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//
// kmerTree.h
// pdsBayesian
//
// Created by Patrick Schloss on 4/3/12.
// Copyright (c) 2012 University of Michigan. All rights reserved.
//
#ifndef pdsBayesian_kmerTree_h
#define pdsBayesian_kmerTree_h
#include "classify.h"
class KmerNode;
class KmerTree : public Classify {
public:
KmerTree(string, string, int, int);
~KmerTree();
string getTaxonomy(Sequence*, string&, bool&);
private:
int addTaxonomyToTree(string, string, vector<int>&);
vector<int> ripKmerProfile(string);
int getMinRiskIndexKmer(vector<int>&, vector<int>&, vector<double>&);
int aggregateThetas();
int sanityCheck(vector<vector<int> >&, vector<int>&);
int kmerSize;
int numPossibleKmers, confidenceThreshold;
vector<KmerNode*> tree;
};
#endif
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