X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=needlemanoverlap.hpp;h=858e70a56c811ceef39e51878b7e68a3e0816840;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=57d3284e80644fbde69f6b5c1e984eebd7384c11;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git

diff --git a/needlemanoverlap.hpp b/needlemanoverlap.hpp
index 57d3284..858e70a 100644
--- a/needlemanoverlap.hpp
+++ b/needlemanoverlap.hpp
@@ -22,6 +22,7 @@
  */
 
 #include "mothur.h"
+#include "alignment.hpp"
 
 /**************************************************************************************************/
 
@@ -31,11 +32,13 @@ public:
 	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);
 };
 
 /**************************************************************************************************/