X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=needlemanoverlap.hpp;h=858e70a56c811ceef39e51878b7e68a3e0816840;hp=ea7bee515bff32685f03b195506fa4416814dddf;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=1244c4907c07baea86b0f0676d098a29d2e95a39

diff --git a/needlemanoverlap.hpp b/needlemanoverlap.hpp
index ea7bee5..858e70a 100644
--- a/needlemanoverlap.hpp
+++ b/needlemanoverlap.hpp
@@ -32,12 +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);
 };
 
 /**************************************************************************************************/