IMSElement.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Anton Pervukhin <Anton.Pervukhin@CeBiTec.Uni-Bielefeld.DE> $
// --------------------------------------------------------------------------
//

#pragma once

#include <string>
#include <iosfwd>
#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