OnDiscMSExperiment.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/INTERFACES/DataStructures.h>
#include <OpenMS/KERNEL/IMSExperimentRandomAccess.h>
 
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
#include <OpenMS/METADATA/ExperimentalSettings.h>
#include <OpenMS/FORMAT/HANDLERS/IndexedMzMLHandler.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
 
#include <vector>
#include <limits>
 
#include <memory>
 
namespace OpenMS
{
  class OPENMS_DLLAPI OnDiscMSExperiment :
    public IMSExperimentRandomAccess
  {
 
  typedef ChromatogramPeak ChromatogramPeakT;
  typedef Peak1D PeakT;
 
public:
 
    OnDiscMSExperiment() = default;
 
    bool openFile(const std::string& filename, bool skipMetaData = false);
 
    OnDiscMSExperiment(const OnDiscMSExperiment& source) :
      IMSExperimentRandomAccess(source),
      filename_(source.filename_),
      indexed_mzml_file_(source.indexed_mzml_file_),
      meta_ms_experiment_(source.meta_ms_experiment_),
      options_(source.options_)
    {
    }
 
    bool operator==(const OnDiscMSExperiment& rhs) const
    {
      if (meta_ms_experiment_ == nullptr || rhs.meta_ms_experiment_ == nullptr) 
      {
        return filename_ == rhs.filename_ &&
               meta_ms_experiment_ == rhs.meta_ms_experiment_;
      }
 
      // check if file and meta information is the same
      return filename_ == rhs.filename_ &&
             (*meta_ms_experiment_) == (*rhs.meta_ms_experiment_);
      // do not check if indexed_mzml_file_ is equal -> they have the same filename...
    }
 
    bool operator!=(const OnDiscMSExperiment& rhs) const
    {
      return !(operator==(rhs));
    }
 
    bool isSortedByRT() const override
    {
      if (!meta_ms_experiment_) return false;
 
      return meta_ms_experiment_->isSorted(false);
    }
 
    inline Size getNrSpectra() const override
    {
      return indexed_mzml_file_.getNrSpectra();
    }
 
    inline Size getNrChromatograms() const override
    {
      return indexed_mzml_file_.getNrChromatograms();
    }
 
    std::shared_ptr<const ExperimentalSettings> getExperimentalSettings() const override
    {
      return std::static_pointer_cast<const ExperimentalSettings>(meta_ms_experiment_);
    }
 
    std::shared_ptr<PeakMap> getMetaData() const
    {
      return meta_ms_experiment_;
    }
 
    inline MSSpectrum operator[](Size n)
    {
      return getSpectrum(n);
    }
 
    MSSpectrum getSpectrum(Size id) override;
 
    MSSpectrum getSpectrumMetadata(Size id) override;
 
    double getSpectrumRT(Size id) const override;
 
    UInt getSpectrumMSLevel(Size id) const override;
 
    std::unique_ptr<IMSExperimentRandomAccess> clone() const override;
 
    OpenMS::Interfaces::SpectrumPtr getSpectrumById(Size id)
    {
      return indexed_mzml_file_.getSpectrumById((int)id);
    }
 
    MSChromatogram getChromatogram(Size id) override;
 
    MSChromatogram getChromatogramByNativeId(const std::string& id);
 
    MSSpectrum getSpectrumByNativeId(const std::string& id);
 
    OpenMS::Interfaces::ChromatogramPtr getChromatogramById(Size id);
 
    void setSkipXMLChecks(bool skip);
 
    PeakFileOptions& getOptions();
 
    const PeakFileOptions& getOptions() const;
 
    void setOptions(const PeakFileOptions& options);
 
private:
 
    OnDiscMSExperiment& operator=(const OnDiscMSExperiment& /* source */);
 
    void loadMetaData_(const std::string& filename);
 
    MSChromatogram getMetaChromatogramById_(const std::string& id);
 
    MSSpectrum getMetaSpectrumById_(const std::string& id);
 
protected:
 
    std::string filename_;
    mutable Internal::IndexedMzMLHandler indexed_mzml_file_;
    std::shared_ptr<PeakMap> meta_ms_experiment_;
    std::unordered_map< std::string, Size > chromatograms_native_ids_;
    std::unordered_map< std::string, Size > spectra_native_ids_;
    PeakFileOptions options_;
  };
 
typedef OpenMS::OnDiscMSExperiment OnDiscPeakMap;
 
} // namespace OpenMS