X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=94d7d29b6117da80862e9fc8b3d0855c4adb8edd;hb=55ec7cde88d5512e177fe9488d5ee13793853bad;hp=21b4c3874c9ccb1f5ab9eab31fe78fbd7f0a40c6;hpb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index 21b4c38..94d7d29 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -26,30 +26,37 @@ public:
 	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();
+	void trim(int);
 	
 	string convert2ints();
 	string getName();
 	string getAligned();
 	string getPairwise();
 	string getUnaligned();
+	string getInlineSeq();
 	int getNumBases();
 	int getStartPos();
 	int getEndPos();
+	void padToPos(int);
+	void padFromPos(int);
 	int getAlignLength();
 	int getAmbigBases();
+	void removeAmbigBases();
 	int getLongHomoPolymer();
 	bool getIsAligned();
 	void printSequence(ostream&);
 	
-	int MPISend(int); //not working at the moment...
-	int MPIRecv(int); //not working at the moment...
-	
 private:
 	MothurOut* m;
 	void initialize();