testing 1.13.0

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index f6d7c869853a17808d8d894466f3d473b18c13d8..c634f78b6522e43742800b0a4541d910eb7d6be3 100644 (file)
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -15,7 +15,7 @@
  */
 
 #include "mothur.h"
-
+#include "mothurout.h"
 
 /**************************************************************************************************/
 
@@ -24,6 +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);
@@ -42,14 +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;