X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=94d7d29b6117da80862e9fc8b3d0855c4adb8edd;hb=8742edef7a51b82834289e570d336f5a81ba1f2b;hp=c634f78b6522e43742800b0a4541d910eb7d6be3;hpb=c27e902ede71ea4d20af65752ef04459c101611b;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index c634f78..94d7d29 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -37,15 +37,19 @@ public:
 	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();