seqAlign.h

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#ifndef SEQALIGN_H
#define SEQALIGN_H

#include <iostream>
#include <string>
#include <vector>
#include <map>
#include <algorithm>

#include "Utils/constants.h"

namespace MTKpp
{

class molecule;
class submolecule;
class atom;

// ============================================================
// Class : seqAlign()
// ------------------------------------------------------------
// ============================================================

class seqAlign
{
public:

    seqAlign();

    virtual ~seqAlign();

    int run();

    int setTemplate(molecule* pMolecule);

    int setQuery(molecule* pMolecule);

    void setPAMFile(std::string pam);

    void setPAMSize(int s);

    void setPAMType(int i, std::string s);

    void setPAMValue(int i, int j, double v);

    void printPAM();

    void setAlgorithmType(int i);

    void setGapPenaltyType(int i);

    void setGapOpen(double d);

    void setGapExtend(double d);

    int* getCorrMap();

    void printResults();

    double getSimScore(std::string i, std::string j);

protected: // functions

    int initMatchMatrix();

    int traceBack();

protected: // data

    molecule* tMol;

    int tNRes;

    char* tCSeq;

    int* tISeq;

    molecule* qMol;

    int qNRes;

    char* qCSeq;

    int* qISeq;

    int algorithmType;

    int gapPenaltyType;

    double gapOpen;

    double gapExtend;

    int maxGap;

    int gapSize;

    std::string pamFile;

    int pamSize;

    char* pamTypes;

    double* pam;

    double* matchMatrix;

    int* maxIndices;

    int bestI;

    int bestJ;

    double bestMatchMatrixValue;

    std::string alignmentA;

    std::string alignmentB;

    int* corrMap;
};

} // MTKpp namespace

#endif // COLLECTION_H