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 map<int, int> getSeqAAlnBaseMap();
34 map<int, int> getSeqBAlnBaseMap();
35 int getCandidateStartPos();
36 int getCandidateEndPos();
37 int getTemplateStartPos();
38 int getTemplateEndPos();
40 int getPairwiseLength();
42 int getnRows() { return nRows; }
43 // int getLongestTemplateGap();
49 int seqAstart, seqAend;
50 int seqBstart, seqBend;
52 int nRows, nCols, lA, lB;
53 vector<vector<AlignmentCell> > alignment;
54 map<int, int> ABaseMap;
55 map<int, int> BBaseMap;
59 /**************************************************************************************************/