void
printFunctionDefinition (unsigned int n, FunctionDefinition_t *fd)
{
const ASTNode_t *math;
char *formula;
if ( FunctionDefinition_isSetMath(fd) )
{
math = FunctionDefinition_getMath(fd);
/* Print function body. */
if (ASTNode_getNumChildren(math) == 0)
{
printf("(no body defined)");
}
else
{
math = ASTNode_getChild(math, ASTNode_getNumChildren(math) - 1);
formula = SBML_formulaToDot(math);
fprintf(fout, "subgraph cluster%u {\n", noClusters);
fprintf(fout, "label=\"FunctionDefinition: %s\";\n%s\n", FunctionDefinition_getId(fd), formula);
free(formula);
noClusters++;
}
}
}
END_TEST
START_TEST (test_FunctionDefinition_setMath1)
{
ASTNode_t *math = SBML_parseFormula("2 * k");
int i = FunctionDefinition_setMath(E, math);
fail_unless( i == LIBSBML_OPERATION_SUCCESS);
fail_unless( FunctionDefinition_getMath(E) != math );
fail_unless( FunctionDefinition_isSetMath(E) );
i = FunctionDefinition_setMath(E, NULL);
fail_unless( i == LIBSBML_OPERATION_SUCCESS);
fail_unless( FunctionDefinition_getMath(E) == NULL );
fail_unless( !FunctionDefinition_isSetMath(E) );
ASTNode_free(math);
}
END_TEST
START_TEST (test_FunctionDefinition_createWith)
{
ASTNode_t *math = SBML_parseFormula("lambda(x, x^3)");
FunctionDefinition_t *fd =
FunctionDefinition_create(2, 4);
FunctionDefinition_setId(fd, "pow3");
FunctionDefinition_setMath(fd, math);
const ASTNode_t * math1;
char * formula;
fail_unless( SBase_getTypeCode((SBase_t *) fd) == SBML_FUNCTION_DEFINITION );
fail_unless( SBase_getMetaId ((SBase_t *) fd) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) fd) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) fd) == NULL );
fail_unless( FunctionDefinition_getName(fd) == NULL );
math1 = FunctionDefinition_getMath(fd);
fail_unless( math1 != NULL );
formula = SBML_formulaToString(math1);
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "lambda(x, x^3)") );
fail_unless( FunctionDefinition_getMath(fd) != math );
fail_unless( FunctionDefinition_isSetMath(fd) );
fail_unless( !strcmp(FunctionDefinition_getId(fd), "pow3") );
fail_unless( FunctionDefinition_isSetId(fd) );
ASTNode_free(math);
safe_free(formula);
FunctionDefinition_free(fd);
}
void
printFunctionDefinition (unsigned int n, const FunctionDefinition_t *fd)
{
const ASTNode_t *math;
char *formula;
if ( FunctionDefinition_isSetMath(fd) )
{
printf("FunctionDefinition %d, %s(", n, FunctionDefinition_getId(fd));
math = FunctionDefinition_getMath(fd);
/* Print function arguments. */
if (ASTNode_getNumChildren(math) > 1)
{
printf("%s", ASTNode_getName( ASTNode_getLeftChild(math) ));
for (n = 1; n < ASTNode_getNumChildren(math) - 1; ++n)
{
printf(", %s", ASTNode_getName( ASTNode_getChild(math, n) ));
}
}
printf(") := ");
/* Print function body. */
if (ASTNode_getNumChildren(math) == 0)
{
printf("(no body defined)");
}
else
{
math = ASTNode_getChild(math, ASTNode_getNumChildren(math) - 1);
formula = SBML_formulaToString(math);
printf("%s\n", formula);
free(formula);
}
}
}
END_TEST
START_TEST (test_FunctionDefinition_setMath)
{
ASTNode_t *math = SBML_parseFormula("lambda(x, x^3)");
const ASTNode_t * math1;
char * formula;
FunctionDefinition_setMath(FD, math);
math1 = FunctionDefinition_getMath(FD);
fail_unless( math1 != NULL );
formula = SBML_formulaToString(math1);
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "lambda(x, x^3)") );
fail_unless( FunctionDefinition_getMath(FD) != math );
fail_unless( FunctionDefinition_isSetMath(FD) );
fail_unless( FunctionDefinition_isSetBody(FD) );
/* Reflexive case (pathological) */
FunctionDefinition_setMath(FD, (ASTNode_t *) FunctionDefinition_getMath(FD));
math1 = FunctionDefinition_getMath(FD);
fail_unless( math1 != NULL );
safe_free(formula);
formula = SBML_formulaToString(math1);
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "lambda(x, x^3)") );
fail_unless( FunctionDefinition_getMath(FD) != math );
FunctionDefinition_setMath(FD, NULL);
fail_unless( !FunctionDefinition_isSetMath(FD) );
fail_unless( !FunctionDefinition_isSetBody(FD) );
if (FunctionDefinition_getMath(FD) != NULL)
{
fail("FunctionDefinition_setMath(FD, NULL) did not clear ASTNode.");
}
ASTNode_free(math);
safe_free(formula);
}
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");
}
}
