Chromosome::Chromosome(Parameters& p,unsigned short cId):chrom(){
for(unsigned short i=0;i<p.getChromLoci(cId);++i){
chrom.push_back(Locus(p,cId));
}
for(unsigned short i=0;i<p.getChromQtls(cId).size();++i){
chrom.push_back(Locus(p,p.getChromQtls(cId)[i].a,p.getChromQtls(cId)[i].b));
}
for(unsigned long i=0;i<(unsigned long)(p.getChromSizes(cId)/p.getMarkerDist());++i){
chrom.push_back(Locus(p,i,p.getMarkerDist()));
}
sort(chrom.begin(),chrom.end(),sortLociChrom());
}
void ContractManager::saveState(FunctionIdentifier::Ptr func, PredicateState::Ptr state) {
if (llvm::isa<BasicPredicateState>(state)) {
contracts->at(func)->push_back(state);
} else if (auto&& chain = llvm::dyn_cast<PredicateStateChain>(state)) {
saveState(func, chain->getBase());
saveState(func, chain->getCurr());
} else if (auto&& stateTerm = stateToTerm(state)) {
auto&& statePred = FN.Predicate->getEqualityPredicate(stateTerm, FN.Term->getTrueTerm(), Locus(), PredicateType::PATH);
auto&& newState = FN.State->Basic({statePred});
Z3::ExprFactory ef;
Z3::Solver s(ef, func->memBounds().first, func->memBounds().second);
auto res = s.isFullGroup(newState);
if (res.isSat()) {
contracts->at(func)->push_back(newState);
}
} else {
errs() << "Unable to save state:" << state << endl;
}
}
void ContractManager::printContracts() const {
auto&& dbg = dbgs();
dbg << "Contract extraction results" << endl;
for (auto&& it : contracts->data()) {
auto&& F = it.first;
auto&& memBounds = F->memBounds();
auto&& merger = MergingTransformer(FN, memBounds, F->calls());
if (F->calls() < MIN_FUNCTION_CALLS) continue;
//analyze each state
for (auto&& st : *contracts->at(F)) {
merger.transform(st);
}
//collect results
auto&& mergedState = merger.getMergedState();
if (not mergedState->isEmpty()) {
if (auto&& contract = stateToTerm(mergedState)) {
auto&& function = functionInfo[F].first;
auto&& fm = functionInfo[F].second;
auto&& contractPredicate = FN.Predicate->getEqualityPredicate(contract, FN.Term->getTrueTerm(), Locus(), PredicateType::REQUIRES);
fm->update(function, FN.State->Basic({contractPredicate}));
}
dbg << "---" << "Function " << F->name() << "---" << endl;
dbg << "State:" << endl;
dbg << mergedState << endl;
dbg << endl;
}
}
dbg << end;
}
/**
* Creates a locus from a splitted line that is taken from
* a .info file.
*
* @param splitted_line A line that has been splitted on ' '.
*
* @return The individual with all its doses that is represented
* by the line.
*/
static Locus
create_locus(const std::vector<std::string> &splitted_line)
{
return Locus( splitted_line[ 0 ], splitted_line[ 1 ], splitted_line[ 2 ] );
}
