8 * Created by Pat Schloss on 12/15/08.
9 * Copyright 2008 Patrick D. Schloss. All rights reserved.
11 * A sequence object has three components: i) an accession number / name, ii) the unaligned primary sequence, iii) a
12 * pairwise aligned sequence, and iv) a sequence that is aligned to a reference alignment. This class has methods
13 * to set and get these values for the other classes where they are needed. *
21 /**************************************************************************************************/
26 Sequence(string, string);
30 void setUnaligned(string);
31 void setPairwise(string);
32 void setAligned(string);
34 void reverseComplement();
36 string convert2ints();
40 string getUnaligned();
46 int getLongHomoPolymer();
48 void printSequence(ostream&);
64 /**************************************************************************************************/