char *species;
char *newIA;
char *newIC;
Species_t *s;
printf("Please enter the id of the species to change: ");
species = get_line(stdin);
species = util_trim(species);
if ( (s = Model_getSpeciesById(m,species) ) ) {
printf("\n");
printf("Id: %s\n", Species_getId(s));
if ( Species_isSetName(s) ) {
printf("Name: %s\n", Species_getName(s));
}
if ( Species_isSetInitialAmount(s) ) {
printf("Initial Amount: %g", Species_getInitialAmount(s));
}
else if (Species_isSetInitialConcentration(s) ) {
printf("Initial Concentration: %g", Species_getInitialConcentration(s));
}
if ( Species_getHasOnlySubstanceUnits(s) ) {
if ( Species_isSetSubstanceUnits(s) ) {
printf("%s ", Species_getSubstanceUnits(s));
}
} else {
if ( Species_isSetSubstanceUnits(s) ) {
printf("%s ", Species_getSubstanceUnits(s));
}
if ( Species_isSetSpatialSizeUnits(s) ) {
printf("%s%s", "/", Species_getSpatialSizeUnits(s));
}
}
if ( Species_getHasOnlySubstanceUnits(s) ) {
printf(" (has only substance units)");
}
printf("\n");
if ( Species_isSetCharge(s) ) {
printf("Charge: %-10d", Species_getCharge(s));
}
printf("\n");
printf("%s ", Species_getBoundaryCondition(s) ?
"Species is a Boundary\n" : "\n");
printf("%s ", Species_getConstant(s) ?
"Species is set constant" : "\n");
printf("\n");
if ( Species_isSetInitialAmount(s) ) {
printf("Please enter new initial Amount: ");
newIA = get_line(stdin);
newIA = util_trim(newIA);
Species_setInitialAmount(s, (float) atof(newIA));
}
else if ( Species_isSetInitialConcentration(s) ) {
printf("Please enter new initial Concentration: ");
newIC = get_line(stdin);
newIC = util_trim(newIC);
Species_setInitialConcentration(s, (float) atof(newIC));
}
}
else {
printf("%s not found.\n", species);
}
}