void System::outputAllObservableCounts(double cSampleTime, int eventCounter)
{
if(!onTheFlyObservables)
{
for(obsIter = obsToOutput.begin(); obsIter != obsToOutput.end(); obsIter++)
{ (*obsIter)->clear(); }
for(molTypeIter = allMoleculeTypes.begin(); molTypeIter != allMoleculeTypes.end(); molTypeIter++ )
{ (*molTypeIter)->addAllToObservables(); }
int match = 0;
// NETGEN -- this bit replaces the commented block below
Complex * complex;
allComplexes.resetComplexIter();
while( (complex = allComplexes.nextComplex()) )
{
if( complex->isAlive() )
{
for(obsIter = speciesObservables.begin(); obsIter != speciesObservables.end(); obsIter++)
{
match = (*obsIter)->isObservable( complex );
for (int k=0; k<match; k++) (*obsIter)->straightAdd();
}
}
}
/*
for(complexIter = allComplexes.begin(); complexIter != allComplexes.end(); complexIter++) {
if((*complexIter)->isAlive()) {
for(obsIter = speciesObservables.begin(); obsIter != speciesObservables.end(); obsIter++) {
match = (*obsIter)->isObservable((*complexIter));
for(int k=0; k<match; k++) (*obsIter)->straightAdd();
}
}
}
*/
}
if(useBinaryOutput) {
double count=0.0; int oTot=0;
outputFileStream.write((char *)&cSampleTime, sizeof(double));
for(obsIter = obsToOutput.begin(); obsIter != obsToOutput.end(); obsIter++) {
count=((double)(*obsIter)->getCount());
outputFileStream.write((char *) &count, sizeof(double));
}
if(outputGlobalFunctionValues)
for( functionIter = globalFunctions.begin(); functionIter != globalFunctions.end(); functionIter++ ) {
count=FuncFactory::Eval((*functionIter)->p);
outputFileStream.write((char *) &count, sizeof(double));
}
if(outputEventCounter) {
count=eventCounter;
outputFileStream.write((char *) &count, sizeof(double));
}
}
else {
if(!csvFormat) {
outputFileStream<<" "<<cSampleTime;
for(obsIter = obsToOutput.begin(); obsIter != obsToOutput.end(); obsIter++) {
outputFileStream<<" "<<((double)(*obsIter)->getCount());
}
if(outputGlobalFunctionValues)
for( functionIter = globalFunctions.begin(); functionIter != globalFunctions.end(); functionIter++ )
outputFileStream<<" "<<FuncFactory::Eval((*functionIter)->p);
if(outputEventCounter) {
outputFileStream<<" "<<eventCounter;
}
outputFileStream<<endl;
} else {
outputFileStream<<cSampleTime;
for(obsIter = obsToOutput.begin(); obsIter != obsToOutput.end(); obsIter++) {
outputFileStream<<", "<<((double)(*obsIter)->getCount());
}
if(outputGlobalFunctionValues)
for( functionIter = globalFunctions.begin(); functionIter != globalFunctions.end(); functionIter++ )
outputFileStream<<", "<<FuncFactory::Eval((*functionIter)->p);
if(outputEventCounter) {
outputFileStream<<", "<<eventCounter;
}
outputFileStream<<endl;
}
}
}
//When you are ready to run the simulation (meaning that all moleculeTypes
//all molecules, and all reactions have been created and registered with
//the system) call this function to populate all the reactant lists and
//observables.
void System::prepareForSimulation()
{
this->selector = new DirectSelector(allReactions);
cout<<"preparing simulation..."<<endl;
//Note!! : the order of preparing the system matters! You have to prepare
//some things before others, because certain things require other
//First, set the observables up correctly, so when functions evaluate, they get the
//correct values
//for(molTypeIter = allMoleculeTypes.begin(); molTypeIter != allMoleculeTypes.end(); molTypeIter++ ) {
// (*molTypeIter)->addAllToObservables();
//}
//First, we have to prep all the functions...
for( functionIter = globalFunctions.begin(); functionIter != globalFunctions.end(); functionIter++ )
(*functionIter)->prepareForSimulation(this);
//cout<<"here 1..."<<endl;
for( int f=0; f<localFunctions.size(); f++)
localFunctions.at(f)->prepareForSimulation(this);
//cout<<"here 2..."<<endl;
for( int f=0; f<compositeFunctions.size(); f++)
compositeFunctions.at(f)->prepareForSimulation(this);
//cout<<"here 3..."<<endl;
//this->printAllFunctions();
// now we prepare all reactions
rxnIndexMap = new int * [allReactions.size()];
for(unsigned int r=0; r<allReactions.size(); r++)
{
rxnIndexMap[r] = new int[allReactions.at(r)->getNumOfReactants()];
allReactions.at(r)->setRxnId(r);
}
//cout<<"here 4..."<<endl;
//This means we aren't going to add any more molecules to the system, so prep the rxns
for(rxnIter = allReactions.begin(); rxnIter != allReactions.end(); rxnIter++ )
(*rxnIter)->prepareForSimulation();
//cout<<"here 5..."<<endl;
//If there are local functions to be had, make sure we set up those local function lists in the molecules
//before we try to add molecules to reactant lists
if(this->localFunctions.size()>0) {
for( molTypeIter = allMoleculeTypes.begin(); molTypeIter != allMoleculeTypes.end(); molTypeIter++ )
(*molTypeIter)->setUpLocalFunctionListForMolecules();
}
//cout<<"here 6..."<<endl;
//prep each molecule type for the simulation
for( molTypeIter = allMoleculeTypes.begin(); molTypeIter != allMoleculeTypes.end(); molTypeIter++ )
(*molTypeIter)->prepareForSimulation();
//cout<<"here 7..."<<endl;
//add all the molecules to the appropriate observables
//NOT NECESSARY - molecules are added to observables when they are prepared
//for(obsIter=obsToOutput.begin(); obsIter != obsToOutput.end(); obsIter++)
// (*obsIter)->clear();
//for(molTypeIter = allMoleculeTypes.begin(); molTypeIter != allMoleculeTypes.end(); molTypeIter++ ) {
// (*molTypeIter)->addAllToObservables();
//}
//Add the complexes to Species observables
int match = 0;
for(obsIter = speciesObservables.begin(); obsIter != speciesObservables.end(); obsIter++)
(*obsIter)->clear();
// NETGEN -- this bit replaces the commented block below
Complex * complex;
allComplexes.resetComplexIter();
while( (complex = allComplexes.nextComplex()) )
{
if( complex->isAlive() )
{
for(obsIter = speciesObservables.begin(); obsIter != speciesObservables.end(); obsIter++)
{
match = (*obsIter)->isObservable( complex );
for (int k=0; k<match; k++) (*obsIter)->straightAdd();
}
}
}
/*
for(complexIter = allComplexes.allComplexes.begin(); complexIter != allComplexes.end(); complexIter++) {
if((*complexIter)->isAlive()) {
for(obsIter = speciesObservables.begin(); obsIter != speciesObservables.end(); obsIter++) {
match = (*obsIter)->isObservable((*complexIter));
for(int k=0; k<match; k++) (*obsIter)->straightAdd();
}
}
}
*/
//cout<<"here 8..."<<endl;
//cout<<"here 9..."<<endl;
//if(BASIC_MESSAGE) cout<<"preparing the system...\n";
//printIndexAndNames();
// if(go!=NULL)
// {
// go->writeGroupKeyFile();
// go->writeOutputFileHeader();
// }
//finally, create the next reaction selector
//this->selector = new LogClassSelector(allReactions);
this->evaluateAllLocalFunctions();
recompute_A_tot();
}
