OpenSwathBase.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest, Justin Sing$
// $Authors: Hannes Roest, Justin Sing$
// --------------------------------------------------------------------------
 
#pragma once
 
// Consumers
#include <OpenMS/FORMAT/DATAACCESS/MSDataWritingConsumer.h>
#include <OpenMS/FORMAT/DATAACCESS/MSDataSqlConsumer.h>
 
// Files
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/FORMAT/SwathFile.h>
#include <OpenMS/ANALYSIS/OPENSWATH/SwathWindowLoader.h>
#include <OpenMS/ANALYSIS/OPENSWATH/TransitionTSVFile.h>
#include <OpenMS/ANALYSIS/OPENSWATH/TransitionPQPFile.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathOSWWriter.h>
 
// Kernel and implementations
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMS.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessTransforming.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SpectrumAccessOpenMSInMemory.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
 
// Helpers
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathHelper.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/DataAccessHelper.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SimpleOpenMSSpectraAccessFactory.h>
 
// Algorithms
#include <OpenMS/ANALYSIS/OPENSWATH/MRMRTNormalizer.h>
#include <OpenMS/ANALYSIS/OPENSWATH/ChromatogramExtractor.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
#include <OpenMS/ANALYSIS/OPENSWATH/MRMTransitionGroupPicker.h>
#include <OpenMS/ANALYSIS/OPENSWATH/SwathMapMassCorrection.h>
 
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathWorkflow.h>
 
#include <cassert>
#include <limits>
 
#include <OpenMS/APPLICATIONS/TOPPBase.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI TOPPOpenSwathBase : public TOPPBase
  {
 
  public:
    struct CalibrationResult
    {
      OpenMS::TransformationDescription rt_trafo;
 
      double ms2_mz_window_ppm{ -1.0 };
 
      double ms2_im_window{ -1.0 };
 
      double ms1_mz_window_ppm{ -1.0 };
 
      double ms1_im_window{ -1.0 };
    };
 
    TOPPOpenSwathBase(String name, String description, bool official = true, const std::vector<Citation>& citations = {});
 
    ~TOPPOpenSwathBase() override;
 
  protected:
    bool loadSwathFiles(const StringList& file_list,
                        boost::shared_ptr<ExperimentalSettings >& exp_meta,
                        std::vector< OpenSwath::SwathMap >& swath_maps,
                        const bool split_file,
                        const String& tmp,
                        const String& readoptions,
                        const String& swath_windows_file,
                        const double min_upper_edge_dist,
                        const bool force,
                        const bool sort_swath_maps,
                        const bool prm,
                        const bool pasef,
                        Interfaces::IMSDataConsumer* plugin_consumer = nullptr);
 
    void prepareChromOutput(Interfaces::IMSDataConsumer ** chromatogramConsumer,
                            const boost::shared_ptr<ExperimentalSettings>& exp_meta,
                            const OpenSwath::LightTargetedExperiment& transition_exp,
                            const String& out_chrom,
                            const UInt64 run_id);
 
    OpenSwath::LightTargetedExperiment loadTransitionList(const FileTypes::Type& tr_type,
                                                          const String& tr_file,
                                                          const Param& tsv_reader_param);
 
    CalibrationResult performCalibration(String trafo_in,
                                         const OpenSwath::LightTargetedExperiment& irt_transitions,
                                         std::vector< OpenSwath::SwathMap > & swath_maps,
                                         double min_rsq,
                                         double min_coverage,
                                         const Param& feature_finder_param,
                                         const ChromExtractParams& cp_irt,
                                         const Param& irt_detection_param,
                                         const Param& calibration_param,
                                         Size debug_level,
                                         bool pasef,
                                         bool load_into_memory,
                                         const String& irt_trafo_out,
                                         const String& irt_mzml_out);
 
  private:
    void loadSwathFiles_(const StringList& file_list,
                         const bool split_file,
                         const String& tmp,
                         const String& readoptions,
                         boost::shared_ptr<ExperimentalSettings > & exp_meta,
                         std::vector< OpenSwath::SwathMap > & swath_maps,
                         Interfaces::IMSDataConsumer* plugin_consumer);
  }; // end TOPPOpenSwathBase
} //  end NS OpenMS