SqMassFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/MSExperiment.h>
 
#include <OpenMS/INTERFACES/IMSDataConsumer.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, MapType& map) const;
 
    void transform(const String& filename_in, Interfaces::IMSDataConsumer* consumer, bool skip_full_count = false, bool skip_first_pass = false) 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_;
  };
}