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#ifndef KMERNODE
#define KMERNODE
/*
* kmerNode.h
* bayesian
*
* Created by Pat Schloss on 10/11/11.
* Copyright 2011 Patrick D. Schloss. All rights reserved.
*
*/
#include "taxonomynode.h"
/**********************************************************************************************************************/
class KmerNode : public TaxonomyNode {
public:
KmerNode(string, int, int);
void loadSequence(vector<int>&);
void printTheta();
double getPxGivenkj_D_j(vector<int>&);
double getSimToConsensus(vector<int>&);
void checkTheta(){};
void setNumUniqueKmers(int num) { numUniqueKmers = num; }
int getNumUniqueKmers();
void addThetas(vector<int>, int);
vector<int> getTheta() { return kmerVector; }
private:
string getKmerBases(int);
int kmerSize; // value of k
int numPossibleKmers; // 4^kmerSize
int numUniqueKmers; // number of unique kmers seen in a group ~ O_kj
int numKmers; // number of kmers in a sequence
vector<int> kmerVector; // counts of kmers across all sequences in a node
};
/**********************************************************************************************************************/
#endif
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