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 2002-2023.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
 
#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