IMSElement.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Stephan Aiche $
// $Authors: Anton Pervukhin <Anton.Pervukhin@CeBiTec.Uni-Bielefeld.DE> $
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//

#ifndef OPENMS_CHEMISTRY_MASSDECOMPOSITION_IMS_IMSELEMENT_H
#define OPENMS_CHEMISTRY_MASSDECOMPOSITION_IMS_IMSELEMENT_H

#include <string>
#include <ostream>
#include <iostream>

#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSIsotopeDistribution.h>

namespace OpenMS
{
  namespace ims
  {

    class OPENMS_DLLAPI IMSElement
    {
public:
      typedef std::string name_type;

      typedef IMSIsotopeDistribution isotopes_type;

      typedef isotopes_type::mass_type mass_type;

      typedef isotopes_type::nominal_mass_type nominal_mass_type;

      typedef isotopes_type::size_type size_type;

      static const mass_type ELECTRON_MASS_IN_U;

      IMSElement()
      {}

      IMSElement(const IMSElement & element) :
        name_(element.name_),
        sequence_(element.sequence_),
        isotopes_(element.isotopes_)
      {}

      IMSElement(const name_type & name,
                 const isotopes_type & isotopes) :
        name_(name),
        sequence_(name),
        isotopes_(isotopes)
      {}

      IMSElement(const name_type & name,
                 mass_type mass) :
        name_(name),
        sequence_(name),
        isotopes_(mass)
      {}

      IMSElement(const name_type & name,
                 nominal_mass_type nominal_mass = 0) :
        name_(name),
        sequence_(name),
        isotopes_(nominal_mass)
      {}

      const name_type & getName() const
      {
        return name_;
      }

      void setName(const name_type & name)
      {
        this->name_ = name;
      }

      const name_type & getSequence() const
      {
        return sequence_;
      }

      void setSequence(const name_type & sequence)
      {
        this->sequence_ = sequence;
      }

      nominal_mass_type getNominalMass() const
      {
        return isotopes_.getNominalMass();
      }

      mass_type getMass(size_type index = 0) const
      {
        return isotopes_.getMass(index);
      }

      mass_type getAverageMass() const
      {
        return isotopes_.getAverageMass();
      }

      mass_type getIonMass(int electrons_number = 1) const
      {
        return this->getMass() - electrons_number * ELECTRON_MASS_IN_U;
      }

      const IMSIsotopeDistribution & getIsotopeDistribution() const
      {
        return isotopes_;
      }

      void setIsotopeDistribution(const IMSIsotopeDistribution & isotopes)
      {
        this->isotopes_ = isotopes;
      }

      IMSElement & operator=(const IMSElement & element);

      bool operator==(const IMSElement & element) const;

      bool operator!=(const IMSElement & element) const;

      virtual ~IMSElement() {}

private:
      name_type name_;

      name_type sequence_;

      isotopes_type isotopes_;
    };

    OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const IMSElement & element);

  } // namespace ims
} // namespace OpenMS

#endif // OPENMS_CHEMISTRY_MASSDECOMPOSITION_IMS_ELEMENT_H