OpenMS  3.0.0
MzMLHandlerHelper.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
40 
41 #include <vector>
42 
43 namespace OpenMS
44 {
45  namespace Internal
46  {
47 
55  class OPENMS_DLLAPI MzMLHandlerHelper
56  {
57 
59  static void warning(int mode, const String & msg, UInt line = 0, UInt column = 0);
60 
61  public:
62 
69  struct BinaryData
70  {
71  // ordered by size (alignment) and cache hotness in 'decode'
72 
73  enum {
76  PRE_64
77  } precision;
78 
79  enum {
83  DT_STRING
84  } data_type;
85 
87 
88  bool compression;
89  double unit_multiplier;
90 
93  std::vector<float> floats_32;
94  std::vector<double> floats_64;
95  std::vector<Int32> ints_32;
96  std::vector<Int64> ints_64;
97  std::vector<String> decoded_char;
98 
100 
103  precision(PRE_NONE),
104  data_type(DT_NONE),
105  np_compression(),
106  compression(false),
107  unit_multiplier(1.0),
108  base64(),
109  size(0),
110  floats_32(),
111  floats_64(),
112  ints_32(),
113  ints_64(),
114  decoded_char(),
115  meta()
116  {
117  }
118 
119  BinaryData(const BinaryData&) = default; // Copy constructor
120  BinaryData(BinaryData&&) = default; // Move constructor
121  BinaryData& operator=(const BinaryData&) & = default; // Copy assignment operator
122  BinaryData& operator=(BinaryData&&) & = default; // Move assignment operator
123  ~BinaryData() = default; // Destructor
124 
125  };
126 
130  static String getCompressionTerm_(const PeakFileOptions& opt,
131  MSNumpressCoder::NumpressConfig np_compression,
132  String indent = "",
133  bool use_numpress = false);
134 
144  static void writeFooter_(std::ostream& os,
145  const PeakFileOptions& options,
146  const std::vector< std::pair<std::string, Int64> > & spectra_offsets,
147  const std::vector< std::pair<std::string, Int64> > & chromatograms_offsets);
148 
155  static void decodeBase64Arrays(std::vector<BinaryData> & data_, const bool skipXMLCheck = false);
156 
167  static void computeDataProperties_(const std::vector<BinaryData>& data_, bool& precision_64, SignedSize& index, const String& index_name);
168 
182  static bool handleBinaryDataArrayCVParam(std::vector<BinaryData>& data_,
183  const String& accession,
184  const String& value,
185  const String& name,
186  const String& unit_accession);
187  };
188 
189 
190  } // namespace Internal
191 } // namespace OpenMS
192 
193 
OpenMS::Internal::MzMLHandlerHelper::BinaryData::BinaryData
BinaryData()
Constructor.
Definition: MzMLHandlerHelper.h:102
OpenMS::Internal::MzMLHandlerHelper::BinaryData::PRE_NONE
unknown precision
Definition: MzMLHandlerHelper.h:74
OpenMS::Internal::MzMLHandlerHelper::BinaryData::ints_64
std::vector< Int64 > ints_64
Definition: MzMLHandlerHelper.h:96
OpenMS::Internal::MzMLHandlerHelper::BinaryData::PRE_32
32bit precision
Definition: MzMLHandlerHelper.h:75
OpenMS::Internal::MzMLHandlerHelper::BinaryData::DT_FLOAT
float data type
Definition: MzMLHandlerHelper.h:81
OpenMS::Internal::MzMLHandlerHelper::BinaryData::decoded_char
std::vector< String > decoded_char
Definition: MzMLHandlerHelper.h:97
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::MetaInfoDescription
Description of the meta data arrays of MSSpectrum.
Definition: MetaInfoDescription.h:48
OpenMS::Internal::MzMLHandlerHelper::BinaryData::size
Size size
Raw data length.
Definition: MzMLHandlerHelper.h:92
OpenMS::Internal::MzMLHandlerHelper::BinaryData::floats_64
std::vector< double > floats_64
Definition: MzMLHandlerHelper.h:94
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Internal::MzMLHandlerHelper::BinaryData
Representation for binary data in mzML.
Definition: MzMLHandlerHelper.h:69
OpenMS::Internal::MzMLHandlerHelper
Helper for mzML file format.
Definition: MzMLHandlerHelper.h:55
OpenMS::Internal::MzMLHandlerHelper::BinaryData::DT_NONE
unknown data type
Definition: MzMLHandlerHelper.h:80
OpenMS::Internal::MzMLHandlerHelper::BinaryData::floats_32
std::vector< float > floats_32
Definition: MzMLHandlerHelper.h:93
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
PeakFileOptions.h
MSNumpressCoder.h
OpenMS::Internal::MzMLHandlerHelper::BinaryData::unit_multiplier
double unit_multiplier
multiplier for unit (e.g. 60 for minutes)
Definition: MzMLHandlerHelper.h:89
OpenMS::Internal::MzMLHandlerHelper::BinaryData::np_compression
MSNumpressCoder::NumpressCompression np_compression
numpress options
Definition: MzMLHandlerHelper.h:86
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::MSNumpressCoder::NumpressConfig
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:88
OpenMS::MSNumpressCoder::NumpressCompression
NumpressCompression
Names of compression schemes.
Definition: MSNumpressCoder.h:74
OpenMS::Internal::MzMLHandlerHelper::BinaryData::compression
bool compression
zlib compression
Definition: MzMLHandlerHelper.h:88
OpenMS::Internal::MzMLHandlerHelper::BinaryData::base64
String base64
Raw data in base64 encoding.
Definition: MzMLHandlerHelper.h:91
OpenMS::Internal::MzMLHandlerHelper::BinaryData::ints_32
std::vector< Int32 > ints_32
Definition: MzMLHandlerHelper.h:95
OpenMS::Internal::MzMLHandlerHelper::BinaryData::DT_INT
integer data type
Definition: MzMLHandlerHelper.h:82
OpenMS::Internal::MzMLHandlerHelper::BinaryData::meta
MetaInfoDescription meta
Meta data description.
Definition: MzMLHandlerHelper.h:99
MetaInfoDescription.h