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 2002-2018.
//
// This software is released under a three-clause BSD license:
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//    may be used to endorse or promote products derived from this software
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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; 
      bool use_lossy_numpress; 
      double linear_fp_mass_acc; 

      SqMassConfig () :
        write_full_meta(true),
        use_lossy_numpress(false),
        linear_fp_mass_acc(-1) {}
    };

    typedef MSExperiment MapType;

    SqMassFile();

    ~SqMassFile();


    void load(const String& filename, MapType& map);

    void store(const String& filename, MapType& map);

    void transform(const String& filename_in, Interfaces::IMSDataConsumer * consumer, bool skip_full_count = false, bool skip_first_pass = false);

    void setConfig(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_;

  };
}