1 #ifndef OVERLAP_H
2 #define OVERLAP_H
3 
4 /*
5  *  overlap.hpp
6  *
7  *
8  *  Created by Pat Schloss on 12/15/08.
9  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
10  *
11  *	This class cleans up the alignment at the 3' end of the alignments.  Because the Gotoh and Needleman-Wunsch
12  *	algorithms start the traceback from the lower-right corner of the dynamic programming matrix, there may be a lot of
13  *	scattered bases in the alignment near the 3' end of the alignment.  Here we basically look for the largest score
14  *	in the last column and row to determine whether there should be exta gaps in sequence A or sequence B.  The gap
15  *	issues at the 5' end of the alignment seem to take care of themselves in the traceback.
16  *
17  */
18 
19 #include "mothur.h"
20 
21 /**************************************************************************************************/
22 
23 class Overlap {
24 
25 public:
Overlap()26 	Overlap(){};
~Overlap()27 	~Overlap(){};
28 	void setOverlap(vector<vector<AlignmentCell> >&, const int, const int, const int);
29 private:
30 	int maxRow(vector<vector<AlignmentCell> >&, const int);
31 	int maxColumn(vector<vector<AlignmentCell> >&, const int);
32 	int lA, lB;
33 };
34 
35 /**************************************************************************************************/
36 
37 #endif
38