added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index 929ca781ba9906c736bc83e2a79b556b583651f2..f6d7c869853a17808d8d894466f3d473b18c13d8 100644 (file)
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -13,7 +13,6 @@
  *     to set and get these values for the other classes where they are needed.  *
  *
  */
-using namespace std;
 
 #include "mothur.h"
 
@@ -31,6 +30,7 @@ public:
        void setPairwise(string);
        void setAligned(string);
        void setLength();
+       void reverseComplement();
        
        string convert2ints();
        string getName();
@@ -48,6 +48,8 @@ public:
        
 private:
        void initialize();
+       string getSequenceString(ifstream&);
+       string getCommentString(ifstream&);
        string name;
        string unaligned;
        string aligned;