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

#ifndef __GTF_GENE_H__
#define __GTF_GENE_H__

#include <fstream>
#include <vector>
#include <set>
#include <map>

#include "item.h"
#include "transcript.h"

using namespace std;

class gene
{
public:
	vector<transcript> transcripts;			
	map<string, int> t2i;

public:
	// build
	int add_transcript(const transcript &t);
	int add_transcript(const item &e);
	int add_exon(const item &e);

	// modify
	int assign(const vector<transcript> &v);
	int sort();
	int shrink();
	int clear();
	int set_gene_id(const string &id);
	int assign_RPKM(double factor);

	// filter
	int filter_single_exon_transcripts();
	int filter_low_coverage_transcripts(double min_coverage);

	set<int32_t> get_exon_boundaries() const;
	PI32 get_bounds() const;
	string get_seqname() const;
	string get_gene_id() const;

	// write
	int write(ofstream &fout) const;	
};

#endif