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

[mothur.git] / needlemanoverlap.hpp

diff --git a/needlemanoverlap.hpp b/needlemanoverlap.hpp
deleted file mode 100644 (file)
index ea7bee5..0000000
--- a/needlemanoverlap.hpp
+++ /dev/null
@@ -1,45 +0,0 @@
-#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