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/*
* Copyright (C) 2015-2018 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>.
*/
#include <cmath>
#include <algorithm>
#include <vector>
#include <stdlib.h>
#include <string.h>
#include <tuple>
#include <unordered_map>
#include <queue>
#include <utility>
#include <iostream>
#include <iomanip>
#include <cctype>
#include <stdexcept>
#include <string>
#include <limits>
#include <assert.h>
#include <ctype.h>
#include "platform.h"
#include "conf.h"
#include "dirtyAllocator.h"
#include "operators.h"
#include "summator.h"
#include "marginalTrek++.h"
#include "isoSpec++.h"
#include "misc.h"
#include "element_tables.h"
using namespace std;
namespace IsoSpec
{
Iso::Iso(
int _dimNumber,
const int* _isotopeNumbers,
const int* _atomCounts,
const double* const * _isotopeMasses,
const double* const * _isotopeProbabilities
) :
disowned(false),
dimNumber(_dimNumber),
isotopeNumbers(array_copy<int>(_isotopeNumbers, _dimNumber)),
atomCounts(array_copy<int>(_atomCounts, _dimNumber)),
confSize(_dimNumber * sizeof(int)),
allDim(0),
marginals(nullptr),
modeLProb(0.0)
{
try{
setupMarginals(_isotopeMasses, _isotopeProbabilities);
}
catch(...)
{
delete[] isotopeNumbers;
delete[] atomCounts;
throw;
}
}
Iso::Iso(Iso&& other) :
disowned(other.disowned),
dimNumber(other.dimNumber),
isotopeNumbers(other.isotopeNumbers),
atomCounts(other.atomCounts),
confSize(other.confSize),
allDim(other.allDim),
marginals(other.marginals),
modeLProb(other.modeLProb)
{
other.disowned = true;
}
Iso::Iso(const Iso& other, bool fullcopy) :
disowned(fullcopy ? throw std::logic_error("Not implemented") : true),
dimNumber(other.dimNumber),
isotopeNumbers(fullcopy ? array_copy<int>(other.isotopeNumbers, dimNumber) : other.isotopeNumbers),
atomCounts(fullcopy ? array_copy<int>(other.atomCounts, dimNumber) : other.atomCounts),
confSize(other.confSize),
allDim(other.allDim),
marginals(fullcopy ? throw std::logic_error("Not implemented") : other.marginals),
modeLProb(other.modeLProb)
{}
inline void Iso::setupMarginals(const double* const * _isotopeMasses, const double* const * _isotopeProbabilities)
{
if (marginals == nullptr)
{
int ii = 0;
try
{
marginals = new Marginal*[dimNumber];
while(ii < dimNumber)
{
allDim += isotopeNumbers[ii];
marginals[ii] = new Marginal(
_isotopeMasses[ii],
_isotopeProbabilities[ii],
isotopeNumbers[ii],
atomCounts[ii]
);
modeLProb += marginals[ii]->getModeLProb();
ii++;
}
}
catch(...)
{
ii--;
while(ii >= 0)
{
delete marginals[ii];
ii--;
}
delete[] marginals;
marginals = nullptr;
throw;
}
}
}
Iso::~Iso()
{
if(!disowned)
{
if (marginals != nullptr)
dealloc_table(marginals, dimNumber);
delete[] isotopeNumbers;
delete[] atomCounts;
}
}
double Iso::getLightestPeakMass() const
{
double mass = 0.0;
for (int ii=0; ii<dimNumber; ii++)
mass += marginals[ii]->getLightestConfMass();
return mass;
}
double Iso::getHeaviestPeakMass() const
{
double mass = 0.0;
for (int ii=0; ii<dimNumber; ii++)
mass += marginals[ii]->getHeaviestConfMass();
return mass;
}
Iso::Iso(const char* formula) :
disowned(false),
allDim(0),
marginals(nullptr),
modeLProb(0.0)
{
std::vector<const double*> isotope_masses;
std::vector<const double*> isotope_probabilities;
dimNumber = parse_formula(formula, isotope_masses, isotope_probabilities, &isotopeNumbers, &atomCounts, &confSize);
setupMarginals(isotope_masses.data(), isotope_probabilities.data());
}
unsigned int parse_formula(const char* formula, std::vector<const double*>& isotope_masses, std::vector<const double*>& isotope_probabilities, int** isotopeNumbers, int** atomCounts, unsigned int* confSize)
{
// This function is NOT guaranteed to be secure against malicious input. It should be used only for debugging.
size_t slen = strlen(formula);
// Yes, it would be more elegant to use std::string here, but it's the only promiment place where it would be used in IsoSpec, and avoiding it here
// means we can run the whole thing through Clang's memory sanitizer without the need for instrumented libc++/libstdc++. That's worth messing with char pointers a
// little bit.
std::vector<std::pair<const char*, size_t> > elements;
std::vector<int> numbers;
if(slen == 0)
throw invalid_argument("Invalid formula: can't be empty");
if(!isdigit(formula[slen-1]))
throw invalid_argument("Invalid formula: every element must be followed by a number - write H2O1 and not H2O for water");
for(size_t ii=0; ii<slen; ii++)
if(!isdigit(formula[ii]) && !isalpha(formula[ii]))
throw invalid_argument("Ivalid formula: contains invalid (non-digit, non-alpha) character");
size_t position = 0;
size_t elem_end = 0;
size_t digit_end = 0;
while(position < slen)
{
elem_end = position;
while(isalpha(formula[elem_end]))
elem_end++;
digit_end = elem_end;
while(isdigit(formula[digit_end]))
digit_end++;
elements.emplace_back(&formula[position], elem_end-position);
numbers.push_back(atoi(&formula[elem_end]));
position = digit_end;
}
std::vector<int> element_indexes;
for (unsigned int i=0; i<elements.size(); i++)
{
int idx = -1;
for(int j=0; j<ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES; j++)
{
if ((strlen(elem_table_symbol[j]) == elements[i].second) && (strncmp(elements[i].first, elem_table_symbol[j], elements[i].second) == 0))
{
idx = j;
break;
}
}
if(idx < 0)
throw invalid_argument("Invalid formula");
element_indexes.push_back(idx);
}
vector<int> _isotope_numbers;
for(vector<int>::iterator it = element_indexes.begin(); it != element_indexes.end(); ++it)
{
int num = 0;
int at_idx = *it;
int atomicNo = elem_table_atomicNo[at_idx];
while(at_idx < ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES && elem_table_atomicNo[at_idx] == atomicNo)
{
at_idx++;
num++;
}
_isotope_numbers.push_back(num);
}
for(vector<int>::iterator it = element_indexes.begin(); it != element_indexes.end(); ++it)
{
isotope_masses.push_back(&elem_table_mass[*it]);
isotope_probabilities.push_back(&elem_table_probability[*it]);
};
const unsigned int dimNumber = elements.size();
*isotopeNumbers = array_copy<int>(_isotope_numbers.data(), dimNumber);
*atomCounts = array_copy<int>(numbers.data(), dimNumber);
*confSize = dimNumber * sizeof(int);
return dimNumber;
}
/*
* ----------------------------------------------------------------------------------------------------------
*/
IsoGenerator::IsoGenerator(Iso&& iso, bool alloc_partials) :
Iso(std::move(iso)),
partialLProbs(alloc_partials ? new double[dimNumber+1] : nullptr),
partialMasses(alloc_partials ? new double[dimNumber+1] : nullptr),
partialProbs(alloc_partials ? new double[dimNumber+1] : nullptr)
{
if(alloc_partials)
{
partialLProbs[dimNumber] = 0.0;
partialMasses[dimNumber] = 0.0;
partialProbs[dimNumber] = 1.0;
}
}
IsoGenerator::~IsoGenerator()
{
if(partialLProbs != nullptr)
delete[] partialLProbs;
if(partialMasses != nullptr)
delete[] partialMasses;
if(partialProbs != nullptr)
delete[] partialProbs;
}
/*
* ----------------------------------------------------------------------------------------------------------
*/
IsoThresholdGenerator::IsoThresholdGenerator(Iso&& iso, double _threshold, bool _absolute, int tabSize, int hashSize, bool reorder_marginals)
: IsoGenerator(std::move(iso)),
Lcutoff(_threshold <= 0.0 ? std::numeric_limits<double>::lowest() : (_absolute ? log(_threshold) : log(_threshold) + modeLProb))
{
counter = new int[dimNumber];
maxConfsLPSum = new double[dimNumber-1];
marginalResultsUnsorted = new PrecalculatedMarginal*[dimNumber];
empty = false;
for(int ii=0; ii<dimNumber; ii++)
{
counter[ii] = 0;
marginalResultsUnsorted[ii] = new PrecalculatedMarginal(std::move(*(marginals[ii])),
Lcutoff - modeLProb + marginals[ii]->getModeLProb(),
true,
tabSize,
hashSize);
if(!marginalResultsUnsorted[ii]->inRange(0))
empty = true;
}
if(reorder_marginals)
{
OrderMarginalsBySizeDecresing comparator(marginalResultsUnsorted);
int* tmpMarginalOrder = new int[dimNumber];
for(int ii=0; ii<dimNumber; ii++)
tmpMarginalOrder[ii] = ii;
std::sort(tmpMarginalOrder, tmpMarginalOrder + dimNumber, comparator);
marginalResults = new PrecalculatedMarginal*[dimNumber];
for(int ii=0; ii<dimNumber; ii++)
marginalResults[ii] = marginalResultsUnsorted[tmpMarginalOrder[ii]];
marginalOrder = new int[dimNumber];
for(int ii = 0; ii<dimNumber; ii++)
marginalOrder[tmpMarginalOrder[ii]] = ii;
delete[] tmpMarginalOrder;
}
else
{
marginalResults = marginalResultsUnsorted;
marginalOrder = nullptr;
}
lProbs_ptr_start = marginalResults[0]->get_lProbs_ptr();
if(dimNumber > 1)
maxConfsLPSum[0] = marginalResults[0]->getModeLProb();
for(int ii=1; ii<dimNumber-1; ii++)
maxConfsLPSum[ii] = maxConfsLPSum[ii-1] + marginalResults[ii]->getModeLProb();
lProbs_ptr = lProbs_ptr_start;
partialLProbs_second = partialLProbs;
partialLProbs_second++;
if(!empty)
{
recalc(dimNumber-1);
counter[0]--;
lProbs_ptr--;
}
else
{
terminate_search();
lcfmsv = std::numeric_limits<double>::infinity();
}
}
void IsoThresholdGenerator::terminate_search()
{
for(int ii=0; ii<dimNumber; ii++)
{
counter[ii] = marginalResults[ii]->get_no_confs()-1;
partialLProbs[ii] = -std::numeric_limits<double>::infinity();
}
partialLProbs[dimNumber] = -std::numeric_limits<double>::infinity();
lProbs_ptr = lProbs_ptr_start + marginalResults[0]->get_no_confs()-1;
}
size_t IsoThresholdGenerator::count_confs()
{
// Smarter algorithm forthcoming in 2.0
size_t ret = 0;
while(advanceToNextConfiguration())
ret++;
reset();
return ret;
}
void IsoThresholdGenerator::reset()
{
if(empty)
{
terminate_search();
return;
}
partialLProbs[dimNumber] = 0.0;
memset(counter, 0, sizeof(int)*dimNumber);
recalc(dimNumber-1);
counter[0]--;
lProbs_ptr = lProbs_ptr_start - 1;
}
/*
* ------------------------------------------------------------------------------------------------------------------------
*/
IsoOrderedGenerator::IsoOrderedGenerator(Iso&& iso, int _tabSize, int _hashSize) :
IsoGenerator(std::move(iso), false), allocator(dimNumber, _tabSize)
{
partialLProbs = ¤tLProb;
partialMasses = ¤tMass;
partialProbs = ¤tProb;
marginalResults = new MarginalTrek*[dimNumber];
for(int i = 0; i<dimNumber; i++)
marginalResults[i] = new MarginalTrek(std::move(*(marginals[i])), _tabSize, _hashSize);
logProbs = new const vector<double>*[dimNumber];
masses = new const vector<double>*[dimNumber];
marginalConfs = new const vector<int*>*[dimNumber];
for(int i = 0; i<dimNumber; i++)
{
masses[i] = &marginalResults[i]->conf_masses();
logProbs[i] = &marginalResults[i]->conf_lprobs();
marginalConfs[i] = &marginalResults[i]->confs();
}
topConf = allocator.newConf();
memset(
reinterpret_cast<char*>(topConf) + sizeof(double),
0,
sizeof(int)*dimNumber
);
*(reinterpret_cast<double*>(topConf)) =
combinedSum(
getConf(topConf),
logProbs,
dimNumber
);
pq.push(topConf);
}
IsoOrderedGenerator::~IsoOrderedGenerator()
{
dealloc_table<MarginalTrek*>(marginalResults, dimNumber);
delete[] logProbs;
delete[] masses;
delete[] marginalConfs;
partialLProbs = nullptr;
partialMasses = nullptr;
partialProbs = nullptr;
}
bool IsoOrderedGenerator::advanceToNextConfiguration()
{
if(pq.size() < 1)
return false;
topConf = pq.top();
pq.pop();
int* topConfIsoCounts = getConf(topConf);
currentLProb = *(reinterpret_cast<double*>(topConf));
currentMass = combinedSum( topConfIsoCounts, masses, dimNumber );
currentProb = exp(currentLProb);
ccount = -1;
for(int j = 0; j < dimNumber; ++j)
{
if(marginalResults[j]->probeConfigurationIdx(topConfIsoCounts[j] + 1))
{
if(ccount == -1)
{
topConfIsoCounts[j]++;
*(reinterpret_cast<double*>(topConf)) = combinedSum(topConfIsoCounts, logProbs, dimNumber);
pq.push(topConf);
topConfIsoCounts[j]--;
ccount = j;
}
else
{
void* acceptedCandidate = allocator.newConf();
int* acceptedCandidateIsoCounts = getConf(acceptedCandidate);
memcpy(acceptedCandidateIsoCounts, topConfIsoCounts, confSize);
acceptedCandidateIsoCounts[j]++;
*(reinterpret_cast<double*>(acceptedCandidate)) = combinedSum(acceptedCandidateIsoCounts, logProbs, dimNumber);
pq.push(acceptedCandidate);
}
}
if(topConfIsoCounts[j] > 0)
break;
}
if(ccount >=0)
topConfIsoCounts[ccount]++;
return true;
}
/*
* ---------------------------------------------------------------------------------------------------
*/
#if !ISOSPEC_BUILDING_R
void printConfigurations(
const std::tuple<double*,double*,int*,int>& results,
int dimNumber,
int* isotopeNumbers
){
int m = 0;
for(int i=0; i<std::get<3>(results); i++){
std::cout << "Mass = " << std::get<0>(results)[i] <<
"\tand log-prob = " << std::get<1>(results)[i] <<
"\tand prob = " << exp(std::get<1>(results)[i]) <<
"\tand configuration =\t";
for(int j=0; j<dimNumber; j++){
for(int k=0; k<isotopeNumbers[j]; k++ )
{
std::cout << std::get<2>(results)[m] << " ";
m++;
}
std::cout << '\t';
}
std::cout << std::endl;
}
}
#endif /* !ISOSPEC_BUILDING_R */
IsoLayeredGenerator::IsoLayeredGenerator( Iso&& iso,
double _targetCoverage,
double _percentageToExpand,
int _tabSize,
int _hashSize,
bool trim
) : IsoGenerator(std::move(iso)),
allocator(dimNumber, _tabSize),
candidate(new int[dimNumber]),
targetCoverage(_targetCoverage >= 1.0 ? 10000.0 : _targetCoverage), // If the user wants the entire spectrum,
// give it to him - and make sure we don't terminate
// early because of rounding errors
percentageToExpand(_percentageToExpand),
do_trim(trim),
layers(0),
generator_position(-1)
{
marginalResults = new MarginalTrek*[dimNumber];
for(int i = 0; i<dimNumber; i++)
marginalResults[i] = new MarginalTrek(std::move(*(marginals[i])), _tabSize, _hashSize);
logProbs = new const vector<double>*[dimNumber];
masses = new const vector<double>*[dimNumber];
marginalConfs = new const vector<int*>*[dimNumber];
for(int i = 0; i<dimNumber; i++)
{
masses[i] = &marginalResults[i]->conf_masses();
logProbs[i] = &marginalResults[i]->conf_lprobs();
marginalConfs[i] = &marginalResults[i]->confs();
}
void* topConf = allocator.newConf();
memset(reinterpret_cast<char*>(topConf) + sizeof(double), 0, sizeof(int)*dimNumber);
*(reinterpret_cast<double*>(topConf)) = combinedSum(getConf(topConf), logProbs, dimNumber);
current = new std::vector<void*>();
next = new std::vector<void*>();
current->push_back(topConf);
lprobThr = (*reinterpret_cast<double*>(topConf));
if(targetCoverage > 0.0)
while(advanceToNextLayer()) {};
}
IsoLayeredGenerator::~IsoLayeredGenerator()
{
if(current != nullptr)
delete current;
if(next != nullptr)
delete next;
delete[] logProbs;
delete[] masses;
delete[] marginalConfs;
delete[] candidate;
dealloc_table(marginalResults, dimNumber);
}
bool IsoLayeredGenerator::advanceToNextLayer()
{
layers += 1;
double maxFringeLprob = -std::numeric_limits<double>::infinity();
if(current == nullptr)
return false;
int accepted_in_this_layer = 0;
Summator prob_in_this_layer(totalProb);
void* topConf;
while(current->size() > 0)
{
topConf = current->back();
current->pop_back();
double top_lprob = getLProb(topConf);
if(top_lprob >= lprobThr)
{
newaccepted.push_back(topConf);
accepted_in_this_layer++;
prob_in_this_layer.add(exp(top_lprob));
}
else
{
next->push_back(topConf);
continue;
}
int* topConfIsoCounts = getConf(topConf);
for(int j = 0; j < dimNumber; ++j)
{
// candidate cannot refer to a position that is
// out of range of the stored marginal distribution.
if(marginalResults[j]->probeConfigurationIdx(topConfIsoCounts[j] + 1))
{
memcpy(candidate, topConfIsoCounts, confSize);
candidate[j]++;
void* acceptedCandidate = allocator.newConf();
int* acceptedCandidateIsoCounts = getConf(acceptedCandidate);
memcpy( acceptedCandidateIsoCounts, candidate, confSize);
double newConfProb = combinedSum(
candidate,
logProbs,
dimNumber
);
*(reinterpret_cast<double*>(acceptedCandidate)) = newConfProb;
if(newConfProb >= lprobThr)
current->push_back(acceptedCandidate);
else
{
next->push_back(acceptedCandidate);
if(newConfProb > maxFringeLprob)
maxFringeLprob = top_lprob;
}
}
if(topConfIsoCounts[j] > 0)
break;
}
}
if(next == nullptr || next->size() < 1)
return false;
else
{
if(prob_in_this_layer.get() < targetCoverage)
{
std::vector<void*>* nnew = current;
nnew->clear();
current = next;
next = nnew;
int howmany = floor(current->size()*percentageToExpand);
lprobThr = getLProb(quickselect(current->data(), howmany, 0, current->size()));
totalProb = prob_in_this_layer;
}
else
{
delete next;
next = nullptr;
delete current;
current = nullptr;
int start = 0;
int end = accepted_in_this_layer - 1;
void* swapspace;
if(do_trim)
{
void** lastLayer = &(newaccepted.data()[newaccepted.size()-accepted_in_this_layer]);
Summator qsprob(totalProb);
while(totalProb.get() < targetCoverage)
{
if(start == end)
break;
// Partition part
int len = end - start;
#if ISOSPEC_BUILDING_R
int pivot = len/2 + start; // We're very definitely NOT switching to R to use a RNG, and if R sees us use C RNG it complains...
#else
int pivot = rand() % len + start;
#endif
void* pval = lastLayer[pivot];
double pprob = getLProb(pval);
mswap(lastLayer[pivot], lastLayer[end-1]);
int loweridx = start;
for(int i=start; i<end-1; i++)
{
if(getLProb(lastLayer[i]) > pprob)
{
mswap(lastLayer[i], lastLayer[loweridx]);
loweridx++;
}
}
mswap(lastLayer[end-1], lastLayer[loweridx]);
// Selection part
Summator leftProb(qsprob);
for(int i=start; i<=loweridx; i++)
{
leftProb.add(exp(getLProb(lastLayer[i])));
}
if(leftProb.get() < targetCoverage)
{
start = loweridx+1;
qsprob = leftProb;
}
else
end = loweridx;
}
int accend = newaccepted.size()-accepted_in_this_layer+start+1;
totalProb = qsprob;
newaccepted.resize(accend);
return true;
}
else // No trimming
{
totalProb = prob_in_this_layer;
return true;
}
}
}
return true;
}
bool IsoLayeredGenerator::advanceToNextConfiguration()
{
generator_position++;
if(generator_position < newaccepted.size())
{
partialLProbs[0] = getLProb(newaccepted[generator_position]);
partialMasses[0] = combinedSum(getConf(newaccepted[generator_position]), masses, dimNumber);
partialProbs[0] = exp(partialLProbs[0]);
return true;
}
else
return false;
}
} // namespace IsoSpec
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