#include <iostream>
#include <fstream>
#include <string>
#include <cmath>
#include <ctime>
#include <vector>
#include <algorithm>
#include <iomanip>
#include <sstream>

using namespace std;

class Seg
{
public:
	int start;
	int end;
	double score;
}; //searched region

void make_Seg(const char* data_name, const char* vector_name, int dim,  int M_L, int M_S, double threshold, const char* outfile_name, int chr, int window)
{
	string line;

	ifstream fin; 
	fin.open(data_name); 
	if (!fin){ cout << "error : file not found" << endl; exit(1); } // if fin==0  file not exist

	ifstream fin2; 
	fin2.open(vector_name); 
	if (!fin2){ cout << "error : file not found" << endl; exit(1); } // if fin2==0  file not exist

	ofstream ofs;
	ofs.open(outfile_name, ios::out | ios::app);

	getline(fin2, line);

	vector<double> v; //feature vector
	stringstream v_buf(line);
	for(int i=0; i<dim; i++)
	{
		double tmp;
		v_buf >> tmp;
		v.push_back(tmp);
	} // read vector file

	getline(fin, line);
	getline(fin, line);

	vector<double> s_row;// score of each position

	//start calculating score of each position

	while(getline(fin, line)) //read data file
	{
		bool z = false;
		stringstream buf(line);
		double tmp;
		double score = 0;
		
		for(int i=0; i<dim; i++)
		{
			buf >> tmp;
			if(tmp == 2)
			{
				z = true;
			}
			score += tmp*v[i];
		}
		if(z)
		{
			s_row.push_back(-1);
		}
		else
		{
			s_row.push_back(score - threshold);
		}
	}
	
	//end calculating score of each position
	
	//start calculating weight sums
	
	vector<double> s_0, l_0, s_1, l_1; //weight sums : w0_short, w0_long, w1_short, w1_long

	int L = 0; 
	L = (int)s_row.size();
	
	s_0.push_back(0);
	s_1.push_back(s_row[0]);
	l_0.push_back(-10000000);
	l_1.push_back(-10000000);
	
	for(int i=1; i<L; i++)
	{
		if(s_0[i-1] > l_1[i-1])
		{
			s_0.push_back(s_0[i-1]);
		}
		else
		{
			s_0.push_back(l_1[i-1]);
		}

		if(s_1[i-1] > l_0[i-1])
		{
			s_1.push_back(s_1[i-1] + s_row[i]);
		}
		else
		{
			s_1.push_back(l_0[i-1] + s_row[i]);
		}

		if(i >= M_S)
		{
			l_0.push_back(s_0[i-M_S+1]);
		}
		else
		{
			l_0.push_back(-10000000);
		}

		if(i >= M_L)
		{
			double tmp = 0;
			tmp = s_1[i-M_L+1];
			for(int j=i-M_L + 2; j<=i; j++)
			{
				tmp += s_row[j];
			}
			l_1.push_back(tmp);
		}
		else
		{
			l_1.push_back(-10000000);
		}
	}
	
	//end calculating weight sums
	
	//start tracing back and search regions
	
	vector<Seg> Seg_row; //searched regions
	int tmp_n = -1;

	int type = 0;
	if(s_0[L-1] > l_1[L-1])
		type = 1;
	else
		type = 4;
	
	int T = L-1;
	
	while(T > 0)
	{
		if(type == 1)
		{
			if(s_0[T-1] > l_1[T-1])
			{
				type = 1;
			}
			else
			{
				type = 4;
			}
			T--;
		}
		else if(type == 2)
		{
			if(s_1[T-1] > l_0[T-1])
			{
				Seg_row[tmp_n].score += s_row[T];
				type = 2;
			}
			else
			{
				Seg_row[tmp_n].score += s_row[T];
				Seg_row[tmp_n].start = T+1;
				type = 3;
			}
			T--;
		}
		else if(type == 3)
		{
			T = T - M_S + 1;
			type = 1;
		}
		else
		{
			Seg tmp_Seg;
			tmp_Seg.end = T+1;
			tmp_Seg.score = 0;
			for(int j = T; j> T-M_L+1; j--)
			{
				tmp_Seg.score += s_row[j];
			}
			Seg_row.push_back(tmp_Seg);
			tmp_n++;
			
			type = 2;
			T = T - M_L+1;
		}
	}

	if(type == 2)
	{
		Seg_row[tmp_n].score += s_row[T];
		Seg_row[tmp_n].start = 1;
	}
	
	//end tracing back and search regions

	for(int i=tmp_n; i>=0; i--)
	{
		ofs << chr << "	" << (Seg_row[i].start-1)*window  << "	" << (Seg_row[i].end-1)*window << "	" << Seg_row[i].score << endl;
	}

	return;

}




int main(int argc, char** argv)
{
	int max = atoi(argv[3]);
	
	int window = 200;
	
	if(argc == 10)
	{
		window = atoi(argv[9]);
	}

	ofstream ofs;
	ofs.open(argv[8]);
	ofs.close();

	for(int i=1; i<max+1;i++)
	{
		string file_name, out_name;
		stringstream ss, ss2;
		ss << string(argv[1]) << i << "_binary.txt";
		file_name = ss.str();

		make_Seg(file_name.c_str(), argv[2], atoi(argv[4]), atoi(argv[5]), atoi(argv[6]), atof(argv[7]), argv[8], i, window);
	}
	
	return 0;
}