END_TEST
START_TEST (test_Species_getsetHasOnlySubstanceUnits)
{
// defaults
fail_unless( Species_getHasOnlySubstanceUnits(S) == 0);
fail_unless( Species_isSetHasOnlySubstanceUnits(S) == 1);
Species_setHasOnlySubstanceUnits(S, 1);
fail_unless( Species_getHasOnlySubstanceUnits(S) == 1);
fail_unless( Species_isSetHasOnlySubstanceUnits(S) == 1);
int ret = Species_unsetHasOnlySubstanceUnits(S);
fail_unless(ret == LIBSBML_UNEXPECTED_ATTRIBUTE);
fail_unless( Species_getHasOnlySubstanceUnits(S) == 0);
fail_unless( Species_isSetHasOnlySubstanceUnits(S) == 1);
Species_setHasOnlySubstanceUnits(S, 0);
fail_unless( Species_getHasOnlySubstanceUnits(S) == 0);
fail_unless( Species_isSetHasOnlySubstanceUnits(S) == 1);
ret = Species_unsetHasOnlySubstanceUnits(S);
fail_unless(ret == LIBSBML_UNEXPECTED_ATTRIBUTE);
fail_unless( Species_getHasOnlySubstanceUnits(S) == 0);
fail_unless( Species_isSetHasOnlySubstanceUnits(S) == 1);
}
END_TEST
START_TEST (test_L3_Species_hasOnlySubstanceUnits)
{
fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 0);
Species_setHasOnlySubstanceUnits(S, 1);
fail_unless(Species_getHasOnlySubstanceUnits(S) == 1);
fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 1);
int ret = Species_unsetHasOnlySubstanceUnits(S);
fail_unless(ret == LIBSBML_OPERATION_SUCCESS);
fail_unless(Species_getHasOnlySubstanceUnits(S) == 1);
fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 0);
Species_setHasOnlySubstanceUnits(S, 0);
fail_unless(Species_getHasOnlySubstanceUnits(S) == 0);
fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 1);
ret = Species_unsetHasOnlySubstanceUnits(S);
fail_unless(ret == LIBSBML_OPERATION_SUCCESS);
fail_unless(Species_getHasOnlySubstanceUnits(S) == 0);
fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 0);
}
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);
}
void post_ev_alter_tree_structure(Model_t *m, ASTNode_t **node_p, ASTNode_t *parent, int child_order){
ASTNode_t *divide_node, *times_node;
ASTNode_t *compartment_node;
ASTNode_t *node, *next_node;
unsigned int i;
Species_t *sp;
node = *node_p;
for(i=0; i<ASTNode_getNumChildren(node); i++){
next_node = ASTNode_getChild(node, i);
post_ev_alter_tree_structure(m, &next_node, *node_p, i);
}
if(ASTNode_getType(node) == AST_NAME){
for(i=0; i<Model_getNumSpecies(m); i++){
sp = (Species_t*)ListOf_get(Model_getListOfSpecies(m), i);
if(strcmp(Species_getId(sp), ASTNode_getName(node)) == 0){
if(!Species_getHasOnlySubstanceUnits(sp) && Compartment_getSpatialDimensions(Model_getCompartmentById(m, Species_getCompartment(sp))) != 0){/* use val/comp in calculation */
divide_node = ASTNode_createWithType(AST_DIVIDE);
compartment_node = ASTNode_createWithType(AST_NAME);
ASTNode_setName(compartment_node, Compartment_getId(Model_getCompartmentById(m, Species_getCompartment(sp))));
ASTNode_addChild(divide_node, node);
ASTNode_addChild(divide_node, compartment_node);
if(parent != NULL){
ASTNode_replaceChild(parent, child_order, divide_node);
}else{
*node_p = divide_node;
}
node = *node_p;
break;
}else if(Species_getHasOnlySubstanceUnits(sp) && Species_isSetInitialConcentration(sp) && Compartment_getSpatialDimensions(Model_getCompartmentById(m, Species_getCompartment(sp))) != 0){/* use val*comp in calculation */
times_node = ASTNode_createWithType(AST_TIMES);
compartment_node = ASTNode_createWithType(AST_NAME);
ASTNode_setName(compartment_node, Compartment_getId(Model_getCompartmentById(m, Species_getCompartment(sp))));
ASTNode_addChild(times_node, node);
ASTNode_addChild(times_node, compartment_node);
if(parent != NULL){
ASTNode_replaceChild(parent, child_order, times_node);
}else{
*node_p = times_node;
}
node = *node_p;
break;
}
}
}
}
return;
}
END_TEST
START_TEST (test_L3_Species_hasOnlySubstanceUnits)
{
fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 0);
Species_setHasOnlySubstanceUnits(S, 1);
fail_unless(Species_getHasOnlySubstanceUnits(S) == 1);
fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 1);
Species_setHasOnlySubstanceUnits(S, 0);
fail_unless(Species_getHasOnlySubstanceUnits(S) == 0);
fail_unless(Species_isSetHasOnlySubstanceUnits(S) == 1);
}
END_TEST
START_TEST (test_Species_setHasOnlySubstanceUnits1)
{
int i = Species_setHasOnlySubstanceUnits(C, 0);
fail_unless( Species_getHasOnlySubstanceUnits(C) == 0 );
fail_unless( i == LIBSBML_UNEXPECTED_ATTRIBUTE );
}
END_TEST
START_TEST (test_Species_setHasOnlySubstanceUnits2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setHasOnlySubstanceUnits(c, 0);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getHasOnlySubstanceUnits(c) == 0 );
i = Species_setHasOnlySubstanceUnits(c, 1);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getHasOnlySubstanceUnits(c) == 1 );
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);
}
END_TEST
START_TEST (test_SBMLConvertStrict_convertToL1)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
/* create model with metaid */
Model_t * m = SBMLDocument_createModel(d);
SBase_setMetaId((SBase_t *) (m), "_m");
/* create a compartment with sbo*/
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
SBase_setSBOTerm((SBase_t *) (c), 240);
/* create a species with hasOnlySubstanceUnits = true*/
Species_t *s = Model_createSpecies(m);
Species_setId(s, "s");
Species_setCompartment(s, "c");
Species_setHasOnlySubstanceUnits(s, 1);
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 1, 2) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 1, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
///* check that attributes that are no longer valid have been removed */
Model_t * m1 = SBMLDocument_getModel(d);
fail_unless (SBase_getMetaId((SBase_t *) (m1)) == NULL);
Compartment_t *c1 = Model_getCompartment(m1, 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c1)) == -1, NULL );
Species_t *s1 = Model_getSpecies(m1, 0);
fail_unless (Species_getHasOnlySubstanceUnits(s1) == 0);
SBMLDocument_free(d);
}
/*
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);
}
}
