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. *
18 #include "mothurout.h"
20 /**************************************************************************************************/
25 Sequence(string, string);
27 Sequence(istringstream&);
29 //these constructors just set the unaligned string to save space
30 Sequence(string, string, string);
31 Sequence(ifstream&, string);
32 Sequence(istringstream&, string);
35 void setUnaligned(string);
36 void setPairwise(string);
37 void setAligned(string);
39 void reverseComplement();
42 string convert2ints();
46 string getUnaligned();
52 void removeAmbigBases();
53 int getLongHomoPolymer();
55 void printSequence(ostream&);
60 string getSequenceString(ifstream&);
61 string getCommentString(ifstream&);
62 string getSequenceString(istringstream&);
63 string getCommentString(istringstream&);
76 /**************************************************************************************************/