ElementDB.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch, Timo Sachsenberg, Chris Bielow $
// --------------------------------------------------------------------------
//

#pragma once

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

namespace OpenMS
{

  class OPENMS_DLLAPI ElementDB
  {
public:
    
    inline static const ElementDB* getInstance()
    {
      static ElementDB db_; // this is thread safe!
      return &db_;
    }

    const Map<String, const Element *> & getNames() const;

    const Map<String, const Element *> & getSymbols() const;

    const Map<UInt, const Element *> & getAtomicNumbers() const;

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

    const Element * getElement(UInt atomic_number) const;


    bool hasElement(const String & name) const;

    bool hasElement(UInt atomic_number) const;

protected:

    /*_ parses a Histogram given as a OpenMS String and return the distribution

            @throw throws exception ParseError
     */
    IsotopeDistribution parseIsotopeDistribution_(const Map<UInt, double>& Z_to_abundance, const Map<UInt, double>& Z_to_mass);

    /*_ calculates the average weight based on isotope abundance and mass
     */
    double calculateAvgWeight_(const Map<UInt, double> & Z_to_abundance, const Map<UInt, double> & Z_to_mass);

    /*_ calculates the mono weight based on the smallest isotope mass
     */
    double calculateMonoWeight_(const Map<UInt, double> & Z_to_mass);

    /*_ read elements from a XML file, formatted as a Param file.

            @throw throws ParseError if the file cannot be parsed
            @throw throws FileNotFound if the file could not be found
     */
    void readFromFile_(const String & file_name);


    void storeElement_(const UInt an, const String& name, const String& symbol, const Map<UInt, double>& Z_to_abundancy, const Map<UInt, double>& Z_to_mass);

    /*_ resets all containers
     */
    void clear_();

    Map<String, const Element *> names_;

    Map<String, const Element *> symbols_;

    Map<UInt, 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