MzMLHandlerHelper.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/FORMAT/MSNumpressCoder.h>
#include <OpenMS/FORMAT/ZstdCompression.h>
#include <OpenMS/METADATA/MetaInfoDescription.h>
 
#include <vector>
 
namespace OpenMS
{
  namespace Internal
  {
 
    class OPENMS_DLLAPI MzMLHandlerHelper
    {
 
      static void warning(int mode, const std::string & msg, UInt line = 0, UInt column = 0);
 
    public:
 
      struct BinaryData
      {
        // ordered by size (alignment) and cache hotness in 'decode'
 
        enum PRECISION{
          PRE_NONE, 
          PRE_32,   
          PRE_64    
        } precision;
 
        enum DATA_TYPE{
          DT_NONE,    
          DT_FLOAT,   
          DT_INT,     
          DT_STRING   
        } data_type;
 
        MSNumpressCoder::NumpressCompression np_compression; 
 
        bool compression; 
        bool zstd_compression; 
        ZstdCompression::ByteTransform zstd_transform; 
        double unit_multiplier; 
 
        std::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<std::string> decoded_char;
 
        MetaInfoDescription meta; 
 
        BinaryData() :
          precision(PRE_NONE),
          data_type(DT_NONE),
          np_compression(),
          compression(false),
          zstd_compression(false),
          zstd_transform(ZstdCompression::ByteTransform::NONE),
          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 std::string getCompressionTerm_(const PeakFileOptions& opt,
                                        MSNumpressCoder::NumpressConfig np_compression,
                                        const std::string& indent = "",
                                        bool use_numpress = false,
                                        bool zstd_byte_shuffle = true);
 
      static void encodeNumericArray(std::vector<float>& in, const PeakFileOptions& opt, std::string& out);
      static void encodeNumericArray(std::vector<double>& in, const PeakFileOptions& opt, std::string& out);
      static void encodeNumericArray(std::vector<Int32>& in, const PeakFileOptions& opt, std::string& out);
      static void encodeNumericArray(std::vector<Int64>& in, const PeakFileOptions& opt, std::string& out);
 
      static void encodeStringArray(const std::vector<std::string>& in, const PeakFileOptions& opt, std::string& out);
 
      static void encodeNumpressArray(const std::vector<double>& in, const PeakFileOptions& opt, const MSNumpressCoder::NumpressConfig& config, std::string& out);
      static void encodeNumpressArray(const std::vector<float>& in, const PeakFileOptions& opt, const MSNumpressCoder::NumpressConfig& config, std::string& out);
 
      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 std::string& index_name);
 
      static bool handleBinaryDataArrayCVParam(std::vector<BinaryData>& data_,
                                               const std::string& accession,
                                               const std::string& value,
                                               const std::string& name,
                                               const std::string& unit_accession);
    };
 
 
  } // namespace Internal
} // namespace OpenMS