timsdata.h

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/**
 * \file pappsomspp/vendors/tims/timsdata.h
 * \date 27/08/2019
 * \author Olivier Langella
 * \brief main Tims data handler
 */
 
/*******************************************************************************
 * Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.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/>.
 *
 ******************************************************************************/
 
#pragma once
 
#include <QDir>
#include <QSqlDatabase>
#include "timsbindec.h"
#include "timsframe.h"
#include "../../massspectrum/qualifiedmassspectrum.h"
#include "../../processing/filters/filterinterface.h"
#include "../../msrun/xiccoord/xiccoordtims.h"
#include <deque>
#include <QMutex>
#include <QSqlQuery>
#include "mzcalibration/mzcalibrationstore.h"
#include "../../msrun/spectrumcollectionhandlerinterface.h"
#include "../../exportinmportconfig.h"
 
 
namespace pappso
{
 
class TimsData;
class TimsDdaPrecursors;
class TimsDiaSlices;
 
/** \brief shared pointer on a TimsData object
 */
typedef std::shared_ptr<TimsData> TimsDataSp;
 
 
struct PMSPP_LIB_DECL FrameIdDescr
{
  std::size_t m_frameId;         // frame id
  std::size_t m_scanCount;       // frame size (number of TOF scans in frame)
  std::size_t m_globalScanIndex; // scan index over the whole file
};
 
/**
 * @todo write docs
 */
class PMSPP_LIB_DECL TimsData
{
  friend TimsDdaPrecursors;
  friend TimsDiaSlices;
 
  public:
  /** @brief build using the tims data directory
   */
  TimsData(QDir timsDataDirectory);
 
  /**
   * Copy constructor
   *
   * @param other TODO
   */
  TimsData(const TimsData &other);
 
  /**
   * Destructor
   */
  virtual ~TimsData();
 
  /** @brief tells if this MS run is a DDA run
   * @result true if it contains DDA precursors
   */
  bool isDdaRun() const;
 
 
  /** @brief tells if this MS run is a DIA run
   * @result true if it contains DIA slices
   */
  bool isDiaRun() const;
 
  /** @brief get a mass spectrum given its spectrum index
   * @param raw_index a number begining at 0, corresponding to a Tims Scan in
   * the order they lies in the binary data file
   */
  [[deprecated("Please use getMassSpectrumCstSPtrByGlobalScanIndex")]] pappso::MassSpectrumCstSPtr
  getMassSpectrumCstSPtrByRawIndex(std::size_t raw_index);
  // FIXME NAMING: Identical to above
  // Not used in i2mcq
  pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtrByGlobalScanIndex(std::size_t index);
 
  /** @brief get a mass spectrum given the tims frame database id and scan
   * number within tims frame
   */
  pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr(std::size_t timsId, std::size_t scanNum);
 
  /** @brief Get total number of frames
   */
  [[deprecated("Please use getFrameCount")]] std::size_t getTotalNumberOfFrames() const;
  // FIXME NAMING : identical to above
  // Not used in i2mcq
  std::size_t getFrameCount() const;
 
  /** @brief get the total number of scans
   */
  [[deprecated("Please use getTotalScanCount")]] std::size_t getTotalNumberOfScans() const;
 
  // FIXME NAMING : identical to above
  // Not used in i2mcq
  std::size_t getTotalScanCount() const;
 
 
  [[deprecated("Please use getMsLevelByGlobalScanIndex")]] unsigned int
  getMsLevelBySpectrumIndex(std::size_t index);
  // FIXME NAMING : identical to above
  // Not used in i2mcq
  unsigned int getMsLevelByGlobalScanIndex(std::size_t index);
 
  [[deprecated("Please use getQualifiedMassSpectrumByGlobalScanIndex")]] void
  getQualifiedMassSpectrumByRawIndex(const MsRunIdCstSPtr &msrun_id,
                                     QualifiedMassSpectrum &mass_spectrum,
                                     std::size_t global_scan_index,
                                     bool want_binary_data);
  // FIXME NAMING : identical to above
  // Not used in i2mcq
  void getQualifiedMassSpectrumByGlobalScanIndex(const MsRunIdCstSPtr &msrun_id,
                                                 QualifiedMassSpectrum &mass_spectrum,
                                                 std::size_t global_scan_index,
                                                 bool want_binary_data);
  Trace getTicChromatogram() const;
 
 
  std::vector<std::size_t> getTimsMS1FrameIdsInRtRange(double rt_begin, double rt_end) const;
 
  std::vector<std::size_t> getTimsMS2FrameIdsInRtRange(double rt_begin, double rt_end) const;
 
 
  /** @brief get a Tims frame with his database ID
   * but look in the cache first
   *
   * thread safe
   */
  TimsFrameCstSPtr getTimsFrameCstSPtrCached(std::size_t timsId);
 
  /** @brief get a Tims frame with his database ID
   *
   * this function is not thread safe
   */
  TimsFrameCstSPtr getTimsFrameCstSPtr(std::size_t timsId);
 
 
  /** @brief get raw signal for a spectrum index
   * only to use to see the raw signal
   *
   * @param spectrum_index spcetrum index
   * @result a map of integers, x=time of flights, y= intensities
   */
  [[deprecated("Please use getScanByGlobalScanIndex")]] TimsDataFastMap &
  getRawMsBySpectrumIndex(std::size_t index);
  // FIXME NAMING: identical to above
  // Not used in i2mcq
  TimsDataFastMap &getScanByGlobalScanIndex(std::size_t index);
 
  /** @brief retention timeline
   * get retention times along the MSrun in seconds
   * @return vector of retention times (seconds)
   */
  [[deprecated("Please use getRetentionTimeLineInSeconds")]] virtual std::vector<double>
  getRetentionTimeLine() const;
  // FIXME NAMING: identical to above
  virtual std::vector<double> getRetentionTimeLineInSeconds() const;
 
 
  const std::vector<FrameIdDescr> &getFrameIdDescrList() const;
  const std::vector<TimsFrameRecord> &getTimsFrameRecordList() const;
 
 
  const QDir &getTimsDataDirectory() const;
 
  TimsDdaPrecursors *getTimsDdaPrecursorsPtr() const;
  TimsDiaSlices *getTimsDiaSlicesPtr() const;
 
  const QVariant &getGlobalMetadataValue(const QString &key) const;
 
  protected:
  QSqlDatabase openDatabaseConnection() const;
 
  TimsBinDec *getTimsBinDecPtr() const;
 
 
  private:
  [[deprecated(
    "Please use getScanCoordinatesByGlobalScanIndex")]] std::pair<std::size_t, std::size_t>
  getScanCoordinateFromRawIndex(std::size_t spectrum_index) const;
  // FIXME NAMING: identical to above
  // Not used in i2mcq
  std::pair<std::size_t, std::size_t> getScanCoordinatesByGlobalScanIndex(std::size_t index) const;
 
  [[deprecated("Please use getGlobalScanIndexByScanCoordinates")]] std::size_t
  getRawIndexFromCoordinate(std::size_t frame_id, std::size_t scan_num) const;
 
  // FIXME NAMING: identical to above
  // Not used in i2mcq
  std::size_t getGlobalScanIndexByScanCoordinates(std::size_t frame_id, std::size_t index) const;
 
 
  /** @brief get a Tims frame base (no binary data file access) with his
   * database ID
   */
  TimsFrameBaseCstSPtr getTimsFrameBaseCstSPtr(std::size_t timsId);
 
 
  TimsFrameBaseCstSPtr getTimsFrameBaseCstSPtrCached(std::size_t timsId);
 
 
  /** @brief private function to fill m_frameIdDescrList
   */
  void fillFrameIdDescrList();
 
 
  QDir m_timsDataDirectory;
  TimsBinDec *mpa_timsBinDec = nullptr;
 
  TimsDdaPrecursors *mpa_timsDdaPrecursors = nullptr;
  TimsDiaSlices *mpa_timsDiaSlices         = nullptr;
  // QSqlDatabase *mpa_qdb      = nullptr;
  std::size_t m_totalScanCount;
  std::size_t m_frameCount;
  std::size_t m_cacheSize = 60;
  std::deque<TimsFrameCstSPtr> m_timsFrameCache;
  std::deque<TimsFrameBaseCstSPtr> m_timsFrameBaseCache;
 
 
  std::map<int, QSqlRecord> m_mapMzCalibrationRecord;
  std::map<int, QSqlRecord> m_mapTimsCalibrationRecord;
  std::vector<TimsFrameRecord> m_mapFramesRecord;
 
  MzCalibrationStore *mpa_mzCalibrationStore;
 
 
  /** @brief store every frame id and corresponding sizes
   */
  std::vector<FrameIdDescr> m_frameIdDescrList;
 
  /** @brief index to find quickly a frameId in the description list with the
   * raw index of spectrum modulo 1000
   * @key thousands of TOF scans
   * @value corresponding m_frameIdDescrList index
   */
  std::map<std::size_t, std::size_t> m_thousandIndexToFrameIdDescrListIndex;
 
 
  /** @brief tells if someone is loading a frame id
   */
  std::vector<std::size_t> m_someoneIsLoadingFrameId;
 
  std::map<QString, QVariant> m_mapGlobalMetadaTable;
 
  QMutex m_mutex;
};
} // namespace pappso