/*
Part of Scallop Transcript Assembler
(c) 2017 by  Mingfu Shao, Carl Kingsford, and Carnegie Mellon University.
See LICENSE for licensing.
*/

#ifndef __REGION_H__
#define __REGION_H__

#include <stdint.h>
#include <vector>
#include "interval_map.h"
#include "partial_exon.h"

using namespace std;

typedef pair<int, int> PI;

class region
{
public:
	region(int32_t _lpos, int32_t _rpos, int _ltype, int _rtype, const split_interval_map *_mmap, const split_interval_map *_imap);
	~region();

public:
	int32_t lpos;					// the leftmost boundary on reference
	int32_t rpos;					// the rightmost boundary on reference
	int ltype;						// type of the left boundary
	int rtype;						// type of the right boundary
	const split_interval_map *mmap;	// pointer to match interval map
	const split_interval_map *imap;	// pointer to indel interval map
	join_interval_map jmap;			// subregion intervals

	vector<partial_exon> pexons;	// generated partial exons

public:
	int print(int index) const;
	bool left_inclusive();
	bool right_inclusive();

private:
	int build_join_interval_map();
	int smooth_join_interval_map();
	int split_join_interval_map();
	bool empty_subregion(int32_t p1, int32_t p2);
	int build_partial_exons();
};

#endif