mods to seq.errror

[mothur.git] / sequence.hpp

diff --git a/sequence.hpp b/sequence.hpp
index 95c3e51839029393798dc2f57848d5e325c6c2df..94d7d29b6117da80862e9fc8b3d0855c4adb8edd 100644 (file)
--- a/sequence.hpp
+++ b/sequence.hpp
@@ -37,17 +37,22 @@ 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();
        int getLongHomoPolymer();
        bool getIsAligned();
        void printSequence(ostream&);