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IsotopeDistributions.h
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//
// Created by Dennis Goldfarb on 6/9/17.
//
#ifndef FRAGMENT_ISOTOPE_DISTRIBUTION_PAPER_ISOTOPEDISTRIBUTIONS_H
#define FRAGMENT_ISOTOPE_DISTRIBUTION_PAPER_ISOTOPEDISTRIBUTIONS_H
#include <OpenMS/KERNEL/Peak1D.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include "SpectrumUtilities.h"
#include "Stats.h"
class IsotopeDistributions {
public :
// Precursor distributions
IsotopeDistributions(std::set<OpenMS::UInt> precursorIsotopes, Ion precursorIon,
const OpenMS::IsotopeSplineDB* isotopeDB,
OpenMS::MSSpectrum<OpenMS::Peak1D> ¤tSpectrumCentroid,
double width, OpenMS::Precursor &precursorInfo)
{
if (precursorIsotopes.size() > 0) {
OpenMS::UInt minIsotope = *std::min_element(precursorIsotopes.begin(), precursorIsotopes.end());
OpenMS::UInt searchDepth = *std::max_element(precursorIsotopes.begin(), precursorIsotopes.end()) + 1;
OpenMS::IsotopeDistribution id = precursorIon.formula.getIsotopeDistribution(searchDepth);
double ionMZ = precursorIon.monoWeight / precursorIon.charge;
for (int i = minIsotope; i < id.size(); ++i) {
double isoMZ = ionMZ + ( OpenMS::Constants::C13C12_MASSDIFF_U / precursorIon.charge ) * i;
exactPrecursorDist.push_back(std::make_pair(isoMZ, id.getContainer()[i].second));
}
exactPrecursorDist = SpectrumUtilities::scaleDistribution(exactPrecursorDist);
SpectrumUtilities::observedDistribution(observedDist, exactPrecursorDist, currentSpectrumCentroid);
scaledObservedDist = SpectrumUtilities::scaleDistribution(observedDist);
}
exactPrecursorX2 = Stats::computeX2(scaledObservedDist, exactPrecursorDist);
}
// Fragment distributions
IsotopeDistributions(std::set<OpenMS::UInt> precursorIsotopes, Ion ion, Ion precursorIon,
const OpenMS::IsotopeSplineDB* isotopeDB, OpenMS::MSSpectrum<OpenMS::Peak1D> ¤tSpectrumCentroid,
OpenMS::Precursor &precursorInfo, double width)
{
SpectrumUtilities::exactConditionalFragmentIsotopeDist(exactConditionalFragmentDist,
precursorIsotopes,
ion,
precursorIon.sequence,
precursorIon.charge);
SpectrumUtilities::approxFragmentFromWeightIsotopeDist(approxFragmentFromWeightDist,
precursorIsotopes,
ion,
precursorIon.sequence,
precursorIon.charge);
SpectrumUtilities::approxFragmentFromWeightAndSIsotopeDist(approxFragmentFromWeightAndSulfurDist,
precursorIsotopes,
ion,
precursorIon.sequence,
precursorIon.charge);
SpectrumUtilities::approxFragmentSplineFromWeightIsotopeDist(approxFragmentSplineFromWeightDist,
precursorIsotopes,
ion,
precursorIon.sequence,
precursorIon.charge,
isotopeDB);
SpectrumUtilities::approxFragmentSplineFromWeightAndSIsotopeDist(approxFragmentSplineFromWeightAndSulfurDist,
precursorIsotopes,
ion,
precursorIon.sequence,
precursorIon.charge,
isotopeDB);
SpectrumUtilities::exactPrecursorIsotopeDist(exactPrecursorDist, precursorIsotopes,
ion);
SpectrumUtilities::approxPrecursorFromWeightIsotopeDist(approxPrecursorFromWeightDist, precursorIsotopes,
ion);
//match theoretical distribution with observed peaks
SpectrumUtilities::observedDistribution(observedDist, exactConditionalFragmentDist, currentSpectrumCentroid);
//scale observed intensities across distribution
scaledObservedDist = SpectrumUtilities::scaleDistribution(observedDist);
//report on matched ion distribution depth
completeFlag = true;
completeAtDepth = 0;
for (int i = 0; i < observedDist.size(); ++i) {
if (observedDist[i].second != 0) {
if (completeFlag) {
++completeAtDepth;
}
} else {
completeFlag = false;
}
}
isValid = true; //SpectrumUtilities::scaledDistributionValid(scaledObservedDist) && completeAtDepth > 1;
//compute chi-squared with observed to Conditional
exactCondFragmentX2 = Stats::computeX2(scaledObservedDist, exactConditionalFragmentDist);
approxFragmentFromWeightX2 = Stats::computeX2(scaledObservedDist, approxFragmentFromWeightDist);
approxFragmentFromWeightAndSulfurX2 = Stats::computeX2(scaledObservedDist, approxFragmentFromWeightAndSulfurDist);
approxFragmentSplineFromWeightX2 = Stats::computeX2(scaledObservedDist, approxFragmentSplineFromWeightDist);
approxFragmentSplineFromWeightAndSulfurX2 = Stats::computeX2(scaledObservedDist, approxFragmentSplineFromWeightAndSulfurDist);
exactPrecursorX2 = Stats::computeX2(scaledObservedDist, exactPrecursorDist);
approxPrecursorX2 = Stats::computeX2(scaledObservedDist, approxPrecursorFromWeightDist);
}
// Precursor or fragment
std::vector<std::pair<double, double> > exactPrecursorDist;
std::vector<std::pair<double, double> > approxPrecursorFromWeightDist;
std::vector<std::pair<double, double> > observedDist;
std::vector<std::pair<double, double> > scaledObservedDist;
// Precursor
std::vector<std::pair<double, double> > approxPrecursorFromWeightAndSulfurDist;
std::vector<std::pair<double, double> > approxPrecursorSplineFromWeightDist;
std::vector<std::pair<double, double> > approxPrecursorSplineFromWeightAndSulfurDist;
// Fragment
std::vector<std::pair<double, double> > approxFragmentFromWeightDist;
std::vector<std::pair<double, double> > approxFragmentFromWeightAndSulfurDist;
std::vector<std::pair<double, double> > approxFragmentSplineFromWeightDist;
std::vector<std::pair<double, double> > approxFragmentSplineFromWeightAndSulfurDist;
std::vector<std::pair<double, double> > exactConditionalFragmentDist;
// Precursor or fragment
double exactPrecursorX2;
double approxPrecursorX2;
// Precursor
double approxPrecursorAndSulfurX2;
double approxPrecursorSplineX2;
double approxPrecursorSplineAndSulfurX2;
// Fragment
double exactCondFragmentX2;
double approxFragmentFromWeightX2;
double approxFragmentFromWeightAndSulfurX2;
double approxFragmentSplineFromWeightX2;
double approxFragmentSplineFromWeightAndSulfurX2;
bool completeFlag;
int completeAtDepth;
bool isValid;
private:
};
#endif //FRAGMENT_ISOTOPE_DISTRIBUTION_PAPER_ISOTOPEDISTRIBUTIONS_H