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#ifndef DPALIGNMENT_H
#define DPALIGNMENT_H
/*
* dpalignment.h
*
*
* Created by Pat Schloss on 12/15/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
* This is a class for an abstract datatype for classes that implement various types of alignment algorithms.
* As of 12/01/21 these included alignments based on needleman-wunsch, and the Gotoh algorithms
*
*/
#include "mothur.h"
#include "alignmentcell.hpp"
#include "currentfile.h"
#include "protein.hpp"
#include "sequence.hpp"
/**************************************************************************************************/
class Alignment {
public:
Alignment(int);
Alignment(int, int);
Alignment();
virtual ~Alignment();
virtual void align(string, string, bool createBaseMap=false) = 0;
virtual void alignPrimer(string, string) {}
virtual void align(Sequence, Protein) {}
string getSeqAAln();
string getSeqBAln();
map<int, int> getSeqAAlnBaseMap();
map<int, int> getSeqBAlnBaseMap();
int getCandidateStartPos();
int getCandidateEndPos();
int getTemplateStartPos();
int getTemplateEndPos();
int getPairwiseLength();
virtual void resize(int);
int getnRows() { return nRows; }
protected:
void traceBack(bool createBaseMap);
void proteinTraceBack(vector<string>, vector<AminoAcid>);
string seqA, seqAaln;
string seqB, seqBaln;
int seqAstart, seqAend;
int seqBstart, seqBend;
int pairwiseLength;
int nRows, nCols, lA, lB;
vector<vector<AlignmentCell> > alignment;
map<int, int> ABaseMap;
map<int, int> BBaseMap;
MothurOut* m;
};
/**************************************************************************************************/
#endif
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