END_TEST
START_TEST (test_KineticLaw_getParameterById)
{
Parameter_t *k1 = Parameter_create(2, 4);
Parameter_t *k2 = Parameter_create(2, 4);
Parameter_setId(k1, "k1");
Parameter_setId(k2, "k2");
Parameter_setValue(k1, 3.14);
Parameter_setValue(k2, 2.72);
KineticLaw_addParameter(kl, k1);
KineticLaw_addParameter(kl, k2);
Parameter_free(k1);
Parameter_free(k2);
fail_unless( KineticLaw_getNumParameters(kl) == 2 );
k1 = KineticLaw_getParameterById(kl, "k1");
k2 = KineticLaw_getParameterById(kl, "k2");
fail_unless( !strcmp(Parameter_getId(k1), "k1") );
fail_unless( !strcmp(Parameter_getId(k2), "k2") );
fail_unless( Parameter_getValue(k1) == 3.14 );
fail_unless( Parameter_getValue(k2) == 2.72 );
}
END_TEST
START_TEST (test_Parameter_setId)
{
char *id = "Km1";
Parameter_setId(P, id);
fail_unless( !strcmp(Parameter_getId(P), id) );
fail_unless( Parameter_isSetId(P) );
if (Parameter_getId(P) == id)
{
fail("Parameter_setId(...) did not make a copy of string.");
}
/* Reflexive case (pathological) */
Parameter_setId(P, Parameter_getId(P));
fail_unless( !strcmp(Parameter_getId(P), id) );
Parameter_setId(P, NULL);
fail_unless( !Parameter_isSetId(P) );
if (Parameter_getId(P) != NULL)
{
fail("Parameter_setId(P, NULL) did not clear string.");
}
}
/* 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;
}
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_Parameter_id)
{
char *id = "mitochondria";
fail_unless( !Parameter_isSetId(P) );
Parameter_setId(P, id);
fail_unless( !strcmp(Parameter_getId(P), id) );
fail_unless( Parameter_isSetId(P) );
if (Parameter_getId(P) == id)
{
fail("Parameter_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_Parameter_setId2)
{
int i = Parameter_setId(P, "cell");
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Parameter_isSetId(P) );
fail_unless( !strcmp(Parameter_getId(P), "cell" ));
i = Parameter_setId(P, NULL);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Parameter_isSetId(P) );
}
END_TEST
START_TEST (test_L3_Parameter_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);
Parameter_t *p =
Parameter_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) p) == SBML_PARAMETER );
fail_unless( SBase_getMetaId ((SBase_t *) p) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) p) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) p) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) p) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) p) == 1 );
fail_unless( Parameter_getNamespaces (p) != NULL );
fail_unless( XMLNamespaces_getLength(Parameter_getNamespaces(p)) == 2 );
fail_unless( Parameter_getId (p) == NULL );
fail_unless( Parameter_getName (p) == NULL );
fail_unless( Parameter_getUnits (p) == NULL );
fail_unless( isnan(Parameter_getValue(p)));
fail_unless( Parameter_getConstant(p) == 1 );
fail_unless( !Parameter_isSetId (p) );
fail_unless( !Parameter_isSetName (p) );
fail_unless( !Parameter_isSetValue (p) );
fail_unless( !Parameter_isSetUnits (p) );
fail_unless( !Parameter_isSetConstant(p) );
Parameter_free(p);
}
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 printReactions(Model_t *m, FILE *f)
{
int i,j,k;
Reaction_t *r;
SpeciesReference_t *sref;
KineticLaw_t *kl;
Rule_t *rl;
AssignmentRule_t *asr;
AlgebraicRule_t *alr;
RateRule_t *rr;
Event_t *e;
EventAssignment_t *ea;
Parameter_t *p;
FunctionDefinition_t *fd;
SBMLTypeCode_t type;
const ASTNode_t *math;
math = NULL;
fprintf(f, "\n");
for(i=0;i<Model_getNumParameters(m);i++){
if(i==0)
fprintf(f, "# Global parameters:\n");
p = Model_getParameter(m,i);
if(Parameter_isSetId(p))
fprintf(f, "%s ", Parameter_getId(p));
if(Parameter_isSetName(p))
fprintf(f, "(%s) ", Parameter_getName(p));
if(Parameter_isSetValue(p))
fprintf(f, "= %g; ", Parameter_getValue(p));
if(Parameter_isSetUnits(p))
fprintf(f, "[%s]; ", Parameter_getUnits(p));
if(!Parameter_getConstant(p))
fprintf(f, "(variable);");
fprintf(f, "\n");
if ( i==Model_getNumParameters(m)-1 )
fprintf(f, "\n");
}
fprintf(f, "# Reactions:\n");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m,i);
fprintf(f, "%s: %s",
Reaction_isSetName(r) ? Reaction_getName(r) : Reaction_getId(r),
Reaction_getFast(r) ? "(fast)" : "");
for ( k=0; k<Reaction_getNumReactants(r); k++ ) {
sref = Reaction_getReactant(r,k);
if ( SpeciesReference_isSetStoichiometryMath(sref) )
fprintf(f, "%s ",
SBML_formulaToString(\
SpeciesReference_getStoichiometryMath(sref)));
else
if ( SpeciesReference_getStoichiometry(sref) != 1. )
fprintf(f, "%g ", SpeciesReference_getStoichiometry(sref));
fprintf(f, "%s", SpeciesReference_getSpecies(sref));
if(k+1<Reaction_getNumReactants(r))
fprintf(f, "%s", " + ");
}
fprintf(f, "%s", Reaction_getReversible(r) ? " <-> " : " -> ");
for ( k=0; k<Reaction_getNumProducts(r); k++ ) {
sref = Reaction_getProduct(r,k);
if ( SpeciesReference_isSetStoichiometryMath(sref) )
fprintf(f, "%s ",
SBML_formulaToString(\
SpeciesReference_getStoichiometryMath(sref)));
else
if ( SpeciesReference_getStoichiometry(sref) != 1. )
fprintf(f, "%g ", SpeciesReference_getStoichiometry(sref));
fprintf(f, "%s", SpeciesReference_getSpecies(sref));
if(k+1<Reaction_getNumProducts(r))
fprintf(f, "%s", " + ");
}
fprintf(f, "; ");
if(Reaction_isSetKineticLaw(r)){
kl = Reaction_getKineticLaw(r);
math = KineticLaw_getMath(kl);
fprintf(f, "%s;", SBML_formulaToString(math));
for(k=0;k<KineticLaw_getNumParameters(kl);k++){
p = KineticLaw_getParameter(kl,k);
fprintf(f, " %s", Parameter_getId(p));
if(Parameter_isSetName(p))
fprintf(f, " (%s)", Parameter_getName(p));
if(Parameter_isSetValue(p))
fprintf(f, " = %g", Parameter_getValue(p));
if(Parameter_isSetUnits(p))
fprintf(f, " [%s]", Parameter_getUnits(p));
if ( !Parameter_getConstant(p) )
fprintf(f, " (variable)");
fprintf(f, ";");
}
/* fprintf(f, "\n"); */
}else
fprintf(f, "# no rate law is set for this reaction.");
fprintf(f, "\n");
}
for(i=0;i<Model_getNumRules(m);i++){
rl = Model_getRule(m,i);
if ( i == 0 ) {
fprintf(f, "# Rules:\n");
}
type = SBase_getTypeCode((SBase_t *)rl);
if ( type == SBML_RATE_RULE ) {
rr = (RateRule_t *) rl;
fprintf(f, " rateRule: d%s/dt = ", RateRule_getVariable(rr));
}
if ( type == SBML_ALGEBRAIC_RULE ) {
alr = (AlgebraicRule_t *) rl;
fprintf(f, " algebraicRule: 0 = ");
}
if ( type == SBML_ASSIGNMENT_RULE ) {
asr = (AssignmentRule_t *) rl;
fprintf(f, " assignmentRule (%s): %s = ",
RuleType_toString(AssignmentRule_getType(asr)),
AssignmentRule_getVariable(asr));
}
if(!Rule_isSetMath(rl)){
if(Rule_isSetFormula(rl)){
Rule_setMathFromFormula(rl);
}
}
if(Rule_isSetMath(rl))
fprintf(f, "%s\n", SBML_formulaToString(Rule_getMath(rl)));
}
fprintf(f, "\n");
for(i=0;i<Model_getNumEvents(m);i++){
if(i==0)
fprintf(f, "# Events:\n");
e = Model_getEvent(m,i);
if(Event_isSetId(e))
fprintf(f, "%s: ", Event_getId(e));
if(Event_isSetName(e))
fprintf(f, "(%s) ", Event_getName(e));
if(Event_isSetTrigger(e)) {
math = Event_getTrigger(e);
fprintf(f, "trigger: %s\n", SBML_formulaToString(math));
}
if(Event_isSetDelay(e))
fprintf(f, "delay: %s;\n", SBML_formulaToString(Event_getDelay(e)));
if(Event_isSetTimeUnits(e))
fprintf(f, "time Units: %s;\n", Event_getTimeUnits(e));
for(k=0;k<Event_getNumEventAssignments(e);k++){
ea = Event_getEventAssignment(e,k);
if(EventAssignment_isSetVariable(ea))
fprintf(f, " event: %s = %s;\n",
EventAssignment_getVariable(ea),
EventAssignment_isSetMath(ea) ?
SBML_formulaToString(EventAssignment_getMath(ea)) :
"# no math set;\n");
}
if(i==Model_getNumEvents(m)-1)
fprintf(f, "\n");
}
for ( i=0; i<Model_getNumFunctionDefinitions(m); i++ ) {
if ( i==0 ) fprintf(f, "# Functions:\n");
fd = Model_getFunctionDefinition(m,i);
if ( FunctionDefinition_isSetName(fd) )
fprintf(f, "%s: ", FunctionDefinition_getName(fd));
if(FunctionDefinition_isSetId(fd) && FunctionDefinition_isSetMath(fd)){
fprintf(f, "%s( ", FunctionDefinition_getId(fd));
math = FunctionDefinition_getMath(fd);
for(j=0;j<ASTNode_getNumChildren(math)-1;j++){
fprintf(f, "%s", SBML_formulaToString(ASTNode_getChild(math, j)));
if(j<ASTNode_getNumChildren(math)-2)
fprintf(f, ", ");
if(j==ASTNode_getNumChildren(math)-2)
fprintf(f, ") = ");
}
fprintf(f, "%s;", SBML_formulaToString(ASTNode_getRightChild(math)));
}
fprintf(f, "\n");
}
}
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;
}
}
}
}
