X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=needlemanoverlap.hpp;h=858e70a56c811ceef39e51878b7e68a3e0816840;hp=a5e21406be2743d8709c9ef5cb81aaa95b49824d;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=bffbd9ad0d837bc9523d95e7b35c34cfd2631046

diff --git a/needlemanoverlap.hpp b/needlemanoverlap.hpp
index a5e2140..858e70a 100644
--- a/needlemanoverlap.hpp
+++ b/needlemanoverlap.hpp
@@ -32,11 +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);
 };
 
 /**************************************************************************************************/