class Bayesian : public Classify {
public:
- Bayesian(string, string, string, int, int, int);
- ~Bayesian() {};
+ Bayesian(string, string, string, int, int, int, int, bool);
+ ~Bayesian();
string getTaxonomy(Sequence*);
private:
vector< vector<float> > wordGenusProb; //vector of maps from genus to probability
- //wordGenusProb[0][392] = probability that a sequence within genus that's index in the tree is 392 would contain kmer 0;
+ //wordGenusProb[0][392] = probability that a sequence within genus that's index in the tree is 392 would contain kmer 0;
vector<int> genusTotals;
vector<int> genusNodes; //indexes in phyloTree where genus' are located
+ vector<diffPair> WordPairDiffArr;
+
int kmerSize, numKmers, confidenceThreshold, iters;
string bootstrapResults(vector<int>, int, int);
int getMostProbableTaxonomy(vector<int>);
void readProbFile(ifstream&, ifstream&, string, string);
+ bool checkReleaseDate(ifstream&, ifstream&, ifstream&, ifstream&);
+ bool isReversed(vector<int>&);
+ vector<int> createWordIndexArr(Sequence*);
+ int generateWordPairDiffArr();
};