8 * Created by Pat Schloss on 12/15/08.
9 * Copyright 2008 Patrick D. Schloss. All rights reserved.
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.
21 /**************************************************************************************************/
28 void setOverlap(vector<vector<AlignmentCell> >&, const int, const int, const int);
30 int maxRow(vector<vector<AlignmentCell> >&, const int);
31 int maxColumn(vector<vector<AlignmentCell> >&, const int);
35 /**************************************************************************************************/