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 2002-2023.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    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
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// 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: 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