END_TEST
START_TEST (test_Event_addEventAssignment4)
{
Event_t *e = Event_create(2, 2);
EventAssignment_t *ea
= EventAssignment_create(2, 2);
EventAssignment_setVariable(ea, "c");
EventAssignment_setMath(ea, SBML_parseFormula("a-n"));
EventAssignment_t *ea1
= EventAssignment_create(2, 2);
EventAssignment_setVariable(ea1, "c");
EventAssignment_setMath(ea1, SBML_parseFormula("a-n"));
int i = Event_addEventAssignment(e, ea);
fail_unless( i == LIBSBML_OPERATION_SUCCESS);
fail_unless( Event_getNumEventAssignments(e) == 1);
i = Event_addEventAssignment(e, ea1);
fail_unless( i == LIBSBML_DUPLICATE_OBJECT_ID);
fail_unless( Event_getNumEventAssignments(e) == 1);
EventAssignment_free(ea);
EventAssignment_free(ea1);
Event_free(e);
}
void
printEventMath (unsigned int n, Event_t *e)
{
char *formula;
unsigned int i;
if ( Event_isSetDelay(e) )
{
formula = SBML_formulaToDot( Delay_getMath(Event_getDelay(e)) );
fprintf(fout, "subgraph cluster%u {\n", noClusters);
fprintf(fout, "label=\"Event %s delay:\";\n%s\n", Event_getId(e), formula);
free(formula);
noClusters++;
}
if ( Event_isSetTrigger(e) )
{
formula = SBML_formulaToDot( Trigger_getMath(Event_getTrigger(e)) );
fprintf(fout, "subgraph cluster%u {\n", noClusters);
fprintf(fout, "label=\"Event %s trigger:\";\n%s\n", Event_getId(e), formula);
noClusters++;
free(formula);
}
for (i = 0; i < Event_getNumEventAssignments(e); ++i)
{
printEventAssignmentMath(i + 1, Event_getEventAssignment(e, i));
}
}
void
printEventMath (unsigned int n, Event_t *e)
{
char *formula;
unsigned int i;
if ( Event_isSetDelay(e) )
{
const Delay_t *delay = Event_getDelay(e);
formula = SBML_formulaToString( Delay_getMath(delay) );
printf("Event %d delay: %s\n", n, formula);
free(formula);
}
if ( Event_isSetTrigger(e) )
{
const Trigger_t *trigger = Event_getTrigger(e);
formula = SBML_formulaToString( Trigger_getMath(trigger) );
printf("Event %d trigger: %s\n", n, formula);
free(formula);
}
for (i = 0; i < Event_getNumEventAssignments(e); ++i)
{
printEventAssignmentMath(i + 1, Event_getEventAssignment(e, i));
}
printf("\n");
}
SBML_ODESOLVER_API int IntegratorInstance_checkTrigger(integratorInstance_t *engine)
{
int i, j, fired;
ASTNode_t *trigger, *assignment;
Event_t *e;
EventAssignment_t *ea;
variableIndex_t *vi;
cvodeSettings_t *opt = engine->opt;
cvodeData_t *data = engine->data;
odeModel_t *om = engine->om;
fired = 0;
for ( i=0; i<Model_getNumEvents(om->simple); i++ ) {
e = Model_getEvent(om->simple, i);
trigger = (ASTNode_t *) Event_getTrigger(e);
if ( data->trigger[i] == 0 && evaluateAST(trigger, data) ) {
if (opt->HaltOnEvent)
SolverError_error(ERROR_ERROR_TYPE,
SOLVER_ERROR_EVENT_TRIGGER_FIRED,
"Event Trigger %d (%s) fired at time %g. "
"Aborting simulation.",
i, SBML_formulaToString(trigger),
data->currenttime);
/* removed AMF 08/11/05
else
SolverError_error(WARNING_ERROR_TYPE,
SOLVER_ERROR_EVENT_TRIGGER_FIRED,
"Event Trigger %d (%s) fired at time %g. ",
i, SBML_formulaToString(trigger),
data->currenttime); */
fired++;
data->trigger[i] = 1;
for ( j=0; j<Event_getNumEventAssignments(e); j++ ) {
ea = Event_getEventAssignment(e, j);
assignment = (ASTNode_t *) EventAssignment_getMath(ea);
vi = ODEModel_getVariableIndex(om,
EventAssignment_getVariable(ea));
IntegratorInstance_setVariableValue(engine, vi,
evaluateAST(assignment, data));
VariableIndex_free(vi);
}
}
else {
data->trigger[i] = 0;
}
}
return fired;
}
END_TEST
START_TEST (test_Event_addEventAssignment3)
{
Event_t *e = Event_create(2, 2);
int i = Event_addEventAssignment(e, NULL);
fail_unless( i == LIBSBML_OPERATION_FAILED);
fail_unless( Event_getNumEventAssignments(e) == 0);
Event_free(e);
}
END_TEST
START_TEST (test_Event_createEventAssignment)
{
Event_t *e = Event_create(2, 2);
EventAssignment_t *ea = Event_createEventAssignment(e);
fail_unless( Event_getNumEventAssignments(e) == 1);
fail_unless( SBase_getLevel((SBase_t *) (ea)) == 2 );
fail_unless( SBase_getVersion((SBase_t *) (ea)) == 2 );
Event_free(e);
}
END_TEST
START_TEST (test_Event_addEventAssignment2)
{
Event_t *e = Event_create(2, 2);
EventAssignment_t *ea
= EventAssignment_create(2, 3);
EventAssignment_setVariable(ea, "f");
EventAssignment_setMath(ea, SBML_parseFormula("a-n"));
int i = Event_addEventAssignment(e, ea);
fail_unless( i == LIBSBML_VERSION_MISMATCH);
fail_unless( Event_getNumEventAssignments(e) == 0);
EventAssignment_free(ea);
Event_free(e);
}
int
main (int argc, char* argv[])
{
unsigned int i,j,errors;
const char* filename = argv[1];
SBMLDocument_t* document;
Model_t* m;
if (argc != 3)
{
printf("\nUsage: unsetNotes <input-filename> <output-filename>\n");
return 1;
}
filename = argv[1];
document = readSBML(filename);
errors = SBMLDocument_getNumErrors(document);
if(errors > 0)
{
SBMLDocument_printErrors(document, stderr);
SBMLDocument_free(document);
return errors;
}
m = SBMLDocument_getModel( document );
SBase_unsetNotes((SBase_t*)m);
for(i=0; i < Model_getNumReactions(m); i++)
{
Reaction_t* re = Model_getReaction(m, i);
SBase_unsetNotes((SBase_t*)re);
for(j=0; j < Reaction_getNumReactants(re); j++)
{
SpeciesReference_t* rt = Reaction_getReactant(re,j);
SBase_unsetNotes((SBase_t*)rt);
}
for(j=0; j < Reaction_getNumProducts(re); j++)
{
SpeciesReference_t* rt = Reaction_getProduct(re,j);
SBase_unsetNotes((SBase_t*)rt);
}
for(j=0; j < Reaction_getNumModifiers(re); j++)
{
SpeciesReference_t* md = Reaction_getModifier(re,j);
SBase_unsetNotes((SBase_t*)md);
}
if(Reaction_isSetKineticLaw(re))
{
KineticLaw_t* kl = Reaction_getKineticLaw(re);
SBase_unsetNotes((SBase_t*)kl);
for(j=0; j < KineticLaw_getNumParameters(kl); j++)
{
Parameter_t* pa = KineticLaw_getParameter(kl, j);
SBase_unsetNotes((SBase_t*)pa);
}
}
}
for(i=0; i < Model_getNumSpecies(m); i++)
{
Species_t* sp = Model_getSpecies(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumCompartments(m); i++)
{
Compartment_t* sp = Model_getCompartment(m,i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumFunctionDefinitions(m); i++)
{
FunctionDefinition_t* sp = Model_getFunctionDefinition(m,i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumUnitDefinitions(m); i++)
{
UnitDefinition_t* sp = Model_getUnitDefinition(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumParameters(m); i++)
{
Parameter_t* sp = Model_getParameter(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumRules(m); i++)
{
Rule_t* sp = Model_getRule(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumInitialAssignments(m); i++)
{
InitialAssignment_t* sp = Model_getInitialAssignment(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumEvents(m); i++)
{
Event_t* sp = Model_getEvent(m, i);
SBase_unsetNotes((SBase_t*)sp);
for(j=0; j < Event_getNumEventAssignments(sp); j++)
{
EventAssignment_t* ea = Event_getEventAssignment(sp, j);
SBase_unsetNotes((SBase_t*)ea);
}
}
for(i=0; i < Model_getNumSpeciesTypes(m); i++)
{
SpeciesType_t* sp = Model_getSpeciesType(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
for(i=0; i < Model_getNumConstraints(m); i++)
{
Constraint_t* sp = Model_getConstraint(m, i);
SBase_unsetNotes((SBase_t*)sp);
}
writeSBML(document, argv[2]);
SBMLDocument_free(document);
return errors;
}
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");
}
}