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

#include <map>
#include <algorithm>
#include <cassert>
#include "gene.h"

int gene::clear()
{
	transcripts.clear();
	t2i.clear();
	return 0;
}

int gene::assign(const vector<transcript> &v)
{
	clear();
	for(int i = 0; i < v.size(); i++)
	{
		add_transcript(v[i]);
	}
	return 0;
}

int gene::add_transcript(const item&e)
{
	assert(e.feature == "transcript");
	if(t2i.find(e.transcript_id) == t2i.end())
	{
		t2i.insert(pair<string, int>(e.transcript_id, t2i.size()));
		transcripts.push_back(transcript(e));
	}
	else
	{
		int k = t2i[e.transcript_id];
		transcripts[k].assign(e);
	}
	return 0;
}

int gene::add_transcript(const transcript &t)
{
	assert(t2i.find(t.transcript_id) == t2i.end());
	t2i.insert(pair<string, int>(t.transcript_id, t2i.size()));
	transcripts.push_back(t);
	return 0;
}

int gene::add_exon(const item&e)
{
	assert(e.feature == "exon");
	if(t2i.find(e.transcript_id) != t2i.end())
	{
		int k = t2i[e.transcript_id];
		transcripts[k].add_exon(e);
	}
	else
	{
		transcript t;
		t.assign(e);
		t.add_exon(e);
		add_transcript(t);
	}
	return 0;
}

int gene::set_gene_id(const string &id) 
{
	for(int i = 0; i < transcripts.size(); i++)
	{
		transcripts[i].gene_id = id;
	}
	return 0;
}

int gene::filter_single_exon_transcripts()
{
	vector<transcript> vv;
	t2i.clear();
	for(int i = 0; i < transcripts.size(); i++)
	{
		if(transcripts[i].exons.size() <= 1) continue;
		t2i.insert(pair<string, int>(transcripts[i].transcript_id, vv.size()));
		vv.push_back(transcripts[i]);
	}
	transcripts = vv;
	return 0;
}

int gene::filter_low_coverage_transcripts(double min_coverage)
{
	vector<transcript> vv;
	t2i.clear();
	for(int i = 0; i < transcripts.size(); i++)
	{
		if(transcripts[i].coverage < min_coverage) continue;
		t2i.insert(pair<string, int>(transcripts[i].transcript_id, vv.size()));
		vv.push_back(transcripts[i]);
	}
	transcripts = vv;
	return 0;
}

int gene::sort()
{
	for(int i = 0; i < transcripts.size(); i++)
	{
		transcripts[i].sort();
	}
	return 0;
}

int gene::shrink()
{
	for(int i = 0; i < transcripts.size(); i++)
	{
		transcripts[i].shrink();
	}
	return 0;
}

int gene::assign_RPKM(double factor)
{
	for(int i = 0; i < transcripts.size(); i++)
	{
		transcripts[i].assign_RPKM(factor);
	}
	return 0;
}

set<int32_t> gene::get_exon_boundaries() const
{
	set<int32_t> s;
	for(int k = 0; k < transcripts.size(); k++)
	{
		const vector<PI32> &v = transcripts[k].exons;
		for(int i = 0; i < v.size(); i++)
		{
			int32_t l = v[i].first;
			int32_t r = v[i].second;
			s.insert(l);
			s.insert(r);
		}
	}
	return s;
}

PI32 gene::get_bounds() const
{
	PI32 pp(-1, -1);
	for(int k = 0; k < transcripts.size(); k++)
	{
		PI32 p = transcripts[k].get_bounds();
		if(pp.first == -1 || pp.first > p.first) pp.first = p.first;
		if(pp.second == -1 || pp.second < p.second) pp.second = p.second;
	}
	return pp;
}

string gene::get_seqname() const
{
	if(transcripts.size() == 0) return "";
	else return transcripts[0].seqname;
}

string gene::get_gene_id() const
{
	if(transcripts.size() == 0) return "";
	else return transcripts[0].gene_id;
}

int gene::write(ofstream &fout) const
{
	for(int i = 0; i < transcripts.size(); i++)
	{
		transcripts[i].write(fout);
	}
	return 0;
}