pat's updates on 7/19/10

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index 904e25aeb7a5b4d3476df576217d12820f95f358..c634f78b6522e43742800b0a4541d910eb7d6be3 100644 (file)
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -13,10 +13,9 @@
  *     to set and get these values for the other classes where they are needed.  *
  *
  */
-using namespace std;
 
 #include "mothur.h"
-
+#include "mothurout.h"
 
 /**************************************************************************************************/
 
@@ -25,6 +24,12 @@ public:
        Sequence();
        Sequence(string, string);
        Sequence(ifstream&);
+       Sequence(istringstream&);
+       
+       //these constructors just set the unaligned string to save space
+       Sequence(string, string, string);  
+       Sequence(ifstream&, string);
+       Sequence(istringstream&, string);
        
        void setName(string);
        void setUnaligned(string);
@@ -43,12 +48,18 @@ public:
        int getEndPos();
        int getAlignLength();
        int getAmbigBases();
+       void removeAmbigBases();
        int getLongHomoPolymer();
        bool getIsAligned();
        void printSequence(ostream&);
        
 private:
+       MothurOut* m;
        void initialize();
+       string getSequenceString(ifstream&);
+       string getCommentString(ifstream&);
+       string getSequenceString(istringstream&);
+       string getCommentString(istringstream&);
        string name;
        string unaligned;
        string aligned;