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

[mothur.git] / overlap.hpp

diff --git a/overlap.hpp b/overlap.hpp
deleted file mode 100644 (file)
index f87f808..0000000
--- a/overlap.hpp
+++ /dev/null
@@ -1,37 +0,0 @@
-#ifndef OVERLAP_H
-#define OVERLAP_H
-
-/*
- *  overlap.hpp
- *  
- *
- *  Created by Pat Schloss on 12/15/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- *     This class cleans up the alignment at the 3' end of the alignments.  Because the Gotoh and Needleman-Wunsch
- *     algorithms start the traceback from the lower-right corner of the dynamic programming matrix, there may be a lot of
- *     scattered bases in the alignment near the 3' end of the alignment.  Here we basically look for the largest score
- *     in the last column and row to determine whether there should be exta gaps in sequence A or sequence B.  The gap
- *     issues at the 5' end of the alignment seem to take care of themselves in the traceback.
- *
- */
-
-#include "mothur.h"
-
-/**************************************************************************************************/
-
-class Overlap {
-       
-public:
-       Overlap(){};
-       ~Overlap(){};
-       void setOverlap(vector<vector<AlignmentCell> >&, const int, const int, const int);
-private:
-       int maxRow(vector<vector<AlignmentCell> >&, const int);
-       int maxColumn(vector<vector<AlignmentCell> >&, const int);
-       int lA, lB;
-};
-
-/**************************************************************************************************/
-
-#endif