1 #ifndef OVERLAP_H 2 #define OVERLAP_H 3 4 /* 5 * overlap.hpp 6 * 7 * 8 * Created by Pat Schloss on 12/15/08. 9 * Copyright 2008 Patrick D. Schloss. All rights reserved. 10 * 11 * This class cleans up the alignment at the 3' end of the alignments. Because the Gotoh and Needleman-Wunsch 12 * algorithms start the traceback from the lower-right corner of the dynamic programming matrix, there may be a lot of 13 * scattered bases in the alignment near the 3' end of the alignment. Here we basically look for the largest score 14 * in the last column and row to determine whether there should be exta gaps in sequence A or sequence B. The gap 15 * issues at the 5' end of the alignment seem to take care of themselves in the traceback. 16 * 17 */ 18 19 #include "mothur.h" 20 21 /**************************************************************************************************/ 22 23 class Overlap { 24 25 public: Overlap()26 Overlap(){}; ~Overlap()27 ~Overlap(){}; 28 void setOverlap(vector<vector<AlignmentCell> >&, const int, const int, const int); 29 private: 30 int maxRow(vector<vector<AlignmentCell> >&, const int); 31 int maxColumn(vector<vector<AlignmentCell> >&, const int); 32 int lA, lB; 33 }; 34 35 /**************************************************************************************************/ 36 37 #endif 38