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&);