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[mothur.git] / needlemanoverlap.hpp

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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);
+
+       
+private:       
+       float gap;
+       float match;
+       float mismatch;
+};
+
+/**************************************************************************************************/
+
+#endif