MzMLFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm, Chris Bielow, Hannes Roest $
// --------------------------------------------------------------------------

#pragma once

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

#include <OpenMS/DATASTRUCTURES/ListUtils.h> // StringList
#include <OpenMS/INTERFACES/IMSDataConsumer.h>

#include <map>

namespace OpenMS
{
  class OPENMS_DLLAPI MzMLFile :
    public Internal::XMLFile,
    public ProgressLogger
  {
public:
    MzMLFile();
    ~MzMLFile() override;

    PeakFileOptions& getOptions();

    const PeakFileOptions& getOptions() const;

    void setOptions(const PeakFileOptions&);

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

    void loadBuffer(const std::string& buffer, PeakMap& map);

    void loadSize(const String & filename, Size& scount, Size& ccount);

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

    void storeBuffer(std::string & output, const PeakMap& map) const;

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

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

    bool isValid(const String& filename, std::ostream& os = std::cerr);

    bool isSemanticallyValid(const String& filename, StringList& errors, StringList& warnings);


    struct SpecInfo
    {
      Size count_centroided = 0;
      Size count_profile = 0;
      Size count_unknown = 0;
    };
      
    std::map<UInt, SpecInfo> getCentroidInfo(const String& filename, const Size first_n_spectra_only = 10);

protected:

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

    void safeParse_(const String & filename, Internal::XMLHandler * handler);

private:

    PeakFileOptions options_;

    String indexed_schema_location_;
  };

} // namespace OpenMS