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

#ifndef __UTIL_H__
#define __UTIL_H__

#include <stdint.h>
#include <map>
#include <sstream>
#include <cassert>
#include <vector>
#include <iostream>
#include <cmath>
#include <cstdlib>

using namespace std;

// macros: using int64_t for two int32_t
#define pack(x, y) (int64_t)((((int64_t)(x)) << 32) | ((int64_t)(y)))
#define high32(x) (int32_t)((x) >> 32)
#define low32(x) (int32_t)(((x) << 32) >> 32)

// definitions
typedef map<int32_t, int32_t> MI32;
typedef pair<int32_t, int32_t> PI32;
typedef map<int32_t, int> MPI;
typedef pair<int32_t, int> PPI;
typedef pair<int, int> PI;
typedef map<int, int> MI;

// common small functions
template<typename T>
string tostring(T t)
{
	ostringstream s;
	s << t;
	return s.str();
}

template<typename T>
T compute_overlap(const pair<T, T> &x, const pair<T, T> &y)
{
	assert(x.first <= x.second);
	assert(y.first <= y.second);
	if(x.first > y.first) return compute_overlap(y, x);
	assert(x.first <= y.first);
	if(y.first >= x.second) return x.second - y.first;
	if(x.second <= y.second) return x.second - y.first;
	else return y.second - y.first;
}

template<typename T>
int reverse(vector<T> &x)
{
	if(x.size() == 0) return 0;
	int i = 0;
	int j = x.size() - 1;
	while(i < j)
	{
		T t = x[i];
		x[i] = x[j];
		x[j] = t;
		i++;
		j--;
	}
	return 0;
}

template<typename T>
int max_element(const vector<T> &x)
{
	if(x.size() == 0) return -1;
	int k = 0;
	for(int i = 1; i < x.size(); i++)
	{
		if(x[i] <= x[k]) continue;
		k = i;
	}
	return k;
}

template<typename T>
int min_element(const vector<T> &x)
{
	if(x.size() == 0) return -1;
	int k = 0;
	for(int i = 1; i < x.size(); i++)
	{
		if(x[i] >= x[k]) continue;
		k = i;
	}
	return k;
}

template<typename T>
int printv(const vector<T> &x)
{
	for(int i = 0; i < x.size(); i++)
	{
		cout<< x[i] <<" ";
	}
	return 0;
}

template<typename T>
int compute_mean_dev(const vector<T> &v, int si, int ti, double &ave, double &dev)
{
	ave = -1;
	dev = -1;
	if(si >= ti) return 0;

	assert(si >= 0 && si < v.size());
	assert(ti > 0 && ti <= v.size());

	T sum = 0;
	for(int i = si; i < ti; i++)
	{
		sum += v[i];
	}

	ave = sum * 1.0 / (ti - si);

	double var;
	for(int i = si ; i < ti; i++)
	{
		var += (v[i] - ave) * (v[i] - ave);
	}

	dev = sqrt(var / (ti - si));
	return 0;
}

template<typename T>
vector<int> consecutive_subset(const vector<T> &ref, const vector<T> &x)
{
	vector<int> v;
	if(x.size() == 0) return v;
	if(ref.size() == 0) return v;
	if(x.size() > ref.size()) return v;
	for(int i = 0; i <= ref.size() - x.size(); i++)
	{
		if(ref[i] != x[0]) continue;
		int k = i;
		bool b = true;
		for(int j = 0; j < x.size(); j++)
		{
			if(x[j] != ref[j + k]) b = false;
			if(b == false) break;
		}
		if(b == false) continue;
		v.push_back(k);
	}
	return v;
}

template<typename K, typename V>
vector<K> get_keys(const map<K, V> &m)
{
	vector<K> v;
    typedef typename std::map<K,V>::const_iterator MIT;
	for(MIT it = m.begin(); it != m.end(); it++)
	{
		v.push_back(it->first);
	}
	return v;
}

vector<int> get_random_permutation(int n);

#endif