END_TEST
START_TEST (test_Compartment_setId)
{
const char *id = "mitochondria";
Compartment_setId(C, id);
fail_unless( !strcmp(Compartment_getId(C), id) );
fail_unless( Compartment_isSetId(C) );
if (Compartment_getId(C) == id)
{
fail("Compartment_setId(...) did not make a copy of string.");
}
/* Reflexive case (pathological) */
Compartment_setId(C, Compartment_getId(C));
fail_unless( !strcmp(Compartment_getId(C), id) );
Compartment_setId(C, NULL);
fail_unless( !Compartment_isSetId(C) );
if (Compartment_getId(C) != NULL)
{
fail("Compartment_setId(C, NULL) did not clear string.");
}
}
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");
}
}
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;
}
/* create contents of myResult object */
myResult *create_myResult(Model_t *m, mySpecies *mySp[], myParameter *myParam[], myCompartment *myComp[], double sim_time, double dt, int print_interval) {
int i;
myResult *result;
int num_of_species = Model_getNumSpecies(m);
int num_of_parameters = Model_getNumParameters(m);
int num_of_compartments = Model_getNumCompartments(m);
int end_cycle = get_end_cycle(sim_time, dt);
result = (myResult *)malloc(sizeof(myResult));
result->error_code = NoError;
result->error_message = NULL;
result->num_of_columns_sp = num_of_species;
result->num_of_columns_param = num_of_parameters;
result->num_of_columns_comp = num_of_compartments;
result->num_of_rows = end_cycle / print_interval + 1;
result->column_name_time = dupstr("time");
result->column_name_sp = (const char **)malloc(sizeof(char *) * num_of_species);
result->column_name_param = (const char **)malloc(sizeof(char *) * num_of_parameters);
result->column_name_comp = (const char **)malloc(sizeof(char *) * num_of_compartments);
result->values_time = (double *)malloc(sizeof(double) * result->num_of_rows);
result->values_sp = (double *)malloc(sizeof(double) * num_of_species * result->num_of_rows);
result->values_param = (double *)malloc(sizeof(double) * num_of_parameters * result->num_of_rows);
result->values_comp = (double *)malloc(sizeof(double) * num_of_compartments * result->num_of_rows);
for(i=0; i<num_of_species; i++){
result->column_name_sp[i] = dupstr(Species_getId(mySp[i]->origin));
}
for(i=0; i<num_of_parameters; i++){
result->column_name_param[i] = dupstr(Parameter_getId(myParam[i]->origin));
}
for(i=0; i<num_of_compartments; i++){
result->column_name_comp[i] = dupstr(Compartment_getId(myComp[i]->origin));
}
return result;
}
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_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 myInitialAssignment_initTarget(
myInitialAssignment *assign,
mySpecies **species, unsigned int num_of_species,
myParameter **parameters, unsigned int num_of_parameters,
myCompartment **compartments, unsigned int num_of_compartments) {
unsigned int i;
InitialAssignment_t *origin;
const char *origin_symbol;
origin = myInitialAssignment_getOrigin(assign);
origin_symbol = InitialAssignment_getSymbol(origin);
for (i = 0; i < num_of_species; i++) {
if (strcmp(origin_symbol, Species_getId(species[i]->origin)) == 0) {
myInitialAssignment_setTargetSpecies(assign, species[i]);
return;
}
}
for (i = 0; i < num_of_parameters; i++) {
if (strcmp(origin_symbol, Parameter_getId(parameters[i]->origin)) == 0) {
myInitialAssignment_setTargetParameter(assign, parameters[i]);
return;
}
}
for (i = 0; i < num_of_compartments; i++) {
if (strcmp(origin_symbol, Compartment_getId(compartments[i]->origin)) == 0) {
myInitialAssignment_setTargetCompartment(assign, compartments[i]);
return;
}
}
}
END_TEST
START_TEST (test_L3_Compartment_id)
{
const char *id = "mitochondria";
fail_unless( !Compartment_isSetId(C) );
Compartment_setId(C, id);
fail_unless( !strcmp(Compartment_getId(C), id) );
fail_unless( Compartment_isSetId(C) );
if (Compartment_getId(C) == id)
{
fail("Compartment_setId(...) did not make a copy of string.");
}
}
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);
}
END_TEST
START_TEST (test_L3_Compartment_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);
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) == 3 );
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_getId (c) == NULL );
fail_unless( Compartment_getName (c) == NULL );
fail_unless( Compartment_getUnits (c) == NULL );
fail_unless( Compartment_getOutside(c) == NULL );
fail_unless( util_isNaN(Compartment_getSpatialDimensionsAsDouble(c)) );
fail_unless( util_isNaN(Compartment_getVolume(c)));
fail_unless( Compartment_getConstant(c) == 1 );
fail_unless( !Compartment_isSetId (c) );
fail_unless( !Compartment_isSetSpatialDimensions (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_isSetConstant(c) );
Compartment_free(c);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
END_TEST
START_TEST (test_Compartment_setId3)
{
Compartment_t *c =
Compartment_create(2, 2);
int i = Compartment_setId(c, "cell");
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Compartment_isSetId(c) );
fail_unless( !strcmp(Compartment_getId(c), "cell" ));
Compartment_free(c);
}
int
main (int argc, char* argv[])
{
unsigned int i,j,errors;
const char* filename;
SBMLDocument_t* document;
Model_t* m;
if (argc != 2)
{
printf("\nUsage: printNotes filename\n\n");
return 1;
}
filename = argv[1];
document = readSBML(filename);
errors = SBMLDocument_getNumErrors( document);
printf("\n%s\n\n", filename);
if(errors > 0)
{
SBMLDocument_printErrors(document, stderr);
SBMLDocument_free(document);
return errors;
}
/* Model */
m = SBMLDocument_getModel(document);
printNotes((SBase_t*)m, Model_getId(m));
for(i=0; i < Model_getNumReactions(m); i++)
{
Reaction_t* re = Model_getReaction( m, i);
printNotes((SBase_t*)re, Reaction_getId(re));
/* SpeciesReference (Reactant) */
for(j=0; j < Reaction_getNumReactants( re); j++)
{
SpeciesReference_t* rt = Reaction_getReactant(re, j);
if (SBase_isSetNotes((SBase_t*) rt)) printf(" ");
printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) );
}
/* SpeciesReference (Product) */
for(j=0; j < Reaction_getNumProducts( re ); j++)
{
SpeciesReference_t* rt = Reaction_getProduct( re, j);
if (SBase_isSetNotes((SBase_t*) rt)) printf(" ");
printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) );
}
/* ModifierSpeciesReference (Modifiers) */
for(j=0; j < Reaction_getNumModifiers( re ); j++)
{
SpeciesReference_t* md = Reaction_getModifier(re, j);
if (SBase_isSetNotes((SBase_t*) md)) printf(" ");
printNotes((SBase_t*)md, SpeciesReference_getSpecies( md ) );
}
/* KineticLaw */
if(Reaction_isSetKineticLaw( re ))
{
KineticLaw_t* kl = Reaction_getKineticLaw( re );
if (SBase_isSetNotes((SBase_t*) kl)) printf(" ");
printNotes((SBase_t*)kl, "");
/* Parameter */
for(j=0; j < KineticLaw_getNumParameters( kl ); j++)
{
Parameter_t* pa = KineticLaw_getParameter( kl, j);
if (SBase_isSetNotes((SBase_t*) pa)) printf(" ");
printNotes((SBase_t*)pa, Parameter_getId(pa));
}
}
}
/* Species */
for(i=0; i < Model_getNumSpecies(m); i++)
{
Species_t* sp = Model_getSpecies(m, i);
printNotes((SBase_t*)sp, Species_getId(sp));
}
/* Compartments */
for(i=0; i < Model_getNumCompartments( m ); i++)
{
Compartment_t* sp = Model_getCompartment(m, i);
printNotes((SBase_t*)sp, Compartment_getId(sp));
}
/* FunctionDefinition */
for(i=0; i < Model_getNumFunctionDefinitions(m); i++)
{
FunctionDefinition_t* sp = Model_getFunctionDefinition(m, i);
printNotes((SBase_t*)sp, FunctionDefinition_getId(sp));
}
/* UnitDefinition */
for(i=0; i < Model_getNumUnitDefinitions(m); i++)
{
UnitDefinition_t* sp = Model_getUnitDefinition( m, i);
printNotes((SBase_t*)sp, UnitDefinition_getId(sp));
}
/* Parameter */
for(i=0; i < Model_getNumParameters( m ); i++)
{
Parameter_t* sp = Model_getParameter( m, i);
printNotes((SBase_t*)sp, Parameter_getId(sp));
}
/* Rule */
for(i=0; i < Model_getNumReactions( m ); i++)
{
Rule_t* sp = Model_getRule(m, i);
printNotes((SBase_t*)sp, "");
}
/* InitialAssignment */
for(i=0; i < Model_getNumInitialAssignments(m); i++)
{
InitialAssignment_t* sp = Model_getInitialAssignment(m, i);
printNotes((SBase_t*)sp, "");
}
/* Event */
for(i=0; i < Model_getNumEvents(m); i++)
{
Event_t* sp = Model_getEvent(m, i);
printNotes((SBase_t*)sp, Event_getId(sp));
/* Trigger */
if(Event_isSetTrigger( sp ))
{
Trigger_t* tg = Event_getTrigger(sp);
if (SBase_isSetNotes( (SBase_t*) tg)) printf( " " );
printNotes((SBase_t*)tg, "");
}
/* Delay */
if(Event_isSetDelay(sp))
{
Delay_t* dl = Event_getDelay(sp);
if (SBase_isSetNotes( (SBase_t*) dl)) printf( " " );
printNotes((SBase_t*) dl, "");
}
/* EventAssignment */
for(j=0; j < Event_getNumEventAssignments(sp); j++)
{
EventAssignment_t* ea = Event_getEventAssignment(sp, j);
if (SBase_isSetNotes( (SBase_t*) ea)) printf( " " );
printNotes((SBase_t*)ea, "");
}
}
/* SpeciesType */
for(i=0; i < Model_getNumSpeciesTypes(m); i++)
{
SpeciesType_t* sp = Model_getSpeciesType(m, i);
printNotes((SBase_t*)sp, SpeciesType_getId(sp));
}
/* Constraints */
for(i=0; i < Model_getNumConstraints(m); i++)
{
Constraint_t* sp = Model_getConstraint(m, i);
printNotes((SBase_t*)sp, "");
}
SBMLDocument_free( document );
return errors;
}
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;
}
}
}
}
