MzXMLFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
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#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/FORMAT/XMLFile.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/INTERFACES/IMSDataConsumer.h>

namespace OpenMS
{
  class String;

  class OPENMS_DLLAPI MzXMLFile :
    public Internal::XMLFile,
    public ProgressLogger
  {
  typedef PeakMap MapType;

public:
    MzXMLFile();
    ~MzXMLFile() override;

    PeakFileOptions & getOptions();

    const PeakFileOptions & getOptions() const;

    void setOptions(const PeakFileOptions &);

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

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

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

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

protected:

    void transformFirstPass_(const String& filename_in, Interfaces::IMSDataConsumer * consumer, bool skip_full_count);

private:

    PeakFileOptions options_;
  };
} // namespace OpenMS