// Author: Joseph Bertolami
// Email: jbertola@uci.edu

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

#include <string.h>
#include <stdio.h>
#include <vector>
#include "dstring.h"

using namespace std;

class DFile
{
public:

	DFile() { buffer=NULL; }
	~DFile() { if ( buffer ) delete buffer; }

	virtual int ReadFile(char *filename);
	int WriteFile(char *filename);

	DString data() { return *buffer; }

protected:

	DString * buffer;
};

typedef struct CGene
{
	DString name;
	DString sequence;
	int neg_range;
	int pos_range;
	int size;

	CGene()
		: neg_range(0), pos_range(0), size(0)
	{}
} CGene;

class DGFile : public DFile
{
public:

	DGFile() 
		: num_genes(0) 
		{}
	~DGFile() {}

	// will simply parse a genomic file
	int ReadGeneFile(char *filename);

	CGene * GetGene(int gene);
	DString * GetGeneData(int gene);

public:

	CGene *genes;
	unsigned long num_genes;

};

#endif