X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=48287af367092715ab999b9ffabf02229c68cacc;hb=f598bd8389840cf030d61f5da7d0b2c3e37c06ba;hp=f6d7c869853a17808d8d894466f3d473b18c13d8;hpb=648ec37228eb16075ace911dd5a5773cdfe683da;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index f6d7c86..48287af 100644
--- 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);
@@ -31,6 +37,7 @@ public:
 	void setAligned(string);
 	void setLength();
 	void reverseComplement();
+	void trim(int);
 	
 	string convert2ints();
 	string getName();
@@ -42,14 +49,18 @@ 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;