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);
string getPairwise();
string getUnaligned();
string getInlineSeq();
+ int getNumNs();
int getNumBases();
int getStartPos();
int getEndPos();
string getCommentString(ifstream&);
string getSequenceString(istringstream&, int&);
string getCommentString(istringstream&);
+ string getSequenceName(ifstream&);
+ string getSequenceName(istringstream&);
string name;
string unaligned;
string aligned;
string pairwise;
+ string comment;
int numBases;
int alignmentLength;
bool isAligned;