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#ifndef GOTOHOVERLAP_H
#define GOTOHOVERLAP_H
/*
* gotohoverlap.h
*
*
* Created by Pat Schloss on 12/15/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
* This class is an Alignment child class that implements the Gotoh pairwise alignment algorithm as described in:
*
* Gotoh O. 1982. An improved algorithm for matching biological sequences. J. Mol. Biol. 162:705-8.
* Myers, EW & Miller, W. 1988. Optimal alignments in linear space. Comput Appl Biosci. 4:11-7.
*
* This method is nice because it allows for an affine gap penalty to be assessed, which is analogous to what is used
* in blast and is an alternative to Needleman-Wunsch, which only charges the same penalty for each gap position.
* Because this method typically has problems at the ends when two sequences do not full overlap, we employ a separate
* method to fix the ends (see Overlap class documentation)
*
*/
#include "mothur.h"
#include "alignment.hpp"
/**************************************************************************************************/
class GotohOverlap : public Alignment {
public:
GotohOverlap(float, float, float, float, int);
void align(string, string, bool createBaseMap=false);
~GotohOverlap() = default;
private:
float gapOpen;
float gapExtend;
float match;
float mismatch;
};
/**************************************************************************************************/
#endif
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