8 * Created by Pat Schloss on 12/15/08.
9 * Copyright 2008 Patrick D. Schloss. All rights reserved.
11 * This is a class for an abstract datatype for classes that implement various types of alignment algorithms.
12 * As of 12/18/08 these included alignments based on blastn, needleman-wunsch, and the Gotoh algorithms
17 #include "alignmentcell.hpp"
19 /**************************************************************************************************/
27 virtual void align(string, string) = 0;
29 // float getAlignmentScore();
32 int getCandidateStartPos();
33 int getCandidateEndPos();
34 int getTemplateStartPos();
35 int getTemplateEndPos();
37 int getPairwiseLength();
38 // int getLongestTemplateGap();
44 int seqAstart, seqAend;
45 int seqBstart, seqBend;
47 int nRows, nCols, lA, lB;
48 vector<vector<AlignmentCell> > alignment;
51 /**************************************************************************************************/