working on pam

[mothur.git] / kmer.hpp

diff --git a/kmer.hpp b/kmer.hpp
index 75ec5384ad2d3724bc61688616a7eb2ca6c9d252..9a3c5a0091b868b7f61ae8043546f39b27e212cb 100644 (file)
--- a/kmer.hpp
+++ b/kmer.hpp
@@ -10,6 +10,8 @@
  *
  */
 
+#include "mothur.h"
+
 /**************************************************************************************************/
 
 class Kmer {
@@ -18,11 +20,11 @@ public:
        Kmer(int);
        string getKmerString(string);
        int getKmerNumber(string, int);
-       
-       
-private:
        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;
@@ -32,4 +34,5 @@ private:
 
 /**************************************************************************************************/
 
+
 #endif