Sequence();
Sequence(string, string);
Sequence(ifstream&);
+ Sequence(ifstream&, string&, bool);
Sequence(istringstream&);
//these constructors just set the unaligned string to save space
Sequence(string, string, string);
int getEndPos();
void padToPos(int);
void padFromPos(int);
+ int filterToPos(int); //any character before the pos is changed to . and aligned and unaligned strings changed
+ int filterFromPos(int); //any character after the pos is changed to . and aligned and unaligned strings changed
int getAlignLength();
int getAmbigBases();
void removeAmbigBases();