EmpiricalFormula.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
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//
#ifndef OPENMS_CHEMISTRY_EMPIRICALFORMULA_H
#define OPENMS_CHEMISTRY_EMPIRICALFORMULA_H

#include <iostream>
#include <vector>

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/CHEMISTRY/IsotopeDistribution.h>
#include <OpenMS/CONCEPT/Types.h>

namespace OpenMS
{
  class Element;
  class ElementDB;
  class OPENMS_DLLAPI EmpiricalFormula
  {

public:


    typedef Map<const Element *, SignedSize>::ConstIterator ConstIterator;
    typedef Map<const Element *, SignedSize>::ConstIterator const_iterator;


    EmpiricalFormula();

    EmpiricalFormula(const EmpiricalFormula & rhs);

    EmpiricalFormula(const String & rhs);

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

    virtual ~EmpiricalFormula();


    DoubleReal getMonoWeight() const;

    DoubleReal getAverageWeight() const;

    IsotopeDistribution getIsotopeDistribution(UInt max_depth) const;

    const Element * getElement(const String & name) const;

    const Element * getElement(UInt atomic_number) const;

    const ElementDB * getElementDB() const;

    Size getNumberOf(UInt atomic_number) const;

    Size getNumberOf(const String & name) const;

    Size getNumberOf(const Element * element) const;

    Size getNumberOfAtoms() const;

    SignedSize getCharge() const;

    void setCharge(SignedSize charge);

    String getString() const;


    EmpiricalFormula & operator=(const EmpiricalFormula & rhs);

    EmpiricalFormula & operator=(const String & rhs);

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

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

    EmpiricalFormula operator*(const SignedSize & times) const;

    EmpiricalFormula operator+(const EmpiricalFormula & rhs) const;

    EmpiricalFormula operator+(const String & rhs) const;

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

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

    EmpiricalFormula operator-(const EmpiricalFormula & rhs) const;

    EmpiricalFormula operator-(const String & rhs) const;


    bool isEmpty() const;

    bool isCharged() const;

    bool hasElement(const Element * element) const;

    bool hasElement(const String & name) const;

    bool hasElement(UInt atomic_number) const;

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

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

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

    bool operator!=(const String & 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(); }

protected:

    void removeZeroedElements_();

    Map<const Element *, SignedSize> formula_;

    SignedSize charge_;

    void readElementsFromFile_(const String & file_name);

    SignedSize parseFormula_(Map<const Element *, SignedSize> & ef, const String & formula) const;

    const ElementDB * element_db_;
  };

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

} // namespace OpenMS
#endif