ElementDB.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: Timo Sachsenberg $
// $Authors: Andreas Bertsch, Timo Sachsenberg, Chris Bielow, Jang Jang Jin$
// --------------------------------------------------------------------------
//

#pragma once

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>

#include <map>
#include <memory>
#include <unordered_map>
#include <string>

namespace OpenMS
{
  class Element;

  class OPENMS_DLLAPI ElementDB
  {
public:

    static ElementDB* getInstance();

    const std::unordered_map<std::string, const Element*>& getNames() const;

    const std::unordered_map<std::string, const Element*>& getSymbols() const;

    const std::unordered_map<unsigned int, const Element*>& getAtomicNumbers() const;

    const Element* getElement(const std::string& name) const;

    const Element* getElement(unsigned int atomic_number) const;

    void addElement(const std::string& name,
                    const std::string& symbol,
                    const unsigned int an,
                    const std::map<unsigned int, double>& abundance,
                    const std::map<unsigned int, double>& mass,
                    bool replace_existing);

    bool hasElement(const std::string& name) const;

    bool hasElement(unsigned int atomic_number) const;

protected:

    IsotopeDistribution parseIsotopeDistribution_(const std::map<unsigned int, double>& abundance, const std::map<unsigned int, double>& mass);

    double calculateAvgWeight_(const std::map<unsigned int, double>& abundance, const std::map<unsigned int, double>& mass);

    double calculateMonoWeight_(const std::map<unsigned int, double>& abundance, const std::map<unsigned int, double>& mass);

    void storeElements_();

    void buildElement_(const std::string& name, const std::string& symbol, const unsigned int an, const std::map<unsigned int, double>& abundance, const std::map<unsigned int, double>& mass);

    void addElementToMaps_(const std::string& name, const std::string& symbol, const unsigned int an, std::unique_ptr<const Element> e);

    void storeIsotopes_(const std::string& name, const std::string& symbol, const unsigned int an, const std::map<unsigned int, double>& Z_to_mass, const IsotopeDistribution& isotopes);

    void clear_();

    std::unordered_map<std::string, const Element*> names_;

    std::unordered_map<std::string, const Element*> symbols_;

    std::unordered_map<unsigned int, const Element*> atomic_numbers_;

private:
    ElementDB();
    ~ElementDB();
    ElementDB(const ElementDB& db) = delete;
    ElementDB(const ElementDB&& db) = delete;
    ElementDB& operator=(const ElementDB& db) = delete;

  };

} // namespace OpenMS