//ProbMatrix.cpp
//Coded by Vishakh (vishakh@uci.edu)
//ICS 175A, Winter 2004
//Project: Motif detection in yeast
//Purpose: Encapsulates the functionality of a probability matrix

#ifndef _PROBMATRIX_H_	// may be included more than once
#define _PROBMATRIX_H_

#include <vector>
#include "GenomicPair.h"	//removing this line leads to errors althought genomicpair isnt used here!
#include "DString.h"

struct MatrixColumn
{
	double a;
	double t;
	double g;
	double c;
};

class ProbMatrix
{
public:
	ProbMatrix(int size);
	ProbMatrix(DString seed);
	int size();
	double getValue(int column, char letter);
	void setValue(int column, char letter, double val);
	void updateMatrix(vector<DString> substrings);
	void print();
	vector<MatrixColumn> getMatrix();

private:
	vector<MatrixColumn> cols;
};

#endif