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;
}
SBML_ODESOLVER_API void CvodeData_initializeValues(cvodeData_t *data)
{
int i;
Parameter_t *p;
Species_t *s;
Compartment_t *c;
odeModel_t *om = data->model;
Model_t *ode = om->simple;
/* First, fill cvodeData_t structure with data from
the derived SBML model */
for ( i=0; i<data->nvalues; i++ ) {
if ( (s = Model_getSpeciesById(ode, om->names[i])) )
data->value[i] = Species_getInitialConcentration(s);
else if ( (c = Model_getCompartmentById(ode, om->names[i])) )
data->value[i] = Compartment_getSize(c);
else if ((p = Model_getParameterById(ode, om->names[i])) )
data->value[i] = Parameter_getValue(p);
}
/* initialize assigned parameters */
for ( i=0; i<om->nass; i++ )
data->value[om->neq+i] = evaluateAST(om->assignment[i],data);
/* set current time to 0 */
data->currenttime = 0.0;
}
SBML_ODESOLVER_API int IntegratorInstance_updateModel(integratorInstance_t *engine)
{
int i;
Species_t *s;
Compartment_t *c;
Parameter_t *p;
odeModel_t *om = engine->om;
cvodeData_t *data = engine->data;
cvodeResults_t *results = engine->results;
int nout = results->nout;
int nvalues = data->nvalues;
Model_t *m = om->m;
for ( i=0; i<nvalues; i++ ) {
if ( (s = Model_getSpeciesById(m, om->names[i]))
!= NULL ) {
Species_setInitialConcentration(s, results->value[i][nout]);
}
else if ( (c = Model_getCompartmentById(m, om->names[i])) != NULL ) {
Compartment_setSize(c, results->value[i][nout]);
}
else if ( (p = Model_getParameterById(m, om->names[i])) != NULL ) {
Parameter_setValue(p, results->value[i][nout]);
}
else
return 0;
}
return 1;
}
static int printXMGLegend(cvodeData_t *data, int nvalues)
{
int i, found;
odeModel_t *om = data->model;
Model_t *m = om->simple;
Species_t *s;
Parameter_t *p;
Compartment_t *c;
for ( i=0; i<nvalues; i++ ) {
found = 0;
if ( (s = Model_getSpeciesById(m, om->names[i])) != NULL ) {
if ( Species_isSetName(s) ) {
GracePrintf("g0.s%d legend \"%s: %s\"\n", i+1,
om->names[i], Species_getName(s));
found++;
}
}
else if ( (c = Model_getCompartmentById(m, om->names[i])) ) {
if ( Compartment_isSetName(c) ) {
GracePrintf("g0.s%d legend \"%s: %s\"\n", i+1,
om->names[i], Compartment_getName(c));
found++;
}
}
else if ( (p = Model_getParameterById(m, om->names[i])) ) {
if ( Parameter_isSetName(p) ) {
GracePrintf("g0.s%d legend \"%s: %s\"\n", i+1,
om->names[i], Parameter_getName(p));
found++;
}
}
if ( found == 0 )
GracePrintf("g0.s%d legend \"%s\"\n", i+1, om->names[i]);
}
GracePrintf("legend 1.155, 0.85");
GracePrintf("legend font 8");
GracePrintf("legend char size 0.6");
return 0;
}
END_TEST
START_TEST (test_SBMLConvert_convertToL1_Species_Concentration)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c =
Compartment_create(2, 1);
Species_t *s =
Species_create(2, 1);
Compartment_setId ( c, sid );
Compartment_setSize ( c, 1.2 );
Model_addCompartment( m, c );
Species_setId ( s, "s" );
Species_setCompartment ( s, sid );
Species_setInitialConcentration( s, 2.34 );
Model_addSpecies ( m, s );
fail_unless( SBMLDocument_setLevelAndVersion(d, 1, 2) == 1, NULL);
/**
* These tests will fail under Cygwin because of a minimal
* setlocale() implementation (see setlocale manpage).
*/
#ifndef CYGWIN
fail_unless( Species_getInitialAmount(Model_getSpecies(m, 0)) == 2.808, NULL );
#endif
Species_t * s1 = Model_getSpecies(m, 0);
fail_unless (s1 != NULL);
fail_unless (!strcmp(Species_getCompartment(s1), "C"));
fail_unless(Compartment_getSize(Model_getCompartmentById(m, "C")) == 1.2);
fail_unless(Species_getInitialConcentration(s1) == 2.34);
fail_unless(Species_isSetInitialConcentration(s1) == 1);
SBMLDocument_free(d);
}
