CoarseIsotopePatternGenerator.h

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// $Maintainer: Chris Bielow $
// $Authors: Clemens Groepl, Andreas Bertsch, Chris Bielow $
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#pragma once

#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopePatternGenerator.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>

#include <set>

namespace OpenMS
{
  class OPENMS_DLLAPI CoarseIsotopePatternGenerator
    : public IsotopePatternGenerator
  {

 public:
    CoarseIsotopePatternGenerator(const Size max_isotope = 0, const bool round_masses = false);

    ~CoarseIsotopePatternGenerator() override;


    void setMaxIsotope(const Size& max_isotope);

    void setRoundMasses(const bool round_masses);

    Size getMaxIsotope() const;

    bool getRoundMasses() const;

    IsotopeDistribution run(const EmpiricalFormula&) const override;

    IsotopeDistribution estimateFromPeptideWeight(double average_weight);

      IsotopeDistribution estimateFromPeptideMonoWeight(double mono_weight);


    IsotopeDistribution estimateFromPeptideWeightAndS(double average_weight, UInt S);

    static IsotopeDistribution approximateFromPeptideWeight(double mass, UInt num_peaks = 20, UInt charge = 1);

    static std::vector<double> approximateIntensities(double mass, UInt num_peaks = 20);

    IsotopeDistribution estimateFromRNAWeight(double average_weight);

   IsotopeDistribution estimateFromRNAMonoWeight(double mono_weight);


    IsotopeDistribution estimateFromDNAWeight(double average_weight);

    IsotopeDistribution estimateFromWeightAndComp(double average_weight, double C, double H, double N, double O, double S, double P);

    IsotopeDistribution estimateFromMonoWeightAndComp(double mono_weight, double C, double H, double N, double O, double S, double P);


    IsotopeDistribution estimateFromWeightAndCompAndS(double average_weight, UInt S, double C, double H, double N, double O, double P);

    IsotopeDistribution estimateForFragmentFromPeptideWeight(double average_weight_precursor, double average_weight_fragment, const std::set<UInt>& precursor_isotopes);

    IsotopeDistribution estimateForFragmentFromPeptideWeightAndS(double average_weight_precursor, UInt S_precursor, double average_weight_fragment, UInt S_fragment, const std::set<UInt>& precursor_isotopes) const;

    IsotopeDistribution estimateForFragmentFromRNAWeight(double average_weight_precursor, double average_weight_fragment, const std::set<UInt>& precursor_isotopes);

    IsotopeDistribution estimateForFragmentFromDNAWeight(double average_weight_precursor, double average_weight_fragment, const std::set<UInt>& precursor_isotopes);

    IsotopeDistribution estimateForFragmentFromWeightAndComp(double average_weight_precursor, double average_weight_fragment, const std::set<UInt>& precursor_isotopes, double C, double H, double N, double O, double S, double P) const;

    IsotopeDistribution calcFragmentIsotopeDist(const IsotopeDistribution& fragment_isotope_dist, const IsotopeDistribution& comp_fragment_isotope_dist, const std::set<UInt>& precursor_isotopes, const double fragment_mono_mass) const;

    CoarseIsotopePatternGenerator& operator=(const CoarseIsotopePatternGenerator& iso);

    IsotopeDistribution::ContainerType convolve(const IsotopeDistribution::ContainerType& left, const IsotopeDistribution::ContainerType& right) const;

  protected:

    IsotopeDistribution::ContainerType convolvePow_(const IsotopeDistribution::ContainerType& input, Size factor) const;

    IsotopeDistribution::ContainerType convolveSquare_(const IsotopeDistribution::ContainerType& input) const;

    IsotopeDistribution::ContainerType correctMass_(const IsotopeDistribution::ContainerType& input, const double mono_weight) const;

    IsotopeDistribution calcFragmentIsotopeDist_(const IsotopeDistribution::ContainerType& fragment_isotope_dist, const IsotopeDistribution::ContainerType& comp_fragment_isotope_dist, const std::set<UInt>& precursor_isotopes) const;

    IsotopeDistribution::ContainerType fillGaps_(const IsotopeDistribution::ContainerType& id) const;

    Size max_isotope_;
    bool round_masses_;

  };

} // namespace OpenMS