END_TEST
START_TEST (test_Compartment_setName)
{
const char *name = "My_Favorite_Factory";
Compartment_setName(C, name);
fail_unless( !strcmp(Compartment_getName(C), name) );
fail_unless( Compartment_isSetName(C) );
if (Compartment_getName(C) == name)
{
fail("Compartment_setName(...) did not make a copy of string.");
}
/* Reflexive case (pathological) */
Compartment_setName(C, Compartment_getName(C));
fail_unless( !strcmp(Compartment_getName(C), name) );
Compartment_setName(C, NULL);
fail_unless( !Compartment_isSetName(C) );
if (Compartment_getName(C) != NULL)
{
fail("Compartment_setName(C, NULL) did not clear string.");
}
}
END_TEST
START_TEST (test_L3_Compartment_name)
{
const char *name = "My_Favorite_Factory";
fail_unless( !Compartment_isSetName(C) );
Compartment_setName(C, name);
fail_unless( !strcmp(Compartment_getName(C), name) );
fail_unless( Compartment_isSetName(C) );
if (Compartment_getName(C) == name)
{
fail("Compartment_setName(...) did not make a copy of string.");
}
Compartment_unsetName(C);
fail_unless( !Compartment_isSetName(C) );
if (Compartment_getName(C) != NULL)
{
fail("Compartment_unsetName(C) did not clear string.");
}
}
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_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");
}
}
static int printXMGLegend(cvodeData_t *data, int nvalues)
{
int i, found;
odeModel_t *om = data->model;
Model_t *m = om->simple;
Species_t *s;
Parameter_t *p;
Compartment_t *c;
for ( i=0; i<nvalues; i++ ) {
found = 0;
if ( (s = Model_getSpeciesById(m, om->names[i])) != NULL ) {
if ( Species_isSetName(s) ) {
GracePrintf("g0.s%d legend \"%s: %s\"\n", i+1,
om->names[i], Species_getName(s));
found++;
}
}
else if ( (c = Model_getCompartmentById(m, om->names[i])) ) {
if ( Compartment_isSetName(c) ) {
GracePrintf("g0.s%d legend \"%s: %s\"\n", i+1,
om->names[i], Compartment_getName(c));
found++;
}
}
else if ( (p = Model_getParameterById(m, om->names[i])) ) {
if ( Parameter_isSetName(p) ) {
GracePrintf("g0.s%d legend \"%s: %s\"\n", i+1,
om->names[i], Parameter_getName(p));
found++;
}
}
if ( found == 0 )
GracePrintf("g0.s%d legend \"%s\"\n", i+1, om->names[i]);
}
GracePrintf("legend 1.155, 0.85");
GracePrintf("legend font 8");
GracePrintf("legend char size 0.6");
return 0;
}
void print_result_list(Model_t *m, mySpecies *mySp[], myParameter *myParam[], myCompartment *myComp[]){
FILE *fp = NULL;
unsigned int i;
int column = 2;
if ((fp = my_fopen(fp, "./simulation_results/result_list.dat", "w")) == NULL) {
return;
}
TRACE(("Result : Species List\n"));
fprintf(fp, "Result : Species List\n");
for(i=0; i<Model_getNumSpecies(m); i++){
/* if(!(Species_getConstant(mySp[i]->origin) && Species_getBoundaryCondition(mySp[i]->origin))){ //XXX must remove this */
fprintf(fp, "column %d : ID=%s Name=%s\n", column, Species_getId(mySp[i]->origin), Species_getName(mySp[i]->origin));
column++;
/* } */
}
TRACE(("\n"));
fprintf(fp, "\n");
fprintf(fp, "Result : Parameter List\n");
column = 2;
for(i=0; i<Model_getNumParameters(m); i++){
/* if(!Parameter_getConstant(myParam[i]->origin)){ //XXX must remove this */
TRACE(("column %d : ID=%s Name=%s\n", column, Parameter_getId(myParam[i]->origin), Parameter_getName(myParam[i]->origin)));
fprintf(fp, "column %d : ID=%s Name=%s\n", column, Parameter_getId(myParam[i]->origin), Parameter_getName(myParam[i]->origin));
column++;
/* } */
}
TRACE(("Result : Compartment List\n"));
fprintf(fp, "Result : Compartment List\n");
column = 2;
for(i=0; i<Model_getNumCompartments(m); i++){
/* if(!Compartment_getConstant(myComp[i]->origin)){ //XXX must remove this */
TRACE(("column %d : ID=%s Name=%s\n", column, Compartment_getId(myComp[i]->origin), Compartment_getName(myComp[i]->origin)));
fprintf(fp, "column %d : ID=%s Name=%s\n", column, Compartment_getId(myComp[i]->origin), Compartment_getName(myComp[i]->origin));
column++;
/* } */
}
fclose(fp);
}
