END_TEST
START_TEST (test_Compartment_initDefaults)
{
Compartment_t *c = Compartment_create(2, 4);
Compartment_setId(c, "A");
Compartment_initDefaults(c);
fail_unless( !strcmp(Compartment_getId (c), "A"));
fail_unless( Compartment_getName (c) == NULL );
fail_unless( Compartment_getUnits (c) == NULL );
fail_unless( Compartment_getOutside(c) == NULL );
fail_unless( Compartment_getSpatialDimensions(c) == 3 );
fail_unless( Compartment_getVolume (c) == 1.0 );
fail_unless( Compartment_getConstant (c) == 1 );
fail_unless( Compartment_isSetId (c) );
fail_unless( !Compartment_isSetName (c) );
fail_unless( !Compartment_isSetSize (c) );
fail_unless( !Compartment_isSetVolume (c) );
fail_unless( !Compartment_isSetUnits (c) );
fail_unless( !Compartment_isSetOutside(c) );
fail_unless( Compartment_isSetSpatialDimensions(c) );
fail_unless( Compartment_isSetConstant(c) );
Compartment_free(c);
}
END_TEST
START_TEST (test_Compartment_getSpatialDimensions)
{
fail_unless( Compartment_isSetSpatialDimensions(C) );
fail_unless( Compartment_getSpatialDimensions(C) == 3);
Compartment_setSpatialDimensions(C, 1);
fail_unless( Compartment_getSpatialDimensions(C) == 1);
fail_unless( Compartment_isSetSpatialDimensions(C) );
fail_unless( Compartment_unsetSpatialDimensions(C) == LIBSBML_UNEXPECTED_ATTRIBUTE);
fail_unless( Compartment_getSpatialDimensions(C) == 3);
fail_unless( Compartment_isSetSpatialDimensions(C) );
}
END_TEST
START_TEST (test_Compartment_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(2,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Compartment_t *c =
Compartment_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) c) == SBML_COMPARTMENT );
fail_unless( SBase_getMetaId ((SBase_t *) c) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) c) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) c) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) c) == 2 );
fail_unless( SBase_getVersion ((SBase_t *) c) == 1 );
fail_unless( Compartment_getNamespaces (c) != NULL );
fail_unless( XMLNamespaces_getLength(Compartment_getNamespaces(c)) == 2 );
fail_unless( Compartment_getName(c) == NULL );
fail_unless( Compartment_getSpatialDimensions(c) == 3 );
fail_unless( Compartment_getConstant(c) == 1 );
Compartment_free(c);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
END_TEST
START_TEST (test_Compartment_createWith)
{
Compartment_t *c = Compartment_create(2, 4);
Compartment_setId(c, "A");
fail_unless( SBase_getTypeCode ((SBase_t *) c) == SBML_COMPARTMENT );
fail_unless( SBase_getMetaId ((SBase_t *) c) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) c) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) c) == NULL );
fail_unless( Compartment_getName(c) == NULL );
fail_unless( Compartment_getSpatialDimensions(c) == 3 );
fail_unless( !strcmp( Compartment_getId (c), "A" ) );
fail_unless( Compartment_getConstant(c) == 1 );
fail_unless( Compartment_isSetId (c) );
fail_unless( !Compartment_isSetName (c) );
Compartment_free(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_Compartment_getSpatialDimensions)
{
Compartment_setSpatialDimensions(C, 1);
fail_unless( Compartment_getSpatialDimensions(C) == 1);
}
END_TEST
START_TEST (test_Compartment_setSpatialDimensions1)
{
int i = Compartment_setSpatialDimensions(C, 2);
fail_unless( i == LIBSBML_UNEXPECTED_ATTRIBUTE );
fail_unless( Compartment_getSpatialDimensions(C) == 3 );
}
END_TEST
START_TEST (test_Compartment_setSpatialDimensions5)
{
Compartment_t *c =
Compartment_create(2, 2);
int i = Compartment_setSpatialDimensionsAsDouble(c, 2.2);
fail_unless( i == LIBSBML_INVALID_ATTRIBUTE_VALUE );
fail_unless( Compartment_getSpatialDimensions(c) == 3 );
Compartment_free(c);
}
END_TEST
START_TEST (test_Compartment_setSpatialDimensions4)
{
Compartment_t *c =
Compartment_create(2, 2);
int i = Compartment_setSpatialDimensionsAsDouble(c, 2.0);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Compartment_getSpatialDimensions(c) == 2 );
Compartment_free(c);
}
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;
}