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;