X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequence.hpp;h=48287af367092715ab999b9ffabf02229c68cacc;hb=c67cf4168e1a124088b6f017946f0aa1fbdf1301;hp=95c3e51839029393798dc2f57848d5e325c6c2df;hpb=b447f829850ae054e42560c7c3ed71b14f3f40bb;p=mothur.git

diff --git a/sequence.hpp b/sequence.hpp
index 95c3e51..48287af 100644
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -37,6 +37,7 @@ public:
 	void setAligned(string);
 	void setLength();
 	void reverseComplement();
+	void trim(int);
 	
 	string convert2ints();
 	string getName();
@@ -48,6 +49,7 @@ public:
 	int getEndPos();
 	int getAlignLength();
 	int getAmbigBases();
+	void removeAmbigBases();
 	int getLongHomoPolymer();
 	bool getIsAligned();
 	void printSequence(ostream&);