fixed problem with class.fy.seqs where group totals did not add up. added constructo...

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index ac9384bf156bf471cc35b3fe8d57f6ecf777e857..95c3e51839029393798dc2f57848d5e325c6c2df 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);
@@ -47,7 +53,12 @@ public:
        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;