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#ifndef BAYESIAN_H
#define BAYESIAN_H
/*
* bayesian.h
* Mothur
*
* Created by westcott on 11/3/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "mothur.h"
#include "classify.h"
/**************************************************************************************************/
class Bayesian : public Classify {
public:
Bayesian(string, string, string, int, int, int, int, bool, bool, string);
~Bayesian();
string getTaxonomy(Sequence*, string&, bool&);
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;
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, string&);
int getMostProbableTaxonomy(vector<int>);
void readProbFile(ifstream&, ifstream&, string, string);
bool isReversed(vector<int>&);
vector<int> createWordIndexArr(Sequence*);
int generateWordPairDiffArr();
};
/**************************************************************************************************/
#endif
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