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#ifndef OVERLAP_H
#define OVERLAP_H
/*
* overlap.hpp
*
*
* Created by Pat Schloss on 12/15/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
* This class cleans up the alignment at the 3' end of the alignments. Because the Gotoh and Needleman-Wunsch
* algorithms start the traceback from the lower-right corner of the dynamic programming matrix, there may be a lot of
* scattered bases in the alignment near the 3' end of the alignment. Here we basically look for the largest score
* in the last column and row to determine whether there should be exta gaps in sequence A or sequence B. The gap
* issues at the 5' end of the alignment seem to take care of themselves in the traceback.
*
*/
#include "mothur.h"
/**************************************************************************************************/
class Overlap {
public:
Overlap(){};
~Overlap(){};
void setOverlap(vector<vector<AlignmentCell> >&, const int, const int, const int);
private:
int maxRow(vector<vector<AlignmentCell> >&, const int);
int maxColumn(vector<vector<AlignmentCell> >&, const int);
int lA, lB;
};
/**************************************************************************************************/
#endif
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