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

#include "dstring.h"
#include "dtable.h"
#include "fileio.h"

using namespace std;

// permutes dstring and stores each permutation into dtable
class Permutation
{
public:
	Permutation();	//constructs count=0
	Permutation(DString dString);	//hashes permuted DString substrings
	~Permutation();

	DString getComplement(DString str);
	void permute(DString dString);	//permutes dString subsequences + adds to dTable
	void permute(DGFile &file);	//permutes dString subsequences via a DGFile + adds to dTable
	int getCount();
	void printDTable();

	DTable dTable;	//genomicPair hash table

private:
	static const int SUBSTR_MIN_LENGTH = 6;
	static const int SUBSTR_MAX_LENGTH = 8;
	int count;	//permutation counter

	void initialize();
};

#endif