#ifndef AFFINITYSCORE_H
#define AFFINITYSCORE_H

//#include <fstream>
//#include <iostream>
#include <stdlib.h>
#include "aaTools.h"

//using namespace std;

// functions followed by an "Msa" comment are ones that
// still depend on the alignment being a multiple alignment
// - these eventually need to be phased out
class AffinityScore {
  public:

    int length;
    float stdDev;
    float avg;
    float *val;

    int subLength;
    char *subName;
    float *subVal;

    AffinityScore(Alignment, Matrix);  // Msa
    void getStats();
    int normVal(float);
    void print();

    void modifyPDB();
    void doAllSub(Alignment, Matrix); // Msa
    void getSub(Alignment, char*); // Msa
    void printSub();
    void getSubN(Alignment, Matrix, char*); // Msa
};

#endif