END_TEST
START_TEST (test_Rule_setMath)
{
ASTNode_t *math = SBML_parseFormula("1 + 1");
Rule_setMath(R, math);
fail_unless( Rule_getMath(R) != math );
fail_unless( Rule_isSetMath(R) );
/* Reflexive case (pathological) */
Rule_setMath(R, (ASTNode_t *) Rule_getMath(R));
fail_unless( Rule_getMath(R) != math );
Rule_setMath(R, NULL);
fail_unless( !Rule_isSetMath(R) );
if (Rule_getMath(R) != NULL)
{
fail("Rule_setMath(R, NULL) did not clear ASTNode.");
}
ASTNode_free(math);
}
END_TEST
START_TEST (test_Rule_setMath1)
{
ASTNode_t *math = ASTNode_createWithType(AST_TIMES);
ASTNode_t *a = ASTNode_create();
ASTNode_t *b = ASTNode_create();
ASTNode_setName(a, "a");
ASTNode_setName(b, "b");
ASTNode_addChild(math, a);
ASTNode_addChild(math, b);
char *formula;
const ASTNode_t *math1;
int i = Rule_setMath(R, math);
fail_unless( i == LIBSBML_OPERATION_SUCCESS);
fail_unless( Rule_isSetMath(R) );
math1 = Rule_getMath(R);
fail_unless( math1 != NULL );
formula = SBML_formulaToString(math1);
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "a * b") );
ASTNode_free(math);
}
END_TEST
START_TEST (test_AssignmentRule_createWithFormula)
{
const ASTNode_t *math;
char *formula;
Rule_t *ar = Rule_createAssignment(2, 4);
Rule_setVariable(ar, "s");
Rule_setFormula(ar, "1 + 1");
fail_unless( SBase_getTypeCode ((SBase_t *) ar) == SBML_ASSIGNMENT_RULE );
fail_unless( SBase_getMetaId ((SBase_t *) ar) == NULL );
fail_unless( !strcmp(Rule_getVariable(ar), "s") );
math = Rule_getMath((Rule_t *) ar);
fail_unless(math != NULL);
formula = SBML_formulaToString(math);
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "1 + 1") );
fail_unless( !strcmp(Rule_getFormula((Rule_t *) ar), formula) );
Rule_free(ar);
safe_free(formula);
}
END_TEST
START_TEST (test_AlgebraicRule_createWithFormula)
{
const ASTNode_t *math;
char *formula;
Rule_t *ar = Rule_createAlgebraic(2, 4);
Rule_setFormula(ar, "1 + 1");
fail_unless( SBase_getTypeCode ((SBase_t *) ar) == SBML_ALGEBRAIC_RULE );
fail_unless( SBase_getMetaId ((SBase_t *) ar) == NULL );
math = Rule_getMath((Rule_t *) ar);
fail_unless(math != NULL);
formula = SBML_formulaToString(math);
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "1 + 1") );
fail_unless( !strcmp(Rule_getFormula((Rule_t *) ar), formula) );
Rule_free(ar);
safe_free(formula);
}
void
printRuleMath (unsigned int n, const Rule_t *r)
{
char *formula;
if ( Rule_isSetMath(r) )
{
formula = SBML_formulaToString( Rule_getMath(r) );
printf("Rule %d, formula: %s\n", n, formula);
free(formula);
}
}
void
printRuleMath (unsigned int n, Rule_t *r)
{
char *formula;
if ( Rule_isSetMath(r) )
{
formula = SBML_formulaToDot( Rule_getMath(r));
fprintf(fout, "subgraph cluster%u {\n", noClusters);
fprintf(fout, "label=\"Rule: %u\";\n%s\n", n, formula);
free(formula);
noClusters++;
}
}
END_TEST
START_TEST (test_AlgebraicRule_createWithMath)
{
ASTNode_t *math = SBML_parseFormula("1 + 1");
Rule_t *ar = Rule_createAlgebraic(2, 4);
Rule_setMath(ar, math);
fail_unless( SBase_getTypeCode ((SBase_t *) ar) == SBML_ALGEBRAIC_RULE );
fail_unless( SBase_getMetaId ((SBase_t *) ar) == NULL );
fail_unless( !strcmp(Rule_getFormula((Rule_t *) ar), "1 + 1") );
fail_unless( Rule_getMath((Rule_t *) ar) != math );
Rule_free(ar);
}
END_TEST
START_TEST (test_AssignmentRule_createWithMath)
{
ASTNode_t *math = SBML_parseFormula("1 + 1");
Rule_t *ar = Rule_createAssignment(2, 4);
Rule_setVariable(ar, "s");
Rule_setMath(ar, math);
fail_unless( SBase_getTypeCode ((SBase_t *) ar) == SBML_ASSIGNMENT_RULE );
fail_unless( SBase_getMetaId ((SBase_t *) ar) == NULL );
fail_unless( !strcmp(Rule_getVariable(ar), "s") );
fail_unless( !strcmp(Rule_getFormula((Rule_t *) ar), "1 + 1") );
fail_unless( Rule_getMath((Rule_t *) ar) != math );
Rule_free(ar);
}
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");
}
}