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[mothur.git] / refchimeratest.h

diff --git a/refchimeratest.h b/refchimeratest.h
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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(vector<Sequence>&);
+       int printHeader(ofstream&);
+       int analyzeQuery(string, string, ofstream&);
+       int getClosestRefIndex();
+private:
+       int getMismatches(string&, vector<vector<int> >&, vector<vector<int> >&, 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;
+       //ofstream chimeraReportFile;
+       
+       MothurOut* m;
+};
+
+#endif