modified trim.seqs command

[mothur.git] / alignment.hpp

diff --git a/alignment.hpp b/alignment.hpp
index 336781244b5a3370c37a7ad6f369cd9553f31618..c033d62cbd8aa94d8ce6b7bc0b429015fd5c3d50 100644 (file)
--- a/alignment.hpp
+++ b/alignment.hpp
@@ -12,7 +12,6 @@
  *     As of 12/18/08 these included alignments based on blastn, needleman-wunsch, and the     Gotoh algorithms
  * 
  */
-using namespace std;
 
 #include "mothur.h"
 #include "alignmentcell.hpp"
@@ -26,7 +25,7 @@ public:
        Alignment();
        virtual void align(string, string) = 0;
        
-       float getAlignmentScore();
+//     float getAlignmentScore();
        string getSeqAAln();
        string getSeqBAln();
        int getCandidateStartPos();