SqMassFile.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/KERNEL/MSExperiment.h>
 
#include <OpenMS/INTERFACES/IMSDataConsumer.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI SqMassFile
  {
public:
 
    struct OPENMS_DLLAPI SqMassConfig 
    {
      bool write_full_meta{true}; 
      bool use_lossy_numpress{false}; 
      double linear_fp_mass_acc{-1}; 
    };
 
    typedef MSExperiment MapType;
 
    SqMassFile();
 
    ~SqMassFile();
 
 
    void load(const String& filename, MapType& map) const;
 
    void store(const String& filename, const MapType& map) const;
 
    void transform(const String& filename_in, Interfaces::IMSDataConsumer* consumer, bool skip_full_count = false, bool skip_first_pass = false) const;
 
    void convertToXICParquet(const String& filename_in,
                const String& xic_filename,
                UInt64 run_id = 0,
                const String& source_file = "",
                const OpenSwath::LightTargetedExperiment& transition_exp = OpenSwath::LightTargetedExperiment()) const;
 
    void setConfig(const SqMassConfig& config) 
    {
      config_ = config;
    }
 
    // maybe later ...
    // static inline void readSpectrumFast(OpenSwath::BinaryDataArrayPtr data1,
    //                                     OpenSwath::BinaryDataArrayPtr data2, std::ifstream& ifs, int& ms_level,
    //                                     double& rt)
 
    // static inline void readChromatogramFast(OpenSwath::BinaryDataArrayPtr data1,
    //                                        OpenSwath::BinaryDataArrayPtr data2, std::ifstream& ifs)
 
protected:
      SqMassConfig config_;
  };
}