tsp_individual_multi::DNA tsp_individual_multi::translateToDnaPhenotypicOrdinal(const DNA trait){
DNA ordinal;
DNA tmp;
for(int i=0;i<trait.size();i++){
tmp.push_back(i);
}
ordinal.resize(trait.size());
for(int i=0;i<trait.size();i++){
ordinal[i] = tmp[trait[i]];
tmp.erase(tmp.begin() + trait[i]);
}
return ordinal;
}
tsp_individual_multi::DNA tsp_individual_multi::translateToDnaPhenotypicTrait(const DNA ordinal){
DNA trait;
DNA tmp;
for(int i=0;i<ordinal.size();i++){
tmp.push_back(i);
}
for(int i=0;i<ordinal.size();i++){
for(int j=0;j<tmp.size();j++){
if(ordinal[i] == tmp[j]){
trait.push_back(j);
tmp.erase(tmp.begin() + j);
break;
}
}
}
return trait;
}
vector<DNA<false>> FrequentWords(const DNA<IsCyclic>& dnaString, int k) {
//Initialize dictionary
unordered_map<DNA<false>, int> counts{ };
size_t n{ dnaString.size() };
//Fill dictionary and count kmer frequencies
int maxCount{ 1 };
for (size_t i = 0; i < n - k + 1; i++) {
DNA<false> part{ dnaString.slice(i, k) };
auto it = counts.find(part);
if (it == end(counts)) {
counts[part] = 1;
} else {
it->second++;
if (maxCount < it->second) maxCount = it->second;
};
};
//Extract most frequent words
vector<DNA<false>> most_frequent_words{ };
for (auto& p : counts) if (p.second == maxCount) most_frequent_words.push_back(p.first);
return most_frequent_words;
};