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#ifndef NEEDLEMAN_H
#define NEEDLEMAN_H
/*
* needleman.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 Needleman-Wunsch pairwise alignment algorithm as
* described in:
*
* Needleman SB & Wunsch CD. 1970. A general method applicable to the search for similarities in the amino acid
* sequence of two proteins. J Mol Biol. 48:443-53.
* Korf I, Yandell M, & Bedell J. 2003. BLAST. O'Reilly & Associates. Sebastopol, CA.
*
* This method is simple as it assesses a consistent 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 NeedlemanOverlap : public Alignment {
public:
NeedlemanOverlap(float, float, float, int);
~NeedlemanOverlap();
void align(string, string, bool createBaseMap=false);
void align(Sequence, Protein);
void alignPrimer(string, string);
private:
float gap;
float match;
float mismatch;
bool isEquivalent(char, char);
};
/**************************************************************************************************/
#endif
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