EmpiricalFormula.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Chris Bielow $
// $Authors: Andreas Bertsch, Chris Bielow $
// --------------------------------------------------------------------------
//
#pragma once

#include <iosfwd>
#include <map>
#include <set>
#include <algorithm>

#include <OpenMS/CONCEPT/Types.h>


namespace OpenMS
{
  class String;
  class Element;
  class ElementDB;
  class IsotopeDistribution;
  class IsotopePatternGenerator;
  class CoarseIsotopePatternGenerator;
  class OPENMS_DLLAPI EmpiricalFormula
  {

protected:
    typedef std::map<const Element*, SignedSize> MapType_;

public:
    typedef MapType_::const_iterator ConstIterator;
    typedef MapType_::const_iterator const_iterator;
    typedef MapType_::iterator Iterator;
    typedef MapType_::iterator iterator;

    EmpiricalFormula();

    EmpiricalFormula(const EmpiricalFormula& rhs);

    explicit EmpiricalFormula(const String& rhs);

    EmpiricalFormula(SignedSize number, const Element* element, SignedSize charge = 0);

    virtual ~EmpiricalFormula();



    double getMonoWeight() const;

    double getAverageWeight() const;

    double calculateTheoreticalIsotopesNumber() const;

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

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


    IsotopeDistribution getIsotopeDistribution(const IsotopePatternGenerator& method) const;    
    
    IsotopeDistribution getConditionalFragmentIsotopeDist(const EmpiricalFormula& precursor, const std::set<UInt>& precursor_isotopes, const CoarseIsotopePatternGenerator& method) const;

    SignedSize getNumberOf(const Element* element) const;

    SignedSize getNumberOfAtoms() const;

    SignedSize getCharge() const;

    void setCharge(SignedSize charge);

    String toString() const;

    std::map<std::string, int> toMap() const;

    EmpiricalFormula& operator=(const EmpiricalFormula& rhs);

    EmpiricalFormula& operator+=(const EmpiricalFormula& rhs);

    EmpiricalFormula operator*(const SignedSize& times) const;

    EmpiricalFormula operator+(const EmpiricalFormula& rhs) const;

    EmpiricalFormula& operator-=(const EmpiricalFormula& rhs);

    EmpiricalFormula operator-(const EmpiricalFormula& rhs) const;


    bool isEmpty() const;

    bool isCharged() const;

    bool hasElement(const Element* element) const;

    bool contains(const EmpiricalFormula& ef);

    bool operator==(const EmpiricalFormula& rhs) const;

    bool operator!=(const EmpiricalFormula& rhs) const;

    bool operator<(const EmpiricalFormula& rhs) const;


    friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const EmpiricalFormula& formula);

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

    inline ConstIterator end() const { return formula_.end(); }
    
    inline Iterator begin() { return formula_.begin(); }

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

protected:

    void removeZeroedElements_();

    MapType_ formula_;

    SignedSize charge_;

    SignedSize parseFormula_(std::map<const Element*, SignedSize>& ef, const String& formula) const;

  };

  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const EmpiricalFormula& formula);

} // namespace OpenMS