*/
#include "mothur.h"
-
+#include "mothurout.h"
/**************************************************************************************************/
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);
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;