MzMLHandlerHelper.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// 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"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
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// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/FORMAT/MSNumpressCoder.h>
#include <OpenMS/METADATA/MetaInfoDescription.h>
 
#include <vector>
 
namespace OpenMS
{
  namespace Internal
  {
 
    class OPENMS_DLLAPI MzMLHandlerHelper
    {
 
      static void warning(int mode, const String & msg, UInt line = 0, UInt column = 0);
 
    public:
 
      struct BinaryData
      {
        // ordered by size (alignment) and cache hotness in 'decode'
 
        enum {
          PRE_NONE, 
          PRE_32,   
          PRE_64    
        } precision;
 
        enum {
          DT_NONE,    
          DT_FLOAT,   
          DT_INT,     
          DT_STRING   
        } data_type;
 
        MSNumpressCoder::NumpressCompression np_compression; 
 
        bool compression; 
        double unit_multiplier; 
 
        String base64; 
        Size size; 
        std::vector<float> floats_32;
        std::vector<double> floats_64;
        std::vector<Int32> ints_32;
        std::vector<Int64> ints_64;
        std::vector<String> decoded_char;
 
        MetaInfoDescription meta; 
 
        BinaryData() :
          precision(PRE_NONE),
          data_type(DT_NONE),
          np_compression(),
          compression(false),
          unit_multiplier(1.0),
          base64(),
          size(0),
          floats_32(),
          floats_64(),
          ints_32(),
          ints_64(),
          decoded_char(),
          meta()
        {
        }
 
        BinaryData(const BinaryData&) = default;               // Copy constructor
        BinaryData(BinaryData&&) = default;                    // Move constructor
        BinaryData& operator=(const BinaryData&) & = default;  // Copy assignment operator
        BinaryData& operator=(BinaryData&&) & = default;       // Move assignment operator
        ~BinaryData() = default;                               // Destructor
 
      };
 
      static String getCompressionTerm_(const PeakFileOptions& opt,
                                        MSNumpressCoder::NumpressConfig np_compression,
                                        String indent = "",
                                        bool use_numpress = false);
 
      static void writeFooter_(std::ostream& os,
                               const PeakFileOptions& options,
                               const std::vector< std::pair<std::string, Int64> > & spectra_offsets,
                               const std::vector< std::pair<std::string, Int64> > & chromatograms_offsets);
 
      static void decodeBase64Arrays(std::vector<BinaryData> & data_, const bool skipXMLCheck = false);
 
      static void computeDataProperties_(const std::vector<BinaryData>& data_, bool& precision_64, SignedSize& index, const String& index_name);
 
      static bool handleBinaryDataArrayCVParam(std::vector<BinaryData>& data_,
                                               const String& accession,
                                               const String& value,
                                               const String& name,
                                               const String& unit_accession);
    };
 
 
  } // namespace Internal
} // namespace OpenMS