Sequence(ifstream&);
Sequence(istringstream&);
+ //these constructors just set the unaligned string to save space
+ Sequence(string, string, string);
+ Sequence(ifstream&, string);
+ Sequence(istringstream&, string);
+
void setName(string);
void setUnaligned(string);
void setPairwise(string);
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&);