moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / gotohoverlap.hpp

diff --git a/gotohoverlap.hpp b/gotohoverlap.hpp
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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);
-       
-       ~GotohOverlap() {}
-       
-private:
-       float gapOpen;
-       float gapExtend;
-       float match;
-       float mismatch;
-};
-
-/**************************************************************************************************/
-
-#endif