changing command name classify.shared to classifyrf.shared

[mothur.git] / needlemanoverlap.hpp

diff --git a/needlemanoverlap.hpp b/needlemanoverlap.hpp
index 57d3284e80644fbde69f6b5c1e984eebd7384c11..858e70a56c811ceef39e51878b7e68a3e0816840 100644 (file)
--- 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);
 };
 
 /**************************************************************************************************/