*/
#include "mothur.h"
+#include "alignment.hpp"
/**************************************************************************************************/
NeedlemanOverlap(float, float, float, int);
~NeedlemanOverlap();
void align(string, string);
+ void alignPrimer(string, string);
private:
float gap;
float match;
float mismatch;
+ bool isEquivalent(char, char);
};
/**************************************************************************************************/