version 1.4

[mothur.git] / alignment.hpp

diff --git a/alignment.hpp b/alignment.hpp
index 336781244b5a3370c37a7ad6f369cd9553f31618..215e4b32f77e1fc21df19ffd61b493b84d89acc6 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"
@@ -24,9 +23,10 @@ class Alignment {
 public:
        Alignment(int);
        Alignment();
+       virtual ~Alignment();
        virtual void align(string, string) = 0;
        
-       float getAlignmentScore();
+//     float getAlignmentScore();
        string getSeqAAln();
        string getSeqBAln();
        int getCandidateStartPos();