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#ifndef REFCHIMERATEST
#define REFCHIMERATEST
/*
* refchimeratest.h
* Mothur
*
* Created by Pat Schloss on 1/31/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "sequence.hpp"
class RefChimeraTest {
public:
RefChimeraTest(){};
~RefChimeraTest(){}
RefChimeraTest(vector<Sequence>&, bool);
string getHeader();
int analyzeQuery(string, string, string&);
int getClosestRefIndex();
string getClosestRefAlignment();
string getQueryAlignment();
private:
int getAlignedMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, int&);
int analyzeAlignedQuery(string, string, string&);
int analyzeUnalignedQuery(string, string, string&);
double alignQueryToReferences(string, string, string&, string&, double&);
int getUnalignedDiffs(string, string, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
int getChimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
int getTrimera(vector<vector<int> >&, vector<vector<int> >&, int&, int&, int&, int&, int&, vector<int>&, vector<int>&, vector<int>&, vector<int>&);
string stitchBimera(int, int, int);
string stitchTrimera(int, int, int, int, int);
double calcDistToChimera(string&, string&);
vector<string> referenceSeqs;
vector<string> referenceNames;
int numRefSeqs;
int alignLength;
int bestMatch;
string bestRefAlignment;
string bestQueryAlignment;
bool aligned;
MothurOut* m;
};
#endif
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