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;
30 // float getAlignmentScore();
33 int getCandidateStartPos();
34 int getCandidateEndPos();
35 int getTemplateStartPos();
36 int getTemplateEndPos();
38 int getPairwiseLength();
40 int getnRows() { return nRows; }
41 // int getLongestTemplateGap();
47 int seqAstart, seqAend;
48 int seqBstart, seqBend;
50 int nRows, nCols, lA, lB;
51 vector<vector<AlignmentCell> > alignment;
55 /**************************************************************************************************/