X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=c634f78b6522e43742800b0a4541d910eb7d6be3;hb=7588ff51d365aad66f455694afb90b6fd3e6639a;hp=929ca781ba9906c736bc83e2a79b556b583651f2;hpb=5b7ac70116137b52dd7884b76c5bca660a5fea38;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index 929ca78..c634f78 100644
--- 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"
 
 /**************************************************************************************************/
 
@@ -25,12 +24,19 @@ 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);
 	void setPairwise(string);
 	void setAligned(string);
 	void setLength();
+	void reverseComplement();
 	
 	string convert2ints();
 	string getName();
@@ -42,12 +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;