IsotopeDistribution.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// For a full list of authors, refer to the file AUTHORS.
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// $Maintainer: Chris Bielow $
// $Authors: Clemens Groepl, Andreas Bertsch, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/Types.h>

#include <utility>
#include <vector>
#include <set>

namespace OpenMS
{
  class OPENMS_DLLAPI IsotopeDistribution
  {
public:


    typedef std::vector<std::pair<Size, double> > ContainerType;
    typedef ContainerType::iterator iterator;
    typedef ContainerType::iterator Iterator;
    typedef ContainerType::const_iterator const_iterator;
    typedef ContainerType::const_iterator ConstIterator;

    typedef ContainerType::reverse_iterator reverse_iterator;
    typedef ContainerType::reverse_iterator ReverseIterator;
    typedef ContainerType::const_reverse_iterator const_reverse_iterator;
    typedef ContainerType::const_reverse_iterator ConstReverseIterator;



    IsotopeDistribution();

    explicit IsotopeDistribution(Size max_isotope);

    IsotopeDistribution(const IsotopeDistribution & isotope_distribution);

    virtual ~IsotopeDistribution();



    void setMaxIsotope(Size max_isotope);

    Size getMaxIsotope() const;

    void set(const ContainerType & distribution);

    const ContainerType & getContainer() const;

    Size getMax() const;

    Size getMin() const;

    Size size() const;

    void clear();

    void estimateFromPeptideWeight(double average_weight);

    void estimateFromPeptideWeightAndS(double average_weight, UInt S);

    void estimateFromRNAWeight(double average_weight);

    void estimateFromDNAWeight(double average_weight);

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

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

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

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

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

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

    void 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);

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

    void renormalize();

    void trimRight(double cutoff);

    void trimLeft(double cutoff);


    IsotopeDistribution & operator=(const IsotopeDistribution & isotope_distribution);

    IsotopeDistribution operator+(const IsotopeDistribution & isotope_distribution) const;

    IsotopeDistribution & operator+=(const IsotopeDistribution & isotope_distribution);

    IsotopeDistribution operator*(Size factor) const;

    IsotopeDistribution & operator*=(Size factor);

    bool operator==(const IsotopeDistribution & isotope_distribution) const;

    bool operator!=(const IsotopeDistribution & isotope_distribution) const;


    inline Iterator begin() { return distribution_.begin(); }

    inline Iterator end()   { return distribution_.end(); }

    inline ConstIterator begin() const { return distribution_.begin(); }

    inline ConstIterator end() const { return distribution_.end(); }

    inline ReverseIterator rbegin() { return distribution_.rbegin(); }

    inline ReverseIterator rend()   { return distribution_.rend(); }

    inline ConstReverseIterator rbegin() const { return distribution_.rbegin(); }

    inline ConstReverseIterator rend() const { return distribution_.rend(); }

protected:

    void convolve_(ContainerType & result, const ContainerType & left, const ContainerType & right) const;

    void convolvePow_(ContainerType & result, const ContainerType & input, Size factor) const;

    void convolveSquare_(ContainerType & result, const ContainerType & input) const;

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

    ContainerType fillGaps_(const ContainerType& id) const;

    Size max_isotope_;

    ContainerType distribution_;
  };

} // namespace OpenMS