ScoreMatrix.h

#ifndef SCORE_MATRIX_H
#define SCORE_MATRIX_H

#include <string>
#include <fstream>
#include <map>
#include <vector>

#define UNKNOWN_SCORE -4

using namespace std;

// Class for loading and accessing substitution scoring matrices

class ScoreMatrix {
public:
    /**
     * Load scoring matrix from a file in csv format
     */
    bool loadFromFile(string filename);
    /**
     * Set all relevant alignment penalties
     */
    void setPenalties(double gapPenalty, double boundaryFsPenalty,
                      double exonFsStopPenalty);
    /**
     * Return score of a specified amino acid pair
     */
    double getScore(char a, char b, bool boundaryFrameshift = false) const;
    /**
     * Return maximum score of an amino acid pair in the matrix
     */
    double getMaxScore() const;
    void print() const;
private:
    map<char, map<char, double> > matrix;
    ifstream inputStream;
    int size;
    vector<char> columnHeaders;
    bool readColumnHeaders();
    bool readRow();
    void processLine(string & line);
    void computeMaxScore();
    double maxScore;
    double gapPenalty;
    double boundaryFsPenalty;
    double exonFsStopPenalty;

};

#endif /* SCORE_MATRIX_H */