changes while testing

[mothur.git] / needlemanoverlap.hpp

diff --git a/needlemanoverlap.hpp b/needlemanoverlap.hpp
index a5e21406be2743d8709c9ef5cb81aaa95b49824d..858e70a56c811ceef39e51878b7e68a3e0816840 100644 (file)
--- 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);
 };
 
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