Revert to previous commit

[mothur.git] / overlap.hpp

diff --git a/overlap.hpp b/overlap.hpp
new file mode 100644 (file)
index 0000000..f87f808
--- /dev/null
+++ b/overlap.hpp
@@ -0,0 +1,37 @@
+#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