| OpenMS 2.5.0

MzMLHandlerHelper.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
38 #include <OpenMS/FORMAT/MSNumpressCoder.h>
39 #include <OpenMS/METADATA/MetaInfoDescription.h>
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 {
74 PRE_NONE,
75 PRE_32,
76 PRE_64
77 } precision;
78
79 enum {
80 DT_NONE,
81 DT_FLOAT,
82 DT_INT,
83 DT_STRING
84 } data_type;
85
86 MSNumpressCoder::NumpressCompression np_compression;
87
88 bool compression;
89 double unit_multiplier;
90
91 String base64;
92 Size size;
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
99 MetaInfoDescription meta;
100
102 BinaryData() :
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::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::Internal::MzMLHandlerHelper::BinaryData::np_compression
MSNumpressCoder::NumpressCompression np_compression
numpress options
Definition: MzMLHandlerHelper.h:86
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Internal::MzMLHandlerHelper::BinaryData::PRE_NONE
unknown precision
Definition: MzMLHandlerHelper.h:74
OpenMS::Internal::MzMLHandlerHelper::BinaryData::meta
MetaInfoDescription meta
Meta data description.
Definition: MzMLHandlerHelper.h:99
MSNumpressCoder.h
OpenMS::Internal::MzMLHandlerHelper::BinaryData::floats_32
std::vector< float > floats_32
Definition: MzMLHandlerHelper.h:93
OpenMS::Internal::MzMLHandlerHelper::BinaryData::decoded_char
std::vector< String > decoded_char
Definition: MzMLHandlerHelper.h:97
OpenMS::MetaInfoDescription
Description of the meta data arrays of MSSpectrum.
Definition: MetaInfoDescription.h:48
OpenMS::Internal::MzMLHandlerHelper::BinaryData::ints_64
std::vector< Int64 > ints_64
Definition: MzMLHandlerHelper.h:96
OpenMS::Internal::MzMLHandlerHelper::BinaryData::DT_FLOAT
float data type
Definition: MzMLHandlerHelper.h:81
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
Representation for binary data in mzML.
Definition: MzMLHandlerHelper.h:69
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::Internal::MzMLHandlerHelper::BinaryData::floats_64
std::vector< double > floats_64
Definition: MzMLHandlerHelper.h:94
OpenMS::Internal::MzMLHandlerHelper::BinaryData::base64
String base64
Raw data in base64 encoding.
Definition: MzMLHandlerHelper.h:91
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::MSNumpressCoder::NumpressCompression
NumpressCompression
Names of compression schemes.
Definition: MSNumpressCoder.h:73
OpenMS::Internal::MzMLHandlerHelper
Helper for mzML file format.
Definition: MzMLHandlerHelper.h:55
OpenMS::Internal::MzMLHandlerHelper::BinaryData::size
Size size
Raw data length.
Definition: MzMLHandlerHelper.h:92
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::Internal::MzMLHandlerHelper::BinaryData::PRE_32
32bit precision
Definition: MzMLHandlerHelper.h:75
OpenMS::Internal::MzMLHandlerHelper::BinaryData::compression
bool compression
zlib compression
Definition: MzMLHandlerHelper.h:88
MetaInfoDescription.h
OpenMS::Internal::MzMLHandlerHelper::BinaryData::DT_NONE
unknown data type
Definition: MzMLHandlerHelper.h:80
PeakFileOptions.h
OpenMS::Internal::MzMLHandlerHelper::BinaryData::DT_INT
integer data type
Definition: MzMLHandlerHelper.h:82
OpenMS::MSNumpressCoder::NumpressConfig
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:87
OpenMS::Internal::MzMLHandlerHelper::BinaryData::ints_32
std::vector< Int32 > ints_32
Definition: MzMLHandlerHelper.h:95
OpenMS::Internal::MzMLHandlerHelper::BinaryData::BinaryData
BinaryData()
Constructor.
Definition: MzMLHandlerHelper.h:102
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127