END_TEST
START_TEST (test_SBML_parseFormula_15)
{
ASTNode_t *r = SBML_parseFormula("foo(1, bar)");
ASTNode_t *c;
fail_unless( ASTNode_getType(r) == AST_FUNCTION , NULL );
fail_unless( !strcmp(ASTNode_getName(r), "foo") , NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
c = ASTNode_getLeftChild(r);
fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (c) == 1, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
c = ASTNode_getRightChild(r);
fail_unless( ASTNode_getType(c) == AST_NAME , NULL );
fail_unless( !strcmp(ASTNode_getName(c), "bar") , NULL );
fail_unless( ASTNode_getNumChildren(c) == 0 , NULL );
ASTNode_free(r);
}
END_TEST
START_TEST (test_FunctionDefinition_getArguments)
{
const ASTNode_t *math;
ASTNode_t* math1 = SBML_parseFormula("lambda(x, y, x^y)");
FunctionDefinition_setMath(FD, math1 );
ASTNode_free(math1);
fail_unless( FunctionDefinition_getNumArguments(FD) == 2 );
math = FunctionDefinition_getArgument(FD, 0);
fail_unless( math != NULL );
fail_unless( ASTNode_isName(math) );
fail_unless( !strcmp(ASTNode_getName(math), "x") );
fail_unless( ASTNode_getNumChildren(math) == 0 );
math = FunctionDefinition_getArgument(FD, 1);
fail_unless( math != NULL );
fail_unless( ASTNode_isName(math) );
fail_unless( !strcmp(ASTNode_getName(math), "y") );
fail_unless( ASTNode_getNumChildren(math) == 0 );
fail_unless( FunctionDefinition_getArgument(FD, 0) ==
FunctionDefinition_getArgumentByName(FD, "x") );
fail_unless( FunctionDefinition_getArgument(FD, 1) ==
FunctionDefinition_getArgumentByName(FD, "y") );
}
END_TEST
START_TEST (test_SBML_parseFormula_6)
{
ASTNode_t *r = SBML_parseFormula("1 + 2");
ASTNode_t *c;
fail_unless( ASTNode_getType (r) == AST_PLUS, NULL );
fail_unless( ASTNode_getCharacter (r) == '+', NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
c = ASTNode_getLeftChild(r);
fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (c) == 1, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
c = ASTNode_getRightChild(r);
fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (c) == 2, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
ASTNode_free(r);
}
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++;
}
}
}
/**
* Visits the given ASTNode as a unary minus. For this node only the
* traversal is preorder.
*/
void
L3FormulaFormatter_visitUMinus ( const ASTNode_t *parent,
const ASTNode_t *node,
StringBuffer_t *sb,
const L3ParserSettings_t *settings )
{
//Unary minus is *not* the highest precedence, since it is superceded by 'power'
unsigned int group;
//If we are supposed to collapse minuses, do so.
if (L3ParserSettings_getParseCollapseMinus(settings)) {
if (ASTNode_getNumChildren(node) == 1 &&
ASTNode_isUMinus(ASTNode_getLeftChild(node))) {
L3FormulaFormatter_visit(parent, ASTNode_getLeftChild(ASTNode_getLeftChild(node)), sb, settings);
return;
}
}
group = L3FormulaFormatter_isGrouped(parent, node, settings);
if (group)
{
StringBuffer_appendChar(sb, '(');
}
StringBuffer_appendChar(sb, '-');
L3FormulaFormatter_visit ( node, ASTNode_getLeftChild(node), sb, settings);
if (group)
{
StringBuffer_appendChar(sb, ')');
}
}
/**
* Visits the given ASTNode as a function. For this node only the
* traversal is preorder.
*/
void
FormulaFormatter_visitFunction ( const ASTNode_t *parent,
const ASTNode_t *node,
StringBuffer_t *sb )
{
unsigned int numChildren = ASTNode_getNumChildren(node);
unsigned int n;
FormulaFormatter_format(sb, node);
StringBuffer_appendChar(sb, '(');
if (numChildren > 0)
{
FormulaFormatter_visit( node, ASTNode_getChild(node, 0), sb );
}
for (n = 1; n < numChildren; n++)
{
StringBuffer_appendChar(sb, ',');
StringBuffer_appendChar(sb, ' ');
FormulaFormatter_visit( node, ASTNode_getChild(node, n), sb );
}
StringBuffer_appendChar(sb, ')');
}
/**
* Since graphviz will interpret identical names as referring to
* the same node presentation-wise it is better if each function node
* has a unique name.
*
* Returns the name of the function with the name of the first child
* prepended
*
* THIS COULD BE DONE BETTER
*/
char *
FormulaGraphvizFormatter_FunctionGetUniqueName (const ASTNode_t *node)
{
char *s;
StringBuffer_t *p = StringBuffer_create(128);
ASTNodeType_t type = ASTNode_getType(node);
if (ASTNode_getNumChildren(node) != 0)
{
const char* name = ASTNode_getName(ASTNode_getChild(node,0));
if (name != NULL)
StringBuffer_append(p, name);
}
else
{
StringBuffer_append(p, "unknown");
}
switch (type)
{
case AST_FUNCTION_ARCCOS:
StringBuffer_append(p, "acos");
break;
case AST_FUNCTION_ARCSIN:
StringBuffer_append(p, "asin");
break;
case AST_FUNCTION_ARCTAN:
StringBuffer_append(p, "atan");
break;
case AST_FUNCTION_CEILING:
StringBuffer_append(p, "ceil");
break;
case AST_FUNCTION_LN:
StringBuffer_append(p, "log");
break;
case AST_FUNCTION_POWER:
StringBuffer_append(p, "pow");
break;
default:
if (ASTNode_getName(node) != NULL)
{
StringBuffer_append(p, ASTNode_getName(node));
}
break;
}
s = StringBuffer_toString(p);
free(p);
return s;
}
END_TEST
START_TEST (test_SBML_parseFormula_10)
{
ASTNode_t *r = SBML_parseFormula("1 + -2e100 / 3");
ASTNode_t *c;
fail_unless( ASTNode_getType (r) == AST_PLUS, NULL );
fail_unless( ASTNode_getCharacter (r) == '+', NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
c = ASTNode_getLeftChild(r);
fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (c) == 1, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
c = ASTNode_getRightChild(r);
fail_unless( ASTNode_getType (c) == AST_DIVIDE, NULL );
fail_unless( ASTNode_getCharacter (c) == '/', NULL );
fail_unless( ASTNode_getNumChildren(c) == 2 , NULL );
c = ASTNode_getLeftChild(c);
fail_unless( ASTNode_getType (c) == AST_REAL_E, NULL );
fail_unless( ASTNode_getMantissa (c) == -2, NULL );
fail_unless( ASTNode_getExponent (c) == 100, NULL );
fail_unless( ASTNode_getReal (c) == -2e+100, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
c = ASTNode_getRightChild( ASTNode_getRightChild(r) );
fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (c) == 3, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
ASTNode_free(r);
}
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_SBML_parseFormula_8)
{
ASTNode_t *r = SBML_parseFormula("(1 - 2) * 3");
ASTNode_t *c;
fail_unless( ASTNode_getType (r) == AST_TIMES, NULL );
fail_unless( ASTNode_getCharacter (r) == '*', NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
c = ASTNode_getLeftChild(r);
fail_unless( ASTNode_getType (c) == AST_MINUS, NULL );
fail_unless( ASTNode_getCharacter (c) == '-', NULL );
fail_unless( ASTNode_getNumChildren(c) == 2, NULL );
c = ASTNode_getRightChild(r);
fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (c) == 3, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
c = ASTNode_getLeftChild( ASTNode_getLeftChild(r) );
fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (c) == 1, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
c = ASTNode_getRightChild( ASTNode_getLeftChild(r) );
fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (c) == 2, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
ASTNode_free(r);
}
END_TEST
START_TEST (test_SBML_parseFormula_2)
{
ASTNode_t *r = SBML_parseFormula("2.1");
fail_unless( ASTNode_getType (r) == AST_REAL, NULL );
fail_unless( ASTNode_getReal (r) == 2.1, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
}
END_TEST
START_TEST (test_SBML_parseFormula_negInf)
{
ASTNode_t *r = SBML_parseFormula("-inf");
fail_unless( ASTNode_getType(r) == AST_REAL, NULL );
fail_unless( util_isInf(ASTNode_getReal(r)) == -1, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
}
END_TEST
START_TEST (test_SBML_parseFormula_1)
{
ASTNode_t *r = SBML_parseFormula("1");
fail_unless( ASTNode_getType (r) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (r) == 1, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
}
END_TEST
START_TEST (test_SBML_parseFormula_negZero)
{
ASTNode_t *r = SBML_parseFormula("-0.0");
fail_unless( ASTNode_getType(r) == AST_REAL, NULL );
fail_unless( util_isNegZero(ASTNode_getReal(r)) == 1, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
}
END_TEST
START_TEST (test_SBML_parseFormula_13)
{
ASTNode_t *r = SBML_parseFormula("foo()");
fail_unless( ASTNode_getType(r) == AST_FUNCTION , NULL );
fail_unless( !strcmp(ASTNode_getName(r), "foo") , NULL );
fail_unless( ASTNode_getNumChildren(r) == 0 , NULL );
ASTNode_free(r);
}
END_TEST
START_TEST (test_SBML_parseFormula_3)
{
ASTNode_t *r = SBML_parseFormula("2.1e5");
fail_unless( ASTNode_getType (r) == AST_REAL_E, NULL );
fail_unless( ASTNode_getMantissa (r) == 2.1, NULL );
fail_unless( ASTNode_getExponent (r) == 5, NULL );
fail_unless( ASTNode_getNumChildren(r) == 0, NULL );
ASTNode_free(r);
}
END_TEST
START_TEST (test_SBML_parseFormula_12)
{
ASTNode_t *r = SBML_parseFormula("2 * foo^bar + 3.0");
ASTNode_t *c;
fail_unless( ASTNode_getType (r) == AST_PLUS, NULL );
fail_unless( ASTNode_getCharacter (r) == '+', NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
c = ASTNode_getLeftChild(r);
fail_unless( ASTNode_getType (c) == AST_TIMES, NULL );
fail_unless( ASTNode_getCharacter (c) == '*', NULL );
fail_unless( ASTNode_getNumChildren(c) == 2 , NULL );
c = ASTNode_getRightChild(r);
fail_unless( ASTNode_getType (c) == AST_REAL, NULL );
fail_unless( ASTNode_getReal (c) == 3.0, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0 , NULL );
c = ASTNode_getLeftChild( ASTNode_getLeftChild(r) );
fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (c) == 2, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
c = ASTNode_getRightChild( ASTNode_getLeftChild(r) );
fail_unless( ASTNode_getType (c) == AST_POWER, NULL );
fail_unless( ASTNode_getCharacter (c) == '^', NULL );
fail_unless( ASTNode_getNumChildren(c) == 2 , NULL );
c = ASTNode_getLeftChild( ASTNode_getRightChild( ASTNode_getLeftChild(r) ) );
fail_unless( ASTNode_getType(c) == AST_NAME , NULL );
fail_unless( !strcmp(ASTNode_getName(c), "foo") , NULL );
fail_unless( ASTNode_getNumChildren(c) == 0 , NULL );
c = ASTNode_getRightChild( ASTNode_getRightChild( ASTNode_getLeftChild(r) ) );
fail_unless( ASTNode_getType(c) == AST_NAME , NULL );
fail_unless( !strcmp(ASTNode_getName(c), "bar") , NULL );
fail_unless( ASTNode_getNumChildren(c) == 0 , NULL );
ASTNode_free(r);
}
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;
}
/**
* Visits the given ASTNode and continues the inorder traversal.
*/
void
L3FormulaFormatter_visitOther ( const ASTNode_t *parent,
const ASTNode_t *node,
StringBuffer_t *sb,
const L3ParserSettings_t *settings )
{
unsigned int numChildren = ASTNode_getNumChildren(node);
unsigned int group = L3FormulaFormatter_isGrouped(parent, node, settings);
unsigned int n;
if (group)
{
StringBuffer_appendChar(sb, '(');
}
if (numChildren == 0) {
L3FormulaFormatter_format(sb, node, settings);
}
else if (numChildren == 1)
{
//I believe this would only be called for invalid ASTNode setups,
// but this could in theory occur. This is the safest
// behavior I can think of.
L3FormulaFormatter_format(sb, node, settings);
StringBuffer_appendChar(sb, '(');
L3FormulaFormatter_visit( node, ASTNode_getChild(node, 0), sb, settings);
StringBuffer_appendChar(sb, ')');
}
else {
L3FormulaFormatter_visit( node, ASTNode_getChild(node, 0), sb, settings);
for (n = 1; n < numChildren; n++)
{
L3FormulaFormatter_format(sb, node, settings);
L3FormulaFormatter_visit( node, ASTNode_getChild(node, n), sb, settings);
}
}
if (group)
{
StringBuffer_appendChar(sb, ')');
}
}
/**
* Visits the given ASTNode as a function. For this node only the
* traversal is preorder.
* Writes the function as a directed graph and appends the result
* to the StringBuffer.
*/
void
FormulaGraphvizFormatter_visitFunction (const ASTNode_t *parent,
const ASTNode_t *node,
StringBuffer_t *sb )
{
unsigned int numChildren = ASTNode_getNumChildren(node);
unsigned int n;
char *name;
char *uniqueName;
uniqueName = FormulaGraphvizFormatter_getUniqueName(node);
name = FormulaGraphvizFormatter_format(node);
StringBuffer_append(sb, uniqueName);
StringBuffer_append(sb, " [shape=box, label=");
StringBuffer_append(sb, name);
StringBuffer_append(sb, "];\n");
if (parent != NULL)
{
name = FormulaGraphvizFormatter_getUniqueName(node);
uniqueName = FormulaGraphvizFormatter_getUniqueName(parent);
if(strcmp(name, uniqueName))
{
StringBuffer_append(sb, uniqueName);
StringBuffer_append(sb, " -> ");
StringBuffer_append(sb, name);
StringBuffer_append(sb, ";\n");
}
}
if (numChildren > 0)
{
FormulaGraphvizFormatter_visit( node, ASTNode_getChild(node, 0), sb );
}
for (n = 1; n < numChildren; n++)
{
FormulaGraphvizFormatter_visit( node, ASTNode_getChild(node, n), sb );
}
}
END_TEST
START_TEST (test_FunctionDefinition_getBody)
{
const ASTNode_t *math;
ASTNode_t * math1 = SBML_parseFormula("lambda(x, x)");
FunctionDefinition_setMath(FD, math1 );
math = FunctionDefinition_getBody(FD);
fail_unless( math != NULL );
fail_unless( ASTNode_isName(math) );
fail_unless( !strcmp(ASTNode_getName(math), "x") );
fail_unless( ASTNode_getNumChildren(math) == 0 );
ASTNode_free(math1);
}
void pre_ev_alter_tree_structure(ASTNode_t **node_p, ASTNode_t *parent, int child_order, ASTNode_t *delay_math){
unsigned int i;
ASTNode_t *node, *next_node, *delay_node;
node = *node_p;
for(i=0; i<ASTNode_getNumChildren(node); i++){
next_node = ASTNode_getChild(node, i);
pre_ev_alter_tree_structure(&next_node, *node_p, i, delay_math);
}
if(ASTNode_getType(node) == AST_NAME){
delay_node = ASTNode_createWithType(AST_FUNCTION_DELAY);
ASTNode_addChild(delay_node, node);
ASTNode_addChild(delay_node, delay_math);
if(parent != NULL){
ASTNode_replaceChild(parent, child_order, delay_node);
}else{
*node_p = delay_node;
}
}
}
/**
* Visits the given ASTNode and continues the inorder traversal.
* Writes the function as a directed graph and appends the result
* to the StringBuffer.
*/
void
FormulaGraphvizFormatter_visitOther (const ASTNode_t *parent,
const ASTNode_t *node,
StringBuffer_t *sb )
{
unsigned int numChildren = ASTNode_getNumChildren(node);
char *name;
char *uniqueName;
if (numChildren > 0)
{
uniqueName = FormulaGraphvizFormatter_getUniqueName(node);
name = FormulaGraphvizFormatter_format(node);
StringBuffer_append(sb, uniqueName);
StringBuffer_append(sb, " [shape=box, label=");
StringBuffer_append(sb, name);
StringBuffer_append(sb, "];\n");
FormulaGraphvizFormatter_visit( node, ASTNode_getLeftChild(node), sb );
}
if (parent != NULL)
{
name = FormulaGraphvizFormatter_getUniqueName(node);
uniqueName = FormulaGraphvizFormatter_getUniqueName(parent);
if(strcmp(name, uniqueName))
{
StringBuffer_append(sb, uniqueName);
StringBuffer_append(sb, " -> ");
StringBuffer_append(sb, name);
StringBuffer_append(sb, ";\n");
}
}
if (numChildren > 1)
{
FormulaGraphvizFormatter_visit( node, ASTNode_getRightChild(node), sb );
}
}
END_TEST
START_TEST (test_SBML_parseFormula_11)
{
ASTNode_t *r = SBML_parseFormula("1 - -foo / 3");
ASTNode_t *c;
fail_unless( ASTNode_getType (r) == AST_MINUS, NULL );
fail_unless( ASTNode_getCharacter (r) == '-', NULL );
fail_unless( ASTNode_getNumChildren(r) == 2 , NULL );
c = ASTNode_getLeftChild(r);
fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (c) == 1, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
c = ASTNode_getRightChild(r);
fail_unless( ASTNode_getType (c) == AST_DIVIDE, NULL );
fail_unless( ASTNode_getCharacter (c) == '/', NULL );
fail_unless( ASTNode_getNumChildren(c) == 2, NULL );
c = ASTNode_getLeftChild( ASTNode_getRightChild(r) );
fail_unless( ASTNode_getType (c) == AST_MINUS, NULL );
fail_unless( ASTNode_getCharacter (c) == '-', NULL );
fail_unless( ASTNode_getNumChildren(c) == 1 , NULL );
c = ASTNode_getLeftChild( ASTNode_getLeftChild( ASTNode_getRightChild(r) ) );
fail_unless( ASTNode_getType(c) == AST_NAME , NULL );
fail_unless( !strcmp(ASTNode_getName(c), "foo") , NULL );
fail_unless( ASTNode_getNumChildren(c) == 0 , NULL );
c = ASTNode_getRightChild( ASTNode_getRightChild(r) );
fail_unless( ASTNode_getType (c) == AST_INTEGER, NULL );
fail_unless( ASTNode_getInteger (c) == 3, NULL );
fail_unless( ASTNode_getNumChildren(c) == 0, NULL );
ASTNode_free(r);
}
//This function determines if the node in question should be
// expressed in the form "functioname(children)" or if
// it should be expressed as "child1 [symbol] child2 [symbol] child3"
// etc.
int
L3FormulaFormatter_isFunction (const ASTNode_t *node,
const L3ParserSettings_t *settings)
{
if (node==NULL) return 0;
switch(ASTNode_getType(node))
{
case AST_PLUS:
case AST_TIMES:
case AST_LOGICAL_AND:
case AST_LOGICAL_OR:
if (ASTNode_getNumChildren(node) >= 2) {
return 0;
}
return 1;
case AST_RELATIONAL_EQ:
case AST_RELATIONAL_GEQ:
case AST_RELATIONAL_GT:
case AST_RELATIONAL_LEQ:
case AST_RELATIONAL_LT:
if (ASTNode_getNumChildren(node) == 2) {
return 0;
}
return 1;
case AST_MINUS:
if (ASTNode_getNumChildren(node) == 1) {
return 0;
}
case AST_DIVIDE:
case AST_RELATIONAL_NEQ:
case AST_POWER:
case AST_FUNCTION_POWER:
if (ASTNode_getNumChildren(node) == 2) {
return 0;
}
return 1;
case AST_LOGICAL_NOT:
if (ASTNode_getNumChildren(node) == 1) {
return 0;
}
return 1;
case AST_INTEGER:
case AST_REAL:
case AST_REAL_E:
case AST_RATIONAL:
case AST_NAME:
case AST_NAME_AVOGADRO:
case AST_NAME_TIME:
case AST_CONSTANT_E:
case AST_CONSTANT_FALSE:
case AST_CONSTANT_PI:
case AST_CONSTANT_TRUE:
/* new elements to the enum that should not get hit */
case AST_QUALIFIER_BVAR:
case AST_QUALIFIER_LOGBASE:
case AST_QUALIFIER_DEGREE:
case AST_SEMANTICS:
case AST_CONSTRUCTOR_PIECE:
case AST_CONSTRUCTOR_OTHERWISE:
return 0;
case AST_LOGICAL_XOR:
case AST_LAMBDA:
case AST_FUNCTION:
case AST_FUNCTION_ABS:
case AST_FUNCTION_ARCCOS:
case AST_FUNCTION_ARCCOSH:
case AST_FUNCTION_ARCCOT:
case AST_FUNCTION_ARCCOTH:
case AST_FUNCTION_ARCCSC:
case AST_FUNCTION_ARCCSCH:
case AST_FUNCTION_ARCSEC:
case AST_FUNCTION_ARCSECH:
case AST_FUNCTION_ARCSIN:
case AST_FUNCTION_ARCSINH:
case AST_FUNCTION_ARCTAN:
case AST_FUNCTION_ARCTANH:
case AST_FUNCTION_CEILING:
case AST_FUNCTION_COS:
case AST_FUNCTION_COSH:
case AST_FUNCTION_COT:
case AST_FUNCTION_COTH:
case AST_FUNCTION_CSC:
case AST_FUNCTION_CSCH:
case AST_FUNCTION_DELAY:
case AST_FUNCTION_EXP:
case AST_FUNCTION_FACTORIAL:
case AST_FUNCTION_FLOOR:
case AST_FUNCTION_LN:
case AST_FUNCTION_LOG:
case AST_FUNCTION_PIECEWISE:
case AST_FUNCTION_ROOT:
case AST_FUNCTION_SEC:
case AST_FUNCTION_SECH:
case AST_FUNCTION_SIN:
case AST_FUNCTION_SINH:
case AST_FUNCTION_TAN:
case AST_FUNCTION_TANH:
case AST_UNKNOWN:
return 1;
/* this one will need work */
case AST_ORIGINATES_IN_PACKAGE:
return 0;
}
//Shouldn't ever get here
assert(0);
return 1;
}
void check_AST(ASTNode_t* node, ASTNode_t* parent) {
unsigned int i;
int type;
ASTNode_t *checker;
if(node == NULL) {
return;
}
checker = parent;
for(i=0; i<ASTNode_getNumChildren(node); i++) {
parent = node;
check_AST(ASTNode_getChild(node, i), parent);
}
type = ASTNode_getType(node);
switch(type) {
case AST_PLUS:
TRACE(("+ "));
break;
case AST_MINUS:
TRACE(("- "));
break;
case AST_TIMES:
TRACE(("* "));
break;
case AST_DIVIDE:
TRACE(("/ "));
break;
case AST_POWER:
TRACE(("pow "));
break;
case AST_INTEGER:
TRACE(("integer(%ld) ", ASTNode_getInteger(node)));
break;
case AST_REAL:
TRACE(("real(%lf) ", ASTNode_getReal(node)));
break;
case AST_REAL_E:
TRACE(("real_E "));
break;
case AST_RATIONAL:
TRACE(("rational "));
break;
case AST_NAME:
TRACE(("name(%s) ", ASTNode_getName(node)));
break;
case AST_NAME_AVOGADRO:
TRACE(("avogadro "));
break;
case AST_NAME_TIME:
TRACE(("time "));
break;
case AST_CONSTANT_E:
TRACE(("constant "));
break;
case AST_CONSTANT_FALSE:
TRACE(("constant_false "));
break;
case AST_CONSTANT_PI:
TRACE(("pi "));
break;
case AST_CONSTANT_TRUE:
TRACE(("constant_true "));
break;
case AST_LAMBDA:
TRACE(("lambda "));
break;
case AST_FUNCTION:
TRACE(("function(%s) ", ASTNode_getName(node)));
break;
case AST_FUNCTION_ABS:
TRACE(("abs "));
break;
case AST_FUNCTION_ARCCOS:
TRACE(("arccos "));
break;
case AST_FUNCTION_ARCCOSH:
TRACE(("arccosh "));
break;
case AST_FUNCTION_ARCCOT:
TRACE(("arccot "));
break;
case AST_FUNCTION_ARCCOTH:
TRACE(("arccoth "));
break;
case AST_FUNCTION_ARCCSC:
TRACE(("arccsc "));
break;
case AST_FUNCTION_ARCCSCH:
TRACE(("arccsch "));
break;
case AST_FUNCTION_ARCSEC:
TRACE(("arcsec "));
break;
case AST_FUNCTION_ARCSECH:
TRACE(("arcsech "));
break;
case AST_FUNCTION_ARCSIN:
TRACE(("arcsin "));
break;
case AST_FUNCTION_ARCSINH:
TRACE(("arcsinh "));
break;
case AST_FUNCTION_ARCTAN:
TRACE(("arctan "));
break;
case AST_FUNCTION_ARCTANH:
TRACE(("arctanh "));
break;
case AST_FUNCTION_CEILING:
TRACE(("ceil "));
break;
case AST_FUNCTION_COS:
TRACE(("cos "));
break;
case AST_FUNCTION_COSH:
TRACE(("cosh "));
break;
case AST_FUNCTION_COT:
TRACE(("cot "));
break;
case AST_FUNCTION_COTH:
TRACE(("coth "));
break;
case AST_FUNCTION_CSC:
TRACE(("csc "));
break;
case AST_FUNCTION_CSCH:
TRACE(("csch "));
break;
case AST_FUNCTION_DELAY:
TRACE(("delay "));
break;
case AST_FUNCTION_EXP:
TRACE(("exp "));
break;
case AST_FUNCTION_FACTORIAL:
TRACE(("! "));
break;
case AST_FUNCTION_FLOOR:
TRACE(("floor "));
break;
case AST_FUNCTION_LN:
TRACE(("ln "));
break;
case AST_FUNCTION_LOG:
TRACE(("log10 "));
break;
case AST_FUNCTION_PIECEWISE:
TRACE(("piecewise "));
break;
case AST_FUNCTION_POWER:
TRACE(("f_pow "));
break;
case AST_FUNCTION_ROOT:
TRACE(("sqrt "));
break;
case AST_FUNCTION_SEC:
TRACE(("sec "));
break;
case AST_FUNCTION_SECH:
TRACE(("sech "));
break;
case AST_FUNCTION_SIN:
TRACE(("sin "));
break;
case AST_FUNCTION_SINH:
TRACE(("sinh "));
break;
case AST_FUNCTION_TAN:
TRACE(("tan "));
break;
case AST_FUNCTION_TANH:
TRACE(("tanh "));
break;
case AST_LOGICAL_AND:
TRACE(("and "));
break;
case AST_LOGICAL_NOT:
TRACE(("not "));
break;
case AST_LOGICAL_OR:
TRACE(("or "));
break;
case AST_LOGICAL_XOR:
TRACE(("xor "));
break;
case AST_RELATIONAL_EQ:
TRACE(("eq "));
break;
case AST_RELATIONAL_GEQ:
TRACE(("geq "));
break;
case AST_RELATIONAL_GT:
TRACE(("gt "));
break;
case AST_RELATIONAL_LEQ:
TRACE(("leq "));
break;
case AST_RELATIONAL_LT:
TRACE(("lt "));
break;
case AST_RELATIONAL_NEQ:
TRACE(("neq "));
break;
case AST_UNKNOWN:
TRACE(("unknown "));
break;
}
if(checker == NULL) {
TRACE(("\n\n"));
}
}
/**
* The function evalAST(ASTNode_t) evaluates the formula of an
* Abstract Syntax Tree by simple recursion and returns the result
* as a double value.
*
* If variables (ASTNodeType_t AST_NAME) occur in the formula the user is
* asked to provide a numerical value. When evaluating ASTs within an SBML
* document or simulating an SBML model this node type includes parameters
* and variables of the model. Parameters should be retrieved from the
* SBML file, time and variables from current values of the simulation.
*
* Not implemented:
*
* - PIECEWISE, LAMBDA, and the SBML model specific functions DELAY and
* TIME and user-defined functions.
*
* - Complex numbers and/or checking for domains of trigonometric and root
* functions.
*
* - Checking for precision and rounding errors.
*
* The Nodetypes AST_TIME, AST_DELAY and AST_PIECEWISE default to 0. The
* SBML DELAY function and unknown functions (SBML user-defined functions)
* use the value of the left child (first argument to function) or 0 if the
* node has no children.
*/
double
evalAST(ASTNode_t *n)
{
int i;
double result;
int childnum = ASTNode_getNumChildren(n);
ASTNode_t **child = (ASTNode_t **) malloc(childnum * sizeof(ASTNode_t*));
for (i = 0; i < childnum; i++)
{
child[i] = ASTNode_getChild(n, i);
}
switch (ASTNode_getType(n))
{
case AST_INTEGER:
result = (double) ASTNode_getInteger(n);
break;
case AST_REAL:
result = ASTNode_getReal(n);
break;
case AST_REAL_E:
result = ASTNode_getReal(n);
break;
case AST_RATIONAL:
result = ASTNode_getReal(n);
break;
case AST_NAME:
{
char *l;
double var;
printf("\n-------------MESSAGE FROM EVALUATION FUNCTION-------------\n");
printf("Please enter a number for the variable!\n");
printf("If you do not enter a valid number (empty or characters), the \n");
printf("evaluation will proceed with a current internal value and the \n");
printf("result will make no sense.\n");
printf("%s=",ASTNode_getName(n));
l = get_line(stdin);
sscanf(l, "%lf", &var);
free(l);
printf("%s = %f\n", ASTNode_getName(n), var);
printf("-----------------------END MESSAGE--------------------------\n\n");
result = var;
}
break;
case AST_FUNCTION_DELAY:
printf("\n-------------MESSAGE FROM EVALUATION FUNCTION-------------\n");
printf("Delays can only be evaluated during a time series simulation.\n");
printf("The value of the first child (ie. the first argument to the function)\n");
printf("is used for this evaluation. If the function node has no children the\n");
printf("value defaults to 0.\n");
printf("-----------------------END MESSAGE--------------------------\n\n");
if(i>0)
result = evalAST(child[0]);
else
result = 0.0;
break;
case AST_NAME_TIME:
printf("\n-------------MESSAGE FROM EVALUATION FUNCTION-------------\n");
printf("The time can only be evaluated during a time series simulation.\n");
printf("The value of defaults to 0\n");
printf("-----------------------END MESSAGE--------------------------\n\n");
result = 0.0;
break;
case AST_CONSTANT_E:
/* exp(1) is used to adjust exponentiale to machine precision */
result = exp(1);
break;
case AST_CONSTANT_FALSE:
result = 0.0;
break;
case AST_CONSTANT_PI:
/* pi = 4 * atan 1 is used to adjust Pi to machine precision */
result = 4.*atan(1.);
break;
case AST_CONSTANT_TRUE:
result = 1.0;
break;
case AST_PLUS:
result = evalAST(child[0]) + evalAST(child[1]);
break;
case AST_MINUS:
if(childnum==1)
result = - (evalAST(child[0]));
else
result = evalAST(child[0]) - evalAST(child[1]);
break;
case AST_TIMES:
result = evalAST(child[0]) * evalAST(child[1]) ;
break;
case AST_DIVIDE:
result = evalAST(child[0]) / evalAST(child[1]);
break;
case AST_POWER:
result = pow(evalAST(child[0]),evalAST(child[1]));
break;
case AST_LAMBDA:
printf("\n-------------MESSAGE FROM EVALUATION FUNCTION-------------\n");
printf("This function is not implemented yet.\n");
printf("The value defaults to 0.\n");
printf("-----------------------END MESSAGE--------------------------\n\n");
result = 0.0;
break;
case AST_FUNCTION:
printf("\n-------------MESSAGE FROM EVALUATION FUNCTION-------------\n");
printf("This function is not known.\n");
printf("Within an SBML document new functions can be defined by the user or \n");
printf("application. The value of the first child (ie. the first argument to \n");
printf("the function) is used for this evaluation. If the function node has\n");
printf("no children the value defaults to 0.\n");
printf("-----------------------END MESSAGE--------------------------\n\n");
if(childnum>0)
result = evalAST(child[0]);
else
result = 0.0;
break;
case AST_FUNCTION_ABS:
result = (double) fabs(evalAST(child[0]));
break;
case AST_FUNCTION_ARCCOS:
result = acos(evalAST(child[0])) ;
break;
case AST_FUNCTION_ARCCOSH:
#ifndef WIN32
result = acosh(evalAST(child[0]));
#else
result = log(evalAST(child[0]) + SQR(evalAST(child[0]) * evalAST(child[0]) - 1.));
#endif
break;
case AST_FUNCTION_ARCCOT:
/* arccot x = arctan (1 / x) */
result = atan(1./ evalAST(child[0]));
break;
case AST_FUNCTION_ARCCOTH:
/* arccoth x = 1/2 * ln((x+1)/(x-1)) */
result = ((1./2.)*log((evalAST(child[0])+1.)/(evalAST(child[0])-1.)) );
break;
case AST_FUNCTION_ARCCSC:
/* arccsc(x) = Arctan(1 / sqrt((x - 1)(x + 1))) */
result = atan( 1. / SQRT( (evalAST(child[0])-1.)*(evalAST(child[0])+1.) ) );
break;
case AST_FUNCTION_ARCCSCH:
/* arccsch(x) = ln((1 + sqrt(1 + x^2)) / x) */
result = log((1.+SQRT((1+SQR(evalAST(child[0]))))) /evalAST(child[0]));
break;
case AST_FUNCTION_ARCSEC:
/* arcsec(x) = arctan(sqrt((x - 1)(x + 1))) */
result = atan( SQRT( (evalAST(child[0])-1.)*(evalAST(child[0])+1.) ) );
break;
case AST_FUNCTION_ARCSECH:
/* arcsech(x) = ln((1 + sqrt(1 - x^2)) / x) */
result = log((1.+pow((1-SQR(evalAST(child[0]))),0.5))/evalAST(child[0]));
break;
case AST_FUNCTION_ARCSIN:
result = asin(evalAST(child[0]));
break;
case AST_FUNCTION_ARCSINH:
#ifndef WIN32
result = asinh(evalAST(child[0]));
#else
result = log(evalAST(child[0]) + SQR(evalAST(child[0]) * evalAST(child[0]) + 1.));
#endif
break;
case AST_FUNCTION_ARCTAN:
result = atan(evalAST(child[0]));
break;
case AST_FUNCTION_ARCTANH:
#ifndef WIN32
result = atanh(evalAST(child[0]));
#else
result = log((1. / evalAST(child[0]) + 1.) / (1. / evalAST(child[0]) - 1.)) / 2.;
#endif
break;
case AST_FUNCTION_CEILING:
result = ceil(evalAST(child[0]));
break;
case AST_FUNCTION_COS:
result = cos(evalAST(child[0]));
break;
case AST_FUNCTION_COSH:
result = cosh(evalAST(child[0]));
break;
case AST_FUNCTION_COT:
/* cot x = 1 / tan x */
result = (1./tan(evalAST(child[0])));
break;
case AST_FUNCTION_COTH:
/* coth x = cosh x / sinh x */
result = cosh(evalAST(child[0])) / sinh(evalAST(child[0]));
break;
case AST_FUNCTION_CSC:
/* csc x = 1 / sin x */
result = (1./sin(evalAST(child[0])));
break;
case AST_FUNCTION_CSCH:
/* csch x = 1 / cosh x */
result = (1./cosh(evalAST(child[0])));
break;
case AST_FUNCTION_EXP:
result = exp(evalAST(child[0]));
break;
case AST_FUNCTION_FACTORIAL:
{
printf("\n-------------MESSAGE FROM EVALUATION FUNCTION-------------\n");
printf("The factorial is only implemented for integer values. If a floating\n");
printf("point number is passed, the floor value is used for calculation!\n");
printf("-----------------------END MESSAGE--------------------------\n\n");
i = (int)floor(evalAST(child[0]));
for(result=1;i>1;--i)
result *= i;
}
break;
case AST_FUNCTION_FLOOR:
result = floor(evalAST(child[0]));
break;
case AST_FUNCTION_LN:
result = log(evalAST(child[0]));
break;
case AST_FUNCTION_LOG:
result = log10(evalAST(child[0]));
break;
case AST_FUNCTION_PIECEWISE:
printf("\n-------------MESSAGE FROM EVALUATION FUNCTION-------------\n");
printf("This function is not implemented yet.\n");
printf("The value defaults to 0.\n");
printf("-----------------------END MESSAGE--------------------------\n\n");
result = 0.0;
break;
case AST_FUNCTION_POWER:
result = pow(evalAST(child[0]),evalAST(child[1]));
break;
case AST_FUNCTION_ROOT:
result = pow(evalAST(child[1]),(1./evalAST(child[0])));
break;
case AST_FUNCTION_SEC:
/* sec x = 1 / cos x */
result = 1./cos(evalAST(child[0]));
break;
case AST_FUNCTION_SECH:
/* sech x = 1 / sinh x */
result = 1./sinh(evalAST(child[0]));
break;
case AST_FUNCTION_SIN:
result = sin(evalAST(child[0]));
break;
case AST_FUNCTION_SINH:
result = sinh(evalAST(child[0]));
break;
case AST_FUNCTION_TAN:
result = tan(evalAST(child[0]));
break;
case AST_FUNCTION_TANH:
result = tanh(evalAST(child[0]));
break;
case AST_LOGICAL_AND:
result = (double) ((evalAST(child[0])) && (evalAST(child[1])));
break;
case AST_LOGICAL_NOT:
result = (double) (!(evalAST(child[0])));
break;
case AST_LOGICAL_OR:
result = (double) ((evalAST(child[0])) || (evalAST(child[1])));
break;
case AST_LOGICAL_XOR:
result = (double) ((!(evalAST(child[0])) && (evalAST(child[1])))
|| ((evalAST(child[0])) && !(evalAST(child[1]))));
break;
case AST_RELATIONAL_EQ :
result = (double) ((evalAST(child[0])) == (evalAST(child[1])));
break;
case AST_RELATIONAL_GEQ:
result = (double) ((evalAST(child[0])) >= (evalAST(child[1])));
break;
case AST_RELATIONAL_GT:
result = (double) ((evalAST(child[0])) > (evalAST(child[1])));
break;
case AST_RELATIONAL_LEQ:
result = (double) ((evalAST(child[0])) <= (evalAST(child[1])));
break;
case AST_RELATIONAL_LT :
result = (double) ((evalAST(child[0])) < (evalAST(child[1])));
break;
default:
result = 0;
break;
}
free(child);
return result;
}
SBML_ODESOLVER_API double evaluateAST(ASTNode_t *n, cvodeData_t *data)
{
int i, j, childnum;
int found, datafound;
int true;
time_series_t *ts=data->model->time_series;
double findtol=1e-5;
ASTNodeType_t type;
/* ASTNode_t **child; */
/* value* are for intermediate values. */
double value1, value2, value3, result;
if ( n == NULL )
{
SolverError_error(FATAL_ERROR_TYPE,
SOLVER_ERROR_AST_UNKNOWN_NODE_TYPE,
"evaluateAST: empty Abstract Syntax Tree (AST).");
return (0);
}
if ( ASTNode_isUnknown(n) )
{
SolverError_error(FATAL_ERROR_TYPE,
SOLVER_ERROR_AST_UNKNOWN_NODE_TYPE,
"evaluateAST: unknown ASTNode type");
}
result = 0;
childnum = ASTNode_getNumChildren(n);
type = ASTNode_getType(n);
switch(type)
{
case AST_INTEGER:
result = (double) ASTNode_getInteger(n);
break;
case AST_REAL:
result = ASTNode_getReal(n);
break;
case AST_REAL_E:
result = ASTNode_getReal(n);
break;
case AST_RATIONAL:
result = ASTNode_getReal(n) ;
break;
case AST_NAME:
/** VARIABLES:
find the value of the variable in the data->value
array. SOSlib's extension to libSBML's AST allows to add the
index of the variable in this array to AST_NAME
(ASTIndexName). If the ASTNode is not indexed, its array
index is searched via the data->model->names array, which
corresponds to the data->value array. For nodes with name
`Time' or `time' the data->currenttime is returned. If no
value is found a fatal error is produced. */
found = 0;
if ( ASTNode_isSetIndex(n) )
{
if ( ASTNode_isSetData(n) )
{
/* if continuous data is observed, obtain interpolated result */
if ( (data->model->discrete_observation_data != 1) || (data->model->compute_vector_v != 1) )
{
result = call(ASTNode_getIndex(n),
data->currenttime, ts);
}
else /* if discrete data is observed, simply obtain value from time_series */
{
datafound = 0;
i = data->TimeSeriesIndex;
if ( fabs(data->currenttime - ts->time[i]) < findtol )
{
result = ts->data[ASTNode_getIndex(n)][i];
datafound++;
}
if ( datafound != 1)
{
SolverError_error(FATAL_ERROR_TYPE,
SOLVER_ERROR_AST_EVALUATION_FAILED_DISCRETE_DATA,
"use of discrete time series data failed; none or several time points matching current time");
result = 0;
/* break; */
}
else found = 1;
}
}
else
{
/* majority case: just return the
according value from data->values
from the index stored by SOSlib
ASTIndexNameNode sub-class of libSBML's ASTNode */
result = data->value[ASTNode_getIndex(n)];
}
found++;
}
if ( found == 0 )
{
for ( j=0; j<data->nvalues; j++ )
{
if ( (strcmp(ASTNode_getName(n),data->model->names[j]) == 0) )
{
result = data->value[j];
found++;
}
}
}
if ( found == 0 )
{
SolverError_error(FATAL_ERROR_TYPE,
SOLVER_ERROR_AST_EVALUATION_FAILED_MISSING_VALUE,
"No value found for AST_NAME %s . Defaults to Zero "
"to avoid program crash", ASTNode_getName(n));
result = 0;
}
break;
case AST_FUNCTION_DELAY:
SolverError_error(FATAL_ERROR_TYPE,
SOLVER_ERROR_AST_EVALUATION_FAILED_DELAY,
"Solving ODEs with Delay is not implemented. "
"Defaults to 0 to avoid program crash");
result = 0.0;
break;
case AST_NAME_TIME:
result = (double) data->currenttime;
break;
case AST_CONSTANT_E:
/** exp(1) is used to adjust exponentiale to machine precision */
result = exp(1.);
break;
case AST_CONSTANT_FALSE:
result = 0.0;
break;
case AST_CONSTANT_PI:
/** pi = 4 * atan 1 is used to adjust Pi to machine precision */
result = 4.*atan(1.);
break;
case AST_CONSTANT_TRUE:
result = 1.0;
break;
case AST_PLUS:
result = 0.0;
for ( i=0; i<childnum; i++)
result += evaluateAST(child(n,i),data);
break;
case AST_MINUS:
if ( childnum<2 )
result = - (evaluateAST(child(n,0),data));
else
result = evaluateAST(child(n,0),data) - evaluateAST(child(n,1),data);
break;
case AST_TIMES:
result = 1.0;
for ( i=0; i<childnum; i++)
{
result *= evaluateAST(child(n,i),data);
if (result == 0.0) break; /* small optimization by skipping the rest of children */
}
break;
case AST_DIVIDE:
result = evaluateAST(child(n,0),data) / evaluateAST(child(n,1),data);
break;
case AST_POWER:
result = pow(evaluateAST(child(n,0),data),evaluateAST(child(n,1),data));
break;
case AST_LAMBDA:
SolverError_error(FATAL_ERROR_TYPE,
SOLVER_ERROR_AST_EVALUATION_FAILED_LAMBDA,
"Lambda can only be used in SBML function definitions."
" Defaults to 0 to avoid program crash");
result = 0.0;
break;
/** FUNCTIONS: */
case AST_FUNCTION:
/** Evaluate external functions, if it was set with
setUserDefinedFunction */
if ( UsrDefFunc == NULL )
{
SolverError_error(FATAL_ERROR_TYPE,
SOLVER_ERROR_AST_EVALUATION_FAILED_FUNCTION,
"The function %s() has not been defined "
"in the SBML input model or as an externally "
"supplied function. Defaults to 0 to avoid "
"program crash",
ASTNode_getName(n));
result = 0.0;
}
else
{
double *func_vals = NULL;
ASSIGN_NEW_MEMORY_BLOCK(func_vals, childnum+1, double, 0);
for ( i=0; i<childnum; i++ )
func_vals[i] = evaluateAST(child(n,i), data);
result = UsrDefFunc((char *)ASTNode_getName(n), childnum, func_vals);
free(func_vals);
}
break;
case AST_FUNCTION_ABS:
result = fabs(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_ARCCOS:
result = acos(evaluateAST(child(n,0),data)) ;
break;
case AST_FUNCTION_ARCCOSH:
result = aCosh(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_ARCCOT:
/** arccot x = arctan (1 / x) */
result = atan(1./ evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_ARCCOTH:
/** arccoth x = 1/2 * ln((x+1)/(x-1)) */
value1 = evaluateAST(child(n,0),data);
result = log((value1 + 1) / (value1 - 1))/2;
break;
case AST_FUNCTION_ARCCSC:
/** arccsc(x) = Arctan(1 / sqrt((x - 1)(x + 1))) */
value1 = evaluateAST(child(n,0),data);
result = atan(1/sqrt((value1-1)*(value1+1)));
break;
case AST_FUNCTION_ARCCSCH:
/** arccsch(x) = ln((1/x) + sqrt((1/(x*x)) + 1)) */
value1 = evaluateAST(child(n,0),data);
result = log(1/value1 + sqrt(1/(value1*value1)+1));
break;
case AST_FUNCTION_ARCSEC:
/** arcsec(x) = arccos(1/x) */
result = acos(1/evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_ARCSECH:
/* arcsech(x) = arccosh(1/x) */
result = aCosh( 1. / evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_ARCSIN:
result = asin(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_ARCSINH:
result = aSinh(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_ARCTAN:
result = atan(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_ARCTANH:
result = aTanh(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_CEILING:
result = ceil(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_COS:
result = cos(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_COSH:
result = cosh(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_COT:
/** cot x = 1 / tan x */
result = (1./tan(evaluateAST(child(n,0),data)));
break;
case AST_FUNCTION_COTH:
/** coth x = cosh x / sinh x */
result = 1/tanh(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_CSC:
/** csc x = 1 / sin x */
result = (1./sin(evaluateAST(child(n,0),data)));
break;
case AST_FUNCTION_CSCH:
/** csch x = 1 / sinh x */
result = (1./sinh(evaluateAST(child(n,0),data)));
break;
case AST_FUNCTION_EXP:
result = exp(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_FACTORIAL:
{
int j;
value1 = evaluateAST(child(n,0),data);
j = floor(value1);
if ( value1 != j )
SolverError_error(FATAL_ERROR_TYPE,
SOLVER_ERROR_AST_EVALUATION_FAILED_FLOAT_FACTORIAL,
"The factorial is only implemented."
"for integer values. The floor value of the "
"passed float is used for calculation!");
for(result=1;j>1;--j)
result *= j;
}
break;
case AST_FUNCTION_FLOOR:
result = floor(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_LN:
result = log(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_LOG:
/** log(x,y) = log10(y)/log10(x) (where x is the base) */
result = log10(evaluateAST(child(n,1),data)) /
log10(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_PIECEWISE:
/** Piecewise: */
found = 0;
/** Go through n pieces with 2 AST children for each piece, */
for ( i=0; i<(childnum-1); i=i+2 )
{
if ( evaluateAST(child(n, i+1), data) )
{
found++;
result = evaluateAST(child(n, i), data);
}
}
/** odd number of AST children: if no piece was true, otherwise remains */
/* i should be equal to childnum for even number piecewise AST
and equal to childnum-1 for odd numbered piecewise ASTs */
if ( i == childnum-1 && found == 0 )
{
found++;
result = evaluateAST(child(n, i), data);
}
if ( found == 0 )
SolverError_error(FATAL_ERROR_TYPE,
SOLVER_ERROR_AST_EVALUATION_FAILED_PIECEWISE,
"Piecewise function failed; no true piece");
if ( found > 1 )
SolverError_error(FATAL_ERROR_TYPE,
SOLVER_ERROR_AST_EVALUATION_FAILED_PIECEWISE,
"Piecewise function failed; several true pieces");
break;
case AST_FUNCTION_POWER:
result = pow(evaluateAST(child(n,0),data),evaluateAST(child(n,1),data));
break;
case AST_FUNCTION_ROOT:
/*!!! ALSO do this in compiled code */
value1 = evaluateAST(child(n,1),data);
value2 = evaluateAST(child(n,0),data);
value3 = floor(value2);
/* for odd root degrees, negative numbers are OK */
if ( value2 == value3 ) /* check whether degree is integer */
{
if ( (value1 < 0) && ((int)value2 % 2 != 0) )
result = - pow(fabs(value1), 1./value2);
else
result = pow(value1, 1./value2);
}
else
result = pow(value1, 1./value2);
break;
case AST_FUNCTION_SEC:
/** sec x = 1 / cos x */
result = 1./cos(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_SECH:
/** sech x = 1 / cosh x */
result = 1./cosh(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_SIN:
result = sin(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_SINH:
result = sinh(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_TAN:
result = tan(evaluateAST(child(n,0),data));
break;
case AST_FUNCTION_TANH:
result = tanh(evaluateAST(child(n,0),data));
break;
case AST_LOGICAL_AND:
/** AND: all children must be true */
true = 0;
for ( i=0; i<childnum; i++ ) true += evaluateAST(child(n,i),data);
if ( true == childnum ) result = 1.0;
else result = 0.0;
break;
case AST_LOGICAL_NOT:
result = (double) (!(evaluateAST(child(n,0),data)));
break;
case AST_LOGICAL_OR:
/** OR: at least one child must be true */
true = 0;
for ( i=0; i<childnum; i++ ) true += evaluateAST(child(n,i),data);
if ( true > 0 ) result = 1.0;
else result = 0.0;
break;
case AST_LOGICAL_XOR:
/* n-ary: true if an odd number of children is true */
true = 0;
for ( i=0; i<childnum; i++ ) true += evaluateAST(child(n,i),data);
if ( true % 2 != 0 ) result = 1.0;
else result = 0.0;
break;
/* !!! check n-ary definitions for relational operators !!! */
case AST_RELATIONAL_EQ:
/** n-ary: all children must be equal */
result = 1.0;
if (childnum <= 1) break;
value1 = evaluateAST(child(n,0),data);
for ( i=1; i<childnum; i++ )
if ( value1 != evaluateAST(child(n,i),data) )
{
result = 0.0;
break;
}
break;
case AST_RELATIONAL_GEQ:
/** n-ary: each child must be greater than or equal to the following */
result = 1.0;
if (childnum <= 1) break;
value2 = evaluateAST(child(n,0),data);
for ( i=1; i<childnum; i++ )
{
value1 = value2;
value2 = evaluateAST(child(n,i),data);
if (value1 < value2)
{
result = 0.0;
break;
}
}
break;
case AST_RELATIONAL_GT:
/** n-ary: each child must be greater than the following */
result = 1.0;
if (childnum <= 1) break;
value2 = evaluateAST(child(n,0),data);
for ( i=1; i<childnum; i++ )
{
value1 = value2;
value2 = evaluateAST(child(n,i),data);
if (value1 <= value2)
{
result = 0.0;
break;
}
}
break;
case AST_RELATIONAL_LEQ:
/** n-ary: each child must be lower than or equal to the following */
result = 1.0;
if (childnum <= 1) break;
value2 = evaluateAST(child(n,0),data);
for ( i=1; i<childnum; i++ )
{
value1 = value2;
value2 = evaluateAST(child(n,i),data);
if (value1 > value2)
{
result = 0.0;
break;
}
}
break;
case AST_RELATIONAL_LT :
/* n-ary: each child must be lower than the following */
result = 1.0;
if (childnum <= 1) break;
value2 = evaluateAST(child(n,0),data);
for ( i=1; i<childnum; i++ )
{
value1 = value2;
value2 = evaluateAST(child(n,i),data);
if (value1 >= value2)
{
result = 0.0;
break;
}
}
break;
case AST_RELATIONAL_NEQ:
/* binary "not equal" */
result = (evaluateAST(child(n, 0), data) != evaluateAST(child(n, 1), data));
break;
default:
SolverError_error(FATAL_ERROR_TYPE,
SOLVER_ERROR_AST_UNKNOWN_NODE_TYPE,
"evaluateAST: unknown ASTNode type: %d", type);
result = 0;
break;
}
return result;
}
/* Used by getL3Precedence and other functions below.
*/
int isTranslatedModulo (const ASTNode_t* node)
{
const ASTNode_t* child;
const ASTNode_t* c2;
const ASTNode_t* x;
const ASTNode_t* y;
//In l3v2 there may be an actual 'modulo' ASTNode, but for now,
// it's all mimicked by the piecewise function:
// piecewise(x - y * ceil(x / y), xor(x < 0, y < 0), x - y * floor(x / y))
if (ASTNode_getType(node) != AST_FUNCTION_PIECEWISE) return 0;
if (ASTNode_getNumChildren(node) != 3) return 0;
//x - y * ceil(x/y)
child = ASTNode_getChild(node, 0);
if (ASTNode_getType(child) != AST_MINUS) return 0;
if (ASTNode_getNumChildren(child) != 2) return 0;
x = ASTNode_getChild(child, 0);
c2 = ASTNode_getChild(child, 1);
if (ASTNode_getType(c2) != AST_TIMES) return 0;
if (ASTNode_getNumChildren(c2) != 2) return 0;
y = ASTNode_getChild(c2, 0);
c2 = ASTNode_getChild(c2, 1);
if (ASTNode_getType(c2) != AST_FUNCTION_CEILING) return 0;
if (ASTNode_getNumChildren(c2) != 1) return 0;
c2 = ASTNode_getChild(c2, 0);
if (ASTNode_getType(c2) != AST_DIVIDE) return 0;
if (ASTNode_getNumChildren(c2) != 2) return 0;
if (!equals(x, ASTNode_getChild(c2, 0))) return 0;
if (!equals(y, ASTNode_getChild(c2, 1))) return 0;
//xor(x<0, y<0)
child = ASTNode_getChild(node, 1);
if (ASTNode_getType(child) != AST_LOGICAL_XOR) return 0;
if (ASTNode_getNumChildren(child) != 2) return 0;
c2 = ASTNode_getChild(child, 0);
if (ASTNode_getType(c2) != AST_RELATIONAL_LT) return 0;
if (ASTNode_getNumChildren(c2) != 2) return 0;
if (!equals(x, ASTNode_getChild(c2, 0))) return 0;
if (ASTNode_getType(ASTNode_getChild(c2, 1)) != AST_INTEGER) return 0;
if (ASTNode_getInteger(ASTNode_getChild(c2, 1)) != 0) return 0;
c2 = ASTNode_getChild(child, 1);
if (ASTNode_getType(c2) != AST_RELATIONAL_LT) return 0;
if (ASTNode_getNumChildren(c2) != 2) return 0;
if (!equals(y, ASTNode_getChild(c2, 0))) return 0;
if (ASTNode_getType(ASTNode_getChild(c2, 1)) != AST_INTEGER) return 0;
if (ASTNode_getInteger(ASTNode_getChild(c2, 1)) != 0) return 0;
//x - y * floor(x/y)
child = ASTNode_getChild(node, 2);
if (ASTNode_getType(child) != AST_MINUS) return 0;
if (ASTNode_getNumChildren(child) != 2) return 0;
if (!equals(x, ASTNode_getChild(child, 0))) return 0;
c2 = ASTNode_getChild(child, 1);
if (ASTNode_getType(c2) != AST_TIMES) return 0;
if (ASTNode_getNumChildren(c2) != 2) return 0;
if (!equals(y, ASTNode_getChild(c2, 0))) return 0;
c2 = ASTNode_getChild(c2, 1);
if (ASTNode_getType(c2) != AST_FUNCTION_FLOOR) return 0;
if (ASTNode_getNumChildren(c2) != 1) return 0;
c2 = ASTNode_getChild(c2, 0);
if (ASTNode_getType(c2) != AST_DIVIDE) return 0;
if (ASTNode_getNumChildren(c2) != 2) return 0;
if (!equals(x, ASTNode_getChild(c2, 0))) return 0;
if (!equals(y, ASTNode_getChild(c2, 1))) return 0;
return 1;
}
/*
* @return the precedence of this ASTNode as defined in the L3 parser documentation.
*/
int getL3Precedence(const ASTNode_t* node)
{
int precedence;
unsigned int numchildren = ASTNode_getNumChildren(node);
if ( !ASTNode_hasCorrectNumberArguments((ASTNode_t*)node) )
{
//If the number of arguments is wrong, it'll be treated like a function call.
precedence = 8;
}
else if ( isTranslatedModulo(node) )
{
precedence = 5;
}
else
{
switch (ASTNode_getType(node))
{
case AST_POWER:
case AST_FUNCTION_POWER:
//Anything other than two children is caught above, since that's the only correct number of arguments.
precedence = 7;
break;
case AST_LOGICAL_NOT:
//Anything other than unary not is caught above, since that's the wrong number of arguments.
precedence = 6;
break;
case AST_DIVIDE:
case AST_TIMES:
if (numchildren < 2) {
//Written in functional form.
precedence = 8;
}
else {
precedence = 5;
}
break;
case AST_MINUS:
if (numchildren == 1) {
//Unary minus
precedence = 6;
break;
}
//Fallthrough to:
case AST_PLUS:
if (numchildren < 2) {
//Written in functional form (unary minus caught above)
precedence = 8;
}
else {
precedence = 4;
}
break;
case AST_RELATIONAL_EQ:
case AST_RELATIONAL_GEQ:
case AST_RELATIONAL_GT:
case AST_RELATIONAL_LEQ:
case AST_RELATIONAL_LT:
case AST_RELATIONAL_NEQ:
//The relational symbols (==, >=, etc.) are only used when there are two children.
if (numchildren == 2) {
precedence = 3;
}
else {
precedence = 8;
}
break;
case AST_LOGICAL_AND:
case AST_LOGICAL_OR:
//The logical symbols && and || are only used when there are two or more children.
if (numchildren < 2) {
precedence = 8;
}
else {
precedence = 2;
}
break;
default:
precedence = 8;
break;
}
}
return precedence;
}