bool variesIn(string id, Model* model, const map<string, vector<double> >& results)
{
if (variesIn(id, results)) return true;
Rule* rule = model->getRule(id);
if (rule != NULL) {
if (rule->getTypeCode() == SBML_RATE_RULE) return true;
return variesIn(rule->getMath(), model, results);
}
if (!getConstant(id, model, results)) {
//The variable might be set by an algebraic rule
for (unsigned long r=0; r<model->getNumRules(); r++) {
if (model->getRule(r)->getTypeCode() == SBML_ALGEBRAIC_RULE) {
if (appearsIn(id, model->getRule(r)->getMath()) &&
variesBesides(id, model->getRule(r)->getMath(), model, results)) return true;
}
}
}
for (unsigned long e=0; e<model->getNumEvents(); e++) {
Event* event = model->getEvent(e);
for (unsigned long ea=0; ea<event->getNumEventAssignments(); ea++) {
if (event->getEventAssignment(ea)->getVariable() == id) return true;
}
}
Species* species = model->getSpecies(id);
if (species==NULL) return false;
if (species->isSetBoundaryCondition() && species->getBoundaryCondition()==true) return false;
for (unsigned long r=0; r<model->getNumReactions(); r++) {
Reaction* rxn = model->getReaction(r);
if (variesIn(id, rxn->getListOfReactants(), results)) return true;
if (variesIn(id, rxn->getListOfProducts(), results)) return true;
}
return false;
}
void checkSpecies(Model* model, set<string>& components, set<string>& tests, const map<string, vector<double> >& results, int type)
{
//Must call this after 'checkCompartments' because we look in 'tests' for 'NonUnityCompartment'.
if (model->getNumSpecies() > 0) {
components.insert("Species");
if (type==0) {
tests.insert("Amount||Concentration");
}
else if (type==2) {
tests.insert("Amount");
}
set<string> compartments;
for (unsigned int s=0; s<model->getNumSpecies(); s++) {
Species* species = model->getSpecies(s);
if (species->isSetBoundaryCondition() && species->getBoundaryCondition()) {
tests.insert("BoundaryCondition");
}
if (species->getConstant()) {
tests.insert("ConstantSpecies");
}
if (species->isSetConversionFactor()) {
tests.insert("ConversionFactors");
}
if (species->isSetHasOnlySubstanceUnits() && species->getHasOnlySubstanceUnits()) {
tests.insert("HasOnlySubstanceUnits");
}
if (!species->isSetInitialAmount() && !species->isSetInitialConcentration()) {
tests.insert("InitialValueReassigned");
}
else if (species->isSetId() && initialOverriddenIn(species->getId(), model, results, tests)) {
tests.insert("InitialValueReassigned");
}
if (species->isSetCompartment()) {
compartments.insert(species->getCompartment());
}
}
if (tests.find("MultiCompartment") != tests.end() && compartments.size()==1 && model->getNumSpecies() > 1) {
cerr << "Error: multiple compartments discovered, but all species are in a single compartment." << endl;
tests.insert("ERRORMultiCompartment");
}
}
}
void
Model::assignRequiredValues()
{
// when converting to L3 some attributes which have default values in L1/L2
// but are required in L3 are not present or set
unsigned int i, n;
if (getNumUnitDefinitions() > 0)
{
for (i = 0; i < getNumUnitDefinitions(); i++)
{
for (n = 0; n < getUnitDefinition(i)->getNumUnits(); n++)
{
Unit *u = getUnitDefinition(i)->getUnit(n);
if (!u->isSetExponent())
u->setExponent(1.0);
if (!u->isSetScale())
u->setScale(0);
if (!u->isSetMultiplier())
u->setMultiplier(1.0);
}
}
}
if (getNumCompartments() > 0)
{
for (i = 0; i < getNumCompartments(); i++)
{
Compartment *c = getCompartment(i);
c->setConstant(c->getConstant());
}
}
if (getNumSpecies() > 0)
{
for (i = 0; i < getNumSpecies(); i++)
{
Species * s = getSpecies(i);
s->setBoundaryCondition(s->getBoundaryCondition());
s->setHasOnlySubstanceUnits(s->getHasOnlySubstanceUnits());
s->setConstant(s->getConstant());
}
}
if (getNumParameters() > 0)
{
for (i = 0; i < getNumParameters(); i++)
{
Parameter * p = getParameter(i);
p->setConstant(p->getConstant());
}
}
if (getNumReactions() > 0)
{
for (i = 0; i < getNumReactions(); i++)
{
Reaction * r = getReaction(i);
r->setFast(r->getFast());
r->setReversible(r->getReversible());
if (r->getNumReactants() > 0)
{
for (n = 0; n < r->getNumReactants(); n++)
{
SpeciesReference *sr = r->getReactant(n);
if (sr->isSetStoichiometryMath())
{
sr->setConstant(false);
}
else
{
sr->setConstant(true);
}
}
}
if (r->getNumProducts() > 0)
{
for (n = 0; n < r->getNumProducts(); n++)
{
SpeciesReference *sr = r->getProduct(n);
if (sr->isSetStoichiometryMath())
{
sr->setConstant(false);
}
else
{
sr->setConstant(true);
}
}
}
}
}
if (getNumEvents() > 0)
{
for (i = 0; i < getNumEvents(); i++)
{
Event * e = getEvent(i);
e->setUseValuesFromTriggerTime(e->getUseValuesFromTriggerTime());
if (e->isSetTrigger())
{
Trigger *t = e->getTrigger();
t->setPersistent(true);
t->setInitialValue(true);
}
}
}
}
/* create MOLECULE */
map< string,Id > SbmlReader::createMolecule( map< string,Id > &idMap )
{
map<string,Id>molMap;
static const Cinfo* moleculeCinfo = initMoleculeCinfo();
static const Finfo* modeFinfo = moleculeCinfo->findFinfo( "mode" );
static const Finfo* nInitFinfo = moleculeCinfo->findFinfo( "nInit" );
static const Cinfo* kincomptCinfo = initKinComptCinfo();
static const Finfo* dimensionFinfo = kincomptCinfo->findFinfo( "numDimensions" );
static const Finfo* sizeFinfo = kincomptCinfo->findFinfo( "size" );
int num_species = model_->getNumSpecies();
//cout << "num species: " << num_species << endl;
for ( int sindex = 0; sindex < num_species; sindex++ )
{
Species* s = model_->getSpecies(sindex);
if (!s){
//cout << "species " << sindex << " is nul" << endl;
continue;
}
std::string compt = "";
if ( s->isSetCompartment() )
compt = s->getCompartment();
if (compt.length()< 1){
cout << "compt is empty for species "<< sindex << endl;
continue;
}
string id = s->getId();
//cout<<"species is :"<<id<<endl;
if (id.length() < 1){
continue;
}
/*std::string name = "";
if ( s->isSetName() ){
name = s->getName();
}*/
Id comptEl = idMap[compt];
molecule_ = Neutral::create( "Molecule",id,comptEl,Id::scratchId() );//create Molecule
molMap[id] = comptEl;
elmtMap_[id] = Eref( molecule_ );
//printNotes(s);
UnitDefinition * ud = s->getDerivedUnitDefinition();
assert(ud != NULL);
/*string udef = UnitDefinition::printUnits(ud);
//cout << "species unit :" << udef << endl;*/
double initvalue =0.0;
if ( s->isSetInitialConcentration() )
initvalue = s->getInitialConcentration();
else if ( s->isSetInitialAmount() )
initvalue = s->getInitialAmount() ;
else {
cout << "Invalid SBML: Either initialConcentration or initialAmount must be set." << endl;
return molMap;
}
double transvalue = transformUnits(1,ud);
//cout << "initAmount: " << initvalue << endl;
transvalue *= initvalue;
//cout << "transvalue: " << transvalue << endl;
unsigned int dimension;
get< unsigned int >( comptEl.eref(), dimensionFinfo,dimension );
bool initconc = s->isSetInitialConcentration();
if ( dimension > 0 && initconc) {
double size;
get< double > (comptEl.eref(),sizeFinfo,size);
transvalue *= size;
}
::set< double >( molecule_, nInitFinfo, transvalue ); //initialAmount
bool cons=s->getConstant();
bool bcondition = s->getBoundaryCondition();
if (cons){
::set< int >( molecule_,modeFinfo,4 );
//cout << "set constant 4" << endl;
}else if (bcondition) {
::set< int >( molecule_,modeFinfo,1 );
//cout << "set constant 1" << endl;
}else {
::set< int >( molecule_,modeFinfo,0 );
//cout << "set constant 0" << endl;
}
}
return molMap;
}
/* create MOLECULE */
const SbmlReader::sbmlStr_mooseId SbmlReader::createMolecule( map< string,Id > &comptSidMIdMap) {
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
map< string, Id >molSidcmptMIdMap;
double transvalue = 0.0;
int num_species = model_->getNumSpecies();
if (num_species == 0) {
baseId = Id();
errorFlag_ = true;
return molSidcmptMIdMap;
}
for ( int sindex = 0; sindex < num_species; sindex++ ) {
Species* spe = model_->getSpecies(sindex);
if (!spe) {
continue;
}
std::string compt = "";
if ( spe->isSetCompartment() ) {
compt = spe->getCompartment();
}
if (compt.length()< 1) {
//cout << "compt is empty for species "<< sindex << endl;
continue;
}
string id = spe->getId();
if (id.length() < 1) {
continue;
}
std::string name = "";
if ( spe->isSetName() ) {
name = spe->getName();
name = nameString(name);
}
if (name.empty())
name = id;
double initvalue =0.0;
if ( spe->isSetInitialConcentration() )
initvalue = spe->getInitialConcentration();
else if ( spe->isSetInitialAmount() )
initvalue = spe->getInitialAmount() ;
else {
unsigned int nr = model_->getNumRules();
bool found = false;
for ( unsigned int r = 0; r < nr; r++ ) {
Rule * rule = model_->getRule(r);
bool assignRule = rule->isAssignment();
if ( assignRule ) {
string rule_variable = rule->getVariable();
if (rule_variable.compare(id) == 0) {
found = true;
break;
}
}
}
if (found == false) {
cout << "Invalid SBML: Either initialConcentration or initialAmount must be set or it should be found in assignmentRule but non happening for " << spe->getName() <<endl;
return molSidcmptMIdMap;
}
}
Id comptEl = comptSidMIdMap[compt];
Id meshEntry = Neutral::child( comptEl.eref(), "mesh" );
bool constant = spe->getConstant();
bool boundaryCondition = spe->getBoundaryCondition();
if (boundaryCondition == true)
cout << "Pools having BoundaryCondition true " << name <<endl;
Id pool;
//If constant is true then its equivalent to BuffPool in moose
if (constant == true)
//if( (boundaryCondition == true) && (constant==false))
pool = shell->doCreate("BufPool",comptEl,name,1);
else
pool = shell->doCreate("Pool", comptEl, name ,1);
molSidcmptMIdMap[id] = comptEl;
//Map to Molecule SBML id to Moose Id
molSidMIdMap_[id] = pool;
//shell->doAddMsg( "OneToOne",pool, "mesh", meshEntry, "mesh" );
bool bcondition = spe->getBoundaryCondition();
if ( constant == true && bcondition == false)
cout <<"The species "<< name << " should not appear in reactant or product as per sbml Rules"<< endl;
unsigned int spatialDimen =Field< unsigned int >::get( comptEl, "numDimensions");
UnitDefinition * ud = spe->getDerivedUnitDefinition();
assert(ud != NULL);
bool hasonlySubUnit = spe->getHasOnlySubstanceUnits();
//double v = Field< double >::get( comptEl.path(), "volume" );
transvalue = transformUnits(1,ud,"substance",hasonlySubUnit);
if (hasonlySubUnit) {
// In Moose, no. of molecules (nInit) and unit is "item"
if (spatialDimen > 0 && spe->isSetInitialAmount() ) {
//transvalue *= initvalue;
initvalue *=transvalue;
Field < double> :: set( pool, "nInit", initvalue);
}
} else {
//transvalue *=initvalue;
initvalue *=transvalue;
Field <double> :: set(pool, "concInit",initvalue);
}
//cout << " poolMap_ "<< name << " " <<transvalue << " "<< hasonlySubUnit;
//poolMap_.insert(make_pair(id,make_tuple(name,transvalue,hasonlySubUnit)));
}
return molSidcmptMIdMap;
}