//genomicPair.h
//Coded by Jeff Weiss (jmweiss@uci.edu)
//ICS 175A, Winter 2004
//Project: Motif detection in yeast
//Purpose: provides a data structure to store genetic squences along with the statistical
//information we for each sequence

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


#include "dstring.h"
//#include "ProbMatrix.h"
#include <iostream>

using namespace std;
class  GenomicPair
{
public:
	GenomicPair();
//	GenomicPair(DString newSequence,int newCount);
	GenomicPair(const DString newSequence, const int newCount);
	GenomicPair(DString newSequence);
	GenomicPair(const GenomicPair& newGenomicPair);
	GenomicPair(DString newSequence,int newCount,int newScore1,int newScore2,int newScore3);
	~GenomicPair();

	void operator=(GenomicPair rhs);
	bool operator<(GenomicPair rhs);
	
	int getCount();
	void setCount(int newCount);
	DString getSequence();
	void setSequence(DString newString);

	void incrementCount();
	void print();
	double score1,score2,score3;
	//ProbMatrix matrix;

protected:
	DString sequence;
	int count;

};

#endif