/*!
* \brief Return a pointer to a vector of newly created individuals.
*/
Individual::Bag::Handle SCHNAPS::Simulation::PopulationManager::getIndividuals() {
schnaps_StackTraceBeginM();
schnaps_NonNullPointerAssertM(mGenerator);
unsigned long lCurrentTime = mGenerator->getClock().getValue();
std::pair<PopulationManager::const_iterator, PopulationManager::const_iterator> lSources = this->equal_range(lCurrentTime);
// if nothing to generate at current time
if (lSources.first == lSources.second) {
return NULL;
}
unsigned int lStartingIndex = mGenerator->getEnvironment().getPopulation().size();
std::stringstream lPrefix;
int lSubPopNumber = 0;
Individual::Bag::Handle lIndividuals = new Individual::Bag();
Individual::Bag::Handle lSubPop;
for (PopulationManager::const_iterator lIt = lSources.first; lIt != lSources.second; lIt++) {
// assign new prefix to sub-population
lPrefix.str("");
lPrefix << "I_" << lCurrentTime << "_" << lSubPopNumber++;
mPrefixes[lPrefix.str()] = lIt->second;
// generate sub-population
lSubPop = mGenerator->generate(lIt->second.mProfile, lIt->second.mSize, lPrefix.str(), lStartingIndex);
lStartingIndex += lSubPop->size();
// add new individuals to time step population
lIndividuals->insert(lIndividuals->end(), lSubPop->begin(), lSubPop->end());
}
if(mGenerator->getSystem().getParameters().hasParameter(CONTACTS_FLAG) || mGenerator->getSystem().getParameters().hasParameter(NBCONTACTS_VARIABLE))
mGenerator->generateContacts(lIndividuals);
return lIndividuals;
schnaps_StackTraceEndM("SCHNAPS::Simulation::Individual::Bag::Handle SCHNAPS::Simulation::PopulationManager::getIndividuals()");
}
/*!
* \brief Apply the recombination operation on a breeding pool, returning a recombined individual.
* \param inBreedingPool Breeding pool to use for the recombination operation.
* \param inChild Node handle associated to child node in the breeder tree.
* \param ioContext Evolutionary context of the recombination operation.
* \return Recombined individual.
*/
Individual::Handle RecombinationOp::breed(Individual::Bag& inBreedingPool,
BreederNode::Handle inChild,
Context& ioContext)
{
Beagle_StackTraceBeginM();
// Generate parents for recombination.
Individual::Bag::Handle lParents = new Individual::Bag;
if(inChild == NULL) {
const unsigned int lNbGenerated =
(mNumberRecomb->getWrappedValue()==0) ? inBreedingPool.size() :
minOf<unsigned int>(inBreedingPool.size(), mNumberRecomb->getWrappedValue());
if(lNbGenerated == inBreedingPool.size()) (*lParents) = inBreedingPool;
else {
std::vector<unsigned int> lIndices(inBreedingPool.size());
for(unsigned int i=0; i<lIndices.size(); ++i) lIndices[i] = i;
std::random_shuffle(lIndices.begin(), lIndices.end(),
ioContext.getSystem().getRandomizer());
for(unsigned int i=0; i<lNbGenerated; ++i) {
lParents->push_back(inBreedingPool[lIndices[i]]);
}
}
} else {
Beagle_NonNullPointerAssertM(inChild->getBreederOp());
const unsigned int lNbGenerated =
(mNumberRecomb->getWrappedValue()==0) ? inBreedingPool.size() :
minOf<unsigned int>(inBreedingPool.size(), mNumberRecomb->getWrappedValue());
for(unsigned int i=0; i<lNbGenerated; ++i) {
Individual::Handle lIndiv = inChild->getBreederOp()->breed(inBreedingPool,
inChild->getFirstChild(),
ioContext);
lParents->push_back(lIndiv);
}
}
// Log parents selected for recombination.
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Recombining ")+uint2str(lParents->size())+std::string(" individuals together")
);
// Do recombination operation on parent and get the resulting child.
Individual::Handle lChildIndiv = recombine(*lParents, ioContext);
if(lChildIndiv->getFitness() != NULL) {
lChildIndiv->getFitness()->setInvalid();
}
// Log information to history, if it is used.
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
if(lHistory != NULL) {
std::vector<HistoryID> lParentNames;
for(unsigned int i=0; i<lParents->size(); ++i) {
HistoryID::Handle lHID = castHandleT<HistoryID>(lParents->at(i)->getMember("HistoryID"));
if(lHID != NULL) lParentNames.push_back(*lHID);
}
lHistory->incrementHistoryVar(*lChildIndiv);
lHistory->trace(ioContext, lParentNames, lChildIndiv, getName(), "recombination");
}
return lChildIndiv;
Beagle_StackTraceEndM();
}
/*!
* \brief Apply the recombination operation on the deme.
* \param ioDeme Current deme of individuals to recombine.
* \param ioContext Context of the evolution.
*/
void RecombinationOp::operate(Deme& ioDeme, Context& ioContext)
{
Beagle_StackTraceBeginM();
Beagle_ValidateParameterM(mRecombProba->getWrappedValue()>=0.0, mRecombProbaName, "<0");
Beagle_LogTraceM(
ioContext.getSystem().getLogger(),
std::string("Recombining individuals of the ")+
uint2ordinal(ioContext.getDemeIndex()+1)+" deme"
);
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("Recombining individuals with probability ")+
dbl2str(mRecombProba->getWrappedValue())
);
History::Handle lHistory = castHandleT<History>(ioContext.getSystem().haveComponent("History"));
Individual::Bag lRecombinedIndiv(ioDeme.size());
for(unsigned int i=0; i<lRecombinedIndiv.size(); ++i) {
if(ioContext.getSystem().getRandomizer().rollUniform() <= mRecombProba->getWrappedValue()) {
Individual::Bag::Handle lParents = new Individual::Bag;
const unsigned int lNbGenerated =
(mNumberRecomb->getWrappedValue()==0) ? ioDeme.size() :
minOf<unsigned int>(ioDeme.size(), mNumberRecomb->getWrappedValue());
if(lNbGenerated == ioDeme.size()) (*lParents) = ioDeme;
else {
std::vector<unsigned int> lIndices(ioDeme.size());
for(unsigned int j=0; j<lIndices.size(); ++j) lIndices[j] = j;
std::random_shuffle(lIndices.begin(), lIndices.end(),
ioContext.getSystem().getRandomizer());
for(unsigned int j=0; j<lNbGenerated; ++j) {
lParents->push_back(ioDeme[lIndices[j]]);
}
}
lRecombinedIndiv[i] = recombine(*lParents, ioContext);
if(lRecombinedIndiv[i]->getFitness() != NULL) {
lRecombinedIndiv[i]->getFitness()->setInvalid();
}
// Log and update history.
Beagle_LogVerboseM(
ioContext.getSystem().getLogger(),
std::string("The ")+uint2ordinal(i+1)+
std::string(" individual as been replaced by recombination")
);
if(lHistory != NULL) {
std::vector<HistoryID> lParentNames;
for(unsigned int j=0; j<lParents->size(); ++j) {
HistoryID::Handle lHID = castHandleT<HistoryID>(lParents->at(j)->getMember("HistoryID"));
if(lHID != NULL) lParentNames.push_back(*lHID);
}
lHistory->incrementHistoryVar(*lRecombinedIndiv[i]);
lHistory->trace(ioContext, lParentNames, lRecombinedIndiv[i], getName(), "recombination");
}
}
}
for(unsigned int i=0; i<ioDeme.size(); ++i) {
if(lRecombinedIndiv[i] != NULL) ioDeme[i] = lRecombinedIndiv[i];
}
Beagle_StackTraceEndM();
}