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[mothur.git] / kmer.hpp

diff --git a/kmer.hpp b/kmer.hpp
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+#ifndef KMER_HPP
+#define KMER_HPP
+
+/*
+ *  kmer.hpp
+ *  
+ *
+ *  Created by Pat Schloss on 12/15/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+
+/**************************************************************************************************/
+
+class Kmer {
+       
+public:
+       Kmer(int);
+       string getKmerString(string);
+       int getKmerNumber(string, int);
+       string getKmerBases(int);
+       int getReverseKmerNumber(int);
+       vector< map<int, int> > getKmerCounts(string sequence);  //for use in chimeraCheck
+       
+private:
+       char getASCII(int);
+       int getNumber(char);
+       int kmerSize;
+       int maxKmer;
+       int nKmers;
+};
+
+/**************************************************************************************************/
+
+
+#endif