isospec 0.1.0+2.6.0

/*
 *   Copyright (C) 2015-2020 Mateusz Łącki and Michał Startek.
 *
 *   This file is part of IsoSpec.
 *
 *   IsoSpec is free software: you can redistribute it and/or modify
 *   it under the terms of the Simplified ("2-clause") BSD licence.
 *
 *   IsoSpec is distributed in the hope that it will be useful,
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 *
 *   You should have received a copy of the Simplified BSD Licence
 *   along with IsoSpec.  If not, see <https://opensource.org/licenses/BSD-2-Clause>.
 */

#pragma once

#include <iostream>
#include <vector>
#include <cstring>
#include <algorithm>
#include "isoMath.h"
#include "pod_vector.h"

namespace IsoSpec
{

inline double combinedSum(
    const int* conf, const std::vector<double>** valuesContainer, int dimNumber
){
    double res = 0.0;
    for(int i = 0; i < dimNumber; i++)
        res += (*(valuesContainer[i]))[conf[i]];
    return res;
}

inline double combinedSum(
    const int* conf, const pod_vector<double>** valuesContainer, int dimNumber
){
    double res = 0.0;
    for(int i = 0; i < dimNumber; i++)
        res += (*(valuesContainer[i]))[conf[i]];
    return res;
}

inline int* getConf(void* conf)
{
    return reinterpret_cast<int*>(
        reinterpret_cast<char*>(conf) + sizeof(double)
    );
}

inline double getLProb(void* conf)
{
    double ret = *reinterpret_cast<double*>(conf);
    return ret;
}


inline double unnormalized_logProb(const int* conf, const double* logProbs, int dim)
{
    double  res = 0.0;

    for(int i = 0; i < dim; i++)
        res += minuslogFactorial(conf[i]) + conf[i] * logProbs[i];

    return res;
}

inline double calc_mass(const int* conf, const double* masses, int dim)
{
    double res = 0.0;

    for(int i = 0; i < dim; i++)
    {
        res += conf[i] * masses[i];
    }

    return res;
}



template<typename T> void printArray(const T* array, size_t size, const char* prefix = "")
{
    if (strlen(prefix) > 0)
        std::cout << prefix << " ";
    for (size_t i = 0; i < size; i++)
        std::cout << array[i] << " ";
    std::cout << std::endl;
}

template<typename T> void printVector(const std::vector<T>& vec)
{
    printArray<T>(vec.data(), vec.size());
}

template<typename T> void printVector(const pod_vector<T>& vec)
{
    printArray<T>(vec.data(), vec.size());
}

template<typename T> void printOffsets(const T** array, size_t size, const T* offset, const char* prefix = "")
{
    if (strlen(prefix) > 0)
        std::cout << prefix << " ";
    for (size_t i = 0; i < size; i++)
        std::cout << array[i] - offset << " ";
    std::cout << std::endl;
}

template<typename T> void printNestedArray(const T** array, const int* shape, size_t size)
{
    for (size_t i = 0; i < size; i++)
        printArray(array[i], shape[i]);
    std::cout << std::endl;
}

//! Quickly select the n'th positional statistic, including the weights.
void* quickselect(void** array, size_t n, size_t start, size_t end);


template <typename T> inline static T* array_copy(const T* A, size_t size)
{
    T* ret = new T[size];
    // memcpy() is declared with __attribute__((nonnull)), so a zero-length copy
    // from a null source is undefined behaviour even though it moves no bytes.
    // A zero-dimensional Iso (e.g. setupIso(0, NULL, ...)) reaches exactly that.
    if(size > 0)
        memcpy(ret, A, size*sizeof(T));
    return ret;
}

template <typename T> inline static T* array_copy_malloc(const T* A, size_t size)
{
    T* ret = reinterpret_cast<T*>(malloc(size * sizeof(T)));
    if(ret == nullptr)
        throw std::bad_alloc();
    memcpy(ret, A, size*sizeof(T));
    return ret;
}


template <typename T> static T* array_copy_nptr(const T* A, size_t size)
{
    if(A == nullptr)
        return nullptr;
    return array_copy(A, size);
}

template <typename T> static T* array_copy_nptr_malloc(const T* A, size_t size)
{
    if(A == nullptr)
        return nullptr;
    return array_copy_malloc(A, size);
}


template<typename T> void dealloc_table(T* tbl, int dim)
{
    for(int i = 0; i < dim; i++)
    {
        delete tbl[i];
    }
    delete[] tbl;
}

template<typename T> void realloc_append(T** array, T what, size_t old_array_size)
{
    T* newT = new T[old_array_size+1];
    // *array may be nullptr when old_array_size == 0 (a default-constructed
    // Iso), and memcpy from a null pointer is undefined even for zero bytes.
    if(old_array_size > 0)
        memcpy(newT, *array, old_array_size*sizeof(T));
    newT[old_array_size] = what;
    delete[] *array;
    *array = newT;
}

template<typename T> size_t* get_order(T* order_array, size_t N)
{
    size_t* arr = new size_t[N];
    for(size_t ii = 0; ii < N; ii++)
        arr[ii] = ii;

    std::sort(arr, arr + N, [&](size_t i, size_t j) { return order_array[i] < order_array[j]; });

    return arr;
}

template<typename T> size_t* get_inverse_order(T* order_array, size_t N)
{
    size_t* arr = new size_t[N];
    for(size_t ii = 0; ii < N; ii++)
        arr[ii] = ii;

    std::sort(arr, arr + N, [&](size_t i, size_t j) { return order_array[i] > order_array[j]; });

    return arr;
}

template<typename TA, typename TB> void impose_order(size_t* O, size_t N, TA* A, TB* B)
{
    for(size_t ii = 0; ii < N; ii++)
    {
        if(ii != O[ii])
        {
            size_t curr_ii = ii;
            TA ta = A[ii];
            TB tb = B[ii];
            size_t next_ii = O[ii];
            while(next_ii != ii)
            {
                A[curr_ii] = A[next_ii];
                B[curr_ii] = B[next_ii];
                O[curr_ii] = curr_ii;
                curr_ii = next_ii;
                next_ii = O[next_ii];
            }
            A[curr_ii] = ta;
            B[curr_ii] = tb;
            O[curr_ii] = curr_ii;
        }
    }
}


}  // namespace IsoSpec