massspectrumid.h

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/*******************************************************************************
 * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
 *
 * This file is part of the PAPPSOms++ library.
 *
 *     PAPPSOms++ is free software: you can redistribute it and/or modify
 *     it under the terms of the GNU General Public License as published by
 *     the Free Software Foundation, either version 3 of the License, or
 *     (at your option) any later version.
 *
 *     PAPPSOms++ is distributed in the hope that it will be useful,
 *     but WITHOUT ANY WARRANTY; without even the implied warranty of
 *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *     GNU General Public License for more details.
 *
 *     You should have received a copy of the GNU General Public License
 *     along with PAPPSOms++.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
 *implementation
 ******************************************************************************/
 
 
#pragma once
 
#include <cstddef>
#include <limits>
 
#include <QString>
 
#include "pappsomspp/export-import-config.h"
 
#include "pappsomspp/core/msrun/msrunid.h"
 
 
namespace pappso
{
 
class PMSPP_LIB_DECL MassSpectrumId
{
  public:
  MassSpectrumId();
 
  MassSpectrumId(const MsRunIdCstSPtr &msrun_id);
 
  MassSpectrumId(const MsRunIdCstSPtr &msrun_id, std::size_t spectrum_index);
 
  MassSpectrumId(const MassSpectrumId &other);
  ~MassSpectrumId();
 
  MassSpectrumId &operator=(const MassSpectrumId &other);
 
  void setMsRunId(MsRunIdCstSPtr other);
  const MsRunIdCstSPtr &getMsRunIdCstSPtr() const;
 
  void setNativeId(const QString &native_id);
  const QString &getNativeId() const;
 
  /** @brief try to find scan id in the native id string
   * @param is_ok true if scan number is found
   * @return integer of the scan number
   */
  std::size_t extractScanNumberFromNativeId(bool *is_ok) const;
 
  void setSpectrumIndex(std::size_t index);
  std::size_t getSpectrumIndex() const;
 
  bool operator==(const MassSpectrumId &other) const;
 
  bool isValid() const;
 
  QString toString() const;
 
  private:
  MsRunIdCstSPtr mcsp_msRunId = nullptr;
 
  // This is the native id string that is stored in the mzML file. Its structure
  // is dependent on the vendor/format of the original data. In some cases, it
  // is possible to ask libpwiz to extract from it the scan number of the
  // spectrum. For water/mdsciex files, this is not possible. We thus need to
  // rely on the index of the spectrum in the spectrum list for the ms run of
  // interest. By combining the run id and the spectrum index, it is possible to
  // unambiguously identify a mass spectrum from a given file.
  QString m_nativeId;
 
  // The index of the mass spectrum in the spectrum list of a given ms run is
  // used when the scan number is not easily usable (see the native id comment
  // above).
  std::size_t m_spectrumIndex = std::numeric_limits<std::size_t>::max();
};
 
 
} // namespace pappso