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[mothur.git] / 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