END_TEST
START_TEST (test_FormulaFormatter_multiOr)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_setType(n, AST_LOGICAL_OR);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "or()"), NULL );
ASTNode_setName(c, "x");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "or(x)"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "y");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "or(x, y)"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "z");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "or(x, y, z)"), NULL );
safe_free(s);
ASTNode_free(n);
}
END_TEST
START_TEST (test_FormulaFormatter_multiPlusTimes)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_setType(n, AST_PLUS);
ASTNode_setName(c, "x");
ASTNode_addChild(n, c);
c = ASTNode_create();
ASTNode_setName(c, "y");
ASTNode_addChild(n, c);
c = ASTNode_create();
ASTNode_setName(c, "z");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "x + y + z"), NULL );
ASTNode_setType(n, AST_TIMES);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "x * y * z"), NULL );
safe_free(s);
ASTNode_free(n);
}
END_TEST
START_TEST (test_FormulaFormatter_multiDivide)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_setType(n, AST_DIVIDE);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, " / "), NULL );
ASTNode_setName(c, "x");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, " / (x)"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "y");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "x / y"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "z");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "x / y / z"), NULL );
safe_free(s);
ASTNode_free(n);
}
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_L3FormulaFormatter_multiGT)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_setType(n, AST_RELATIONAL_GT);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "gt()"), NULL );
ASTNode_setName(c, "x");
ASTNode_addChild(n, c);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "gt(x)"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "y");
ASTNode_addChild(n, c);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "x > y"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "z");
ASTNode_addChild(n, c);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "gt(x, y, z)"), NULL );
safe_free(s);
ASTNode_free(n);
}
END_TEST
START_TEST (test_L3FormulaFormatter_multiAnd)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_setType(n, AST_LOGICAL_AND);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "and()"), NULL );
ASTNode_setName(c, "x");
ASTNode_addChild(n, c);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "and(x)"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "y");
ASTNode_addChild(n, c);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "x && y"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "z");
ASTNode_addChild(n, c);
s = SBML_formulaToL3String(n);
fail_unless( !strcmp(s, "x && y && z"), NULL );
safe_free(s);
ASTNode_free(n);
}
END_TEST
START_TEST (test_SpeciesReference_setStoichiometryMath5)
{
SpeciesReference_t *sr1 =
SpeciesReference_create(1, 2);
StoichiometryMath_t * sm = StoichiometryMath_create(2, 4);
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);
StoichiometryMath_setMath(sm, math);
int i = SpeciesReference_setStoichiometryMath(sr1, sm);
fail_unless( i == LIBSBML_UNEXPECTED_ATTRIBUTE);
fail_unless( !SpeciesReference_isSetStoichiometryMath(sr1) );
StoichiometryMath_free(sm);
SpeciesReference_free(sr1);
}
END_TEST
START_TEST (test_SpeciesReference_setStoichiometryMath1)
{
StoichiometryMath_t * sm = StoichiometryMath_create(2, 4);
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);
StoichiometryMath_setMath(sm, math);
int i = SpeciesReference_setStoichiometryMath(sr, sm);
fail_unless( i == LIBSBML_OPERATION_SUCCESS);
fail_unless( SpeciesReference_isSetStoichiometryMath(sr) );
fail_unless( SpeciesReference_getStoichiometry(sr) == 1 );
i = SpeciesReference_unsetStoichiometryMath(sr);
fail_unless( i == LIBSBML_OPERATION_SUCCESS);
fail_unless( !SpeciesReference_isSetStoichiometryMath(sr) );
StoichiometryMath_free(sm);
}
END_TEST
START_TEST (test_FormulaFormatter_multiAnd)
{
char *s;
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_setType(n, AST_LOGICAL_AND);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "and()"), NULL );
safe_free(s);
ASTNode_setName(c, "x");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "and(x)"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "y");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "and(x, y)"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "z");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "and(x, y, z)"), NULL );
safe_free(s);
ASTNode_free(n);
}
END_TEST
START_TEST (test_FormulaFormatter_multiPlus)
{
char *s;
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_setType(n, AST_PLUS);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "0"), NULL );
safe_free(s);
ASTNode_setName(c, "x");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "x"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "y");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "x + y"), NULL );
safe_free(s);
c = ASTNode_create();
ASTNode_setName(c, "z");
ASTNode_addChild(n, c);
s = SBML_formulaToString(n);
fail_unless( !strcmp(s, "x + y + z"), NULL );
safe_free(s);
ASTNode_free(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;
}
END_TEST
START_TEST (test_Rule_setMath2)
{
ASTNode_t *math = ASTNode_createWithType(AST_DIVIDE);
ASTNode_t *a = ASTNode_create();
ASTNode_setName(a, "a");
ASTNode_addChild(math, a);
int i = Rule_setMath(R, math);
fail_unless( i == LIBSBML_INVALID_OBJECT);
fail_unless( !Rule_isSetMath(R) );
ASTNode_free(math);
}
END_TEST
START_TEST (test_KineticLaw_setMath2)
{
ASTNode_t *math = ASTNode_createWithType(AST_TIMES);
ASTNode_t *a = ASTNode_create();
ASTNode_setName(a, "a");
ASTNode_addChild(math, a);
int i = KineticLaw_setMath(kl, math);
fail_unless( i == LIBSBML_INVALID_OBJECT);
fail_unless( !KineticLaw_isSetMath(kl) );
ASTNode_free(math);
}
END_TEST
START_TEST (test_L3FormulaFormatter_collapseMinus)
{
StringBuffer_t *sb = StringBuffer_create(42);
char *s = StringBuffer_getBuffer(sb);
ASTNode_t *n = ASTNode_create();
ASTNode_t *c = ASTNode_create();
ASTNode_t *c2 = ASTNode_create();
ASTNode_t *c3 = ASTNode_create();
ASTNode_t *c4 = ASTNode_create();
L3ParserSettings_t* l3ps = L3ParserSettings_create();
ASTNode_setType(n, AST_MINUS);
ASTNode_setType(c, AST_MINUS);
ASTNode_addChild(n, c);
ASTNode_setType(c2, AST_MINUS);
ASTNode_addChild(c, c2);
ASTNode_setType(c3, AST_MINUS);
ASTNode_addChild(c2, c3);
ASTNode_setName(c4, "x");
ASTNode_addChild(c3, c4);
//default (false)
s = SBML_formulaToL3StringWithSettings(n, l3ps);
fail_unless( !strcmp(s, "----x"), NULL );
safe_free(s);
//explicit false
L3ParserSettings_setParseCollapseMinus(l3ps, 0);
s = SBML_formulaToL3StringWithSettings(n, l3ps);
fail_unless( !strcmp(s, "----x"), NULL );
safe_free(s);
//explicit true
L3ParserSettings_setParseCollapseMinus(l3ps, 1);
s = SBML_formulaToL3StringWithSettings(n, l3ps);
fail_unless( !strcmp(s, "x"), NULL );
safe_free(s);
ASTNode_free(n);
L3ParserSettings_free(l3ps);
}
END_TEST
START_TEST (test_SpeciesReference_setStoichiometryMath2)
{
StoichiometryMath_t * sm = StoichiometryMath_create(2, 4);
ASTNode_t *math = ASTNode_createWithType(AST_TIMES);
ASTNode_t *a = ASTNode_create();
ASTNode_setName(a, "a");
ASTNode_addChild(math, a);
StoichiometryMath_setMath(sm, math);
int i = SpeciesReference_setStoichiometryMath(sr, sm);
/* once the StoichiometryMath_setMath function does not set
* an invalid ASTNode this changes to i == LIBSBML_OPERATION_SUCCESS
fail_unless( i == LIBSBML_INVALID_OBJECT);
*/
fail_unless ( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( SpeciesReference_isSetStoichiometryMath(sr) );
StoichiometryMath_free(sm);
}
void ev_alter_tree_structure(Model_t *m, ASTNode_t **node_p, ASTNode_t *parent, int child_order, copied_AST *cp_AST){
ASTNode_t *zero_node;
ASTNode_t *node, *next_node;
ASTNode_t *pc_eq, *pc_cd, *times_node, *and_node, *not_node;
unsigned int i, j;
int p;
ASTNode_t *arg_node_list[MAX_ARG_NUM];
unsigned int arg_node_num;
FunctionDefinition_t *fd;
ASTNode_t *fd_arg;
ASTNode_t *fd_body;
node = *node_p;
for(i=0; i<ASTNode_getNumChildren(node); i++){
next_node = ASTNode_getChild(node, i);
if(ASTNode_getNumChildren(node) == 1 && ASTNode_getType(node) == AST_MINUS){
zero_node = ASTNode_create();
ASTNode_setType(zero_node, AST_REAL);
ASTNode_setReal(zero_node, 0);
ASTNode_replaceChild(node, 0, zero_node);
ASTNode_addChild(*node_p, next_node);
}else{
ev_alter_tree_structure(m, &next_node, *node_p, i, cp_AST);
}
}
if(ASTNode_getType(node) == AST_FUNCTION){
arg_node_num = ASTNode_getNumChildren(node);
for(i=0; i<arg_node_num; i++){
arg_node_list[i] = ASTNode_getChild(node, i);
}
for(i=0; i<Model_getNumFunctionDefinitions(m); i++){
fd = (FunctionDefinition_t*)ListOf_get(Model_getListOfFunctionDefinitions(m), i);
fd_body = (ASTNode_t*)FunctionDefinition_getBody(fd);
if(strcmp(FunctionDefinition_getId(fd), ASTNode_getName(node)) == 0){
fd_body = ASTNode_deepCopy(fd_body);
cp_AST->ast[cp_AST->num_of_copied_AST++] = fd_body;
for(j=0; j<FunctionDefinition_getNumArguments(fd); j++){
fd_arg = (ASTNode_t*)FunctionDefinition_getArgument(fd, j);
ASTNode_replaceArgument(fd_body, (char*)ASTNode_getName(fd_arg), arg_node_list[j]);
}
/* check_AST(fd_body, NULL); */
if(parent != NULL){
ASTNode_replaceChild(parent, child_order, fd_body);
}else{
*node_p = fd_body;
}
node = *node_p;
break;
}
}
}
if(ASTNode_getType(node) == AST_FUNCTION_PIECEWISE){
ASTNode_setType(node, AST_PLUS);
ASTNode_setName(node, NULL);
times_node = ASTNode_createWithType(AST_TIMES);
pc_eq = ASTNode_getRightChild(node);
ASTNode_addChild(times_node, pc_eq);
if(ASTNode_getNumChildren(node) > 3){
and_node = ASTNode_createWithType(AST_LOGICAL_AND);
ASTNode_addChild(times_node, and_node);
for(p=(int)ASTNode_getNumChildren(node)-2; p >= 1; p = p-2){
pc_cd = ASTNode_getChild(node, p);
not_node = ASTNode_createWithType(AST_LOGICAL_NOT);
ASTNode_addChild(not_node, pc_cd);
ASTNode_addChild(and_node, not_node);
}
ASTNode_reduceToBinary(and_node);
}else{
pc_cd = ASTNode_getChild(node, 1);
not_node = ASTNode_createWithType(AST_LOGICAL_NOT);
ASTNode_addChild(not_node, pc_cd);
ASTNode_addChild(times_node, not_node);
}
ASTNode_replaceChild(node, ASTNode_getNumChildren(node)-1, times_node);
for(p=ASTNode_getNumChildren(node)-2; p >= 1; p = p-2){
times_node = ASTNode_createWithType(AST_TIMES);
pc_eq = ASTNode_getChild(node, p-1);
pc_cd = ASTNode_getChild(node, p);
ASTNode_addChild(times_node, pc_eq);
ASTNode_addChild(times_node, ASTNode_deepCopy(pc_cd));
ASTNode_removeChild(node, p);
ASTNode_replaceChild(node ,p-1, times_node);
}
ASTNode_reduceToBinary(node);
}
return;
}
