OpenMS  3.0.0
CachedMzMLHandler.h
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34 
35 #pragma once
36 
38 
40 #include <OpenMS/CONCEPT/Types.h>
42 #include <OpenMS/CONCEPT/Macros.h>
43 
46 
47 #include <fstream>
48 
49 #define CACHED_MZML_FILE_IDENTIFIER 8094
50 
51 namespace OpenMS
52 {
53 
54 namespace Internal
55 {
56 
66  class OPENMS_DLLAPI CachedMzMLHandler :
67  public ProgressLogger
68  {
69  typedef int IntType;
70  typedef double DoubleType;
71 
72 public:
73 
74  typedef PeakMap MapType;
77 
78  // using double precision to store all data (has to agree with type of BinaryDataArrayPtr)
79  typedef double DatumSingleton;
80 
81  typedef std::vector<DatumSingleton> Datavector;
82 
88 
90  ~CachedMzMLHandler() override;
91 
93  CachedMzMLHandler& operator=(const CachedMzMLHandler& rhs);
95 
99 
101  void writeMemdump(const MapType& exp, const String& out) const;
102 
104  void writeMetadata(MapType exp, String out_meta, bool addCacheMetaValue=false);
105 
107  void writeMetadata_x(const MapType& exp, const String& out_meta, bool addCacheMetaValue=false);
108 
110  void readMemdump(MapType& exp_reading, String filename) const;
112 
116  void createMemdumpIndex(String filename);
118 
120  const std::vector<std::streampos>& getSpectraIndex() const;
121 
123  const std::vector<std::streampos>& getChromatogramIndex() const;
125 
129 
142  std::ifstream& ifs,
143  int& ms_level,
144  double& rt)
145  {
146  std::vector<OpenSwath::BinaryDataArrayPtr> data = readSpectrumFast(ifs, ms_level, rt);
147  data1 = data[0];
148  data2 = data[1];
149  }
150 
160  static std::vector<OpenSwath::BinaryDataArrayPtr> readSpectrumFast(std::ifstream& ifs, int& ms_level, double& rt);
161 
171  OpenSwath::BinaryDataArrayPtr& data2, std::ifstream& ifs)
172  {
173  std::vector<OpenSwath::BinaryDataArrayPtr> data = readChromatogramFast(ifs);
174  data1 = data[0];
175  data2 = data[1];
176  }
177 
185  static std::vector<OpenSwath::BinaryDataArrayPtr> readChromatogramFast(std::ifstream& ifs);
187 
196  static void readSpectrum(SpectrumType& spectrum, std::ifstream& ifs);
197 
206  static void readChromatogram(ChromatogramType& chromatogram, std::ifstream& ifs);
207 
208 protected:
209 
211  void writeSpectrum_(const SpectrumType& spectrum, std::ofstream& ofs) const;
212 
214  void writeChromatogram_(const ChromatogramType& chromatogram, std::ofstream& ofs) const;
215 
217  static inline void readDataFast_(std::ifstream& ifs, std::vector<OpenSwath::BinaryDataArrayPtr>& data, const Size& data_size,
218  const Size& nr_float_arrays);
219 
221  std::vector<std::streampos> spectra_index_;
222  std::vector<std::streampos> chrom_index_;
223 
224  };
225 }
226 }
227 
OpenMS::Internal::CachedMzMLHandler::IntType
int IntType
Definition: CachedMzMLHandler.h:69
OpenMS::Internal::CachedMzMLHandler::Datavector
std::vector< DatumSingleton > Datavector
Definition: CachedMzMLHandler.h:81
OpenMS::Internal::CachedMzMLHandler::SpectrumType
MSSpectrum SpectrumType
Definition: CachedMzMLHandler.h:75
OpenMS::Internal::CachedMzMLHandler::DoubleType
double DoubleType
Definition: CachedMzMLHandler.h:70
Types.h
OpenMS::Internal::CachedMzMLHandler::readSpectrumFast
static void readSpectrumFast(OpenSwath::BinaryDataArrayPtr &data1, OpenSwath::BinaryDataArrayPtr &data2, std::ifstream &ifs, int &ms_level, double &rt)
fast access to a spectrum (a direct copy of the data into the provided arrays)
Definition: CachedMzMLHandler.h:140
OpenMS::String
A more convenient string class.
Definition: String.h:58
ISpectrumAccess.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Macros.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Exception.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenSwath::BinaryDataArrayPtr
boost::shared_ptr< BinaryDataArray > BinaryDataArrayPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:79
OpenMS::Internal::CachedMzMLHandler::chrom_index_
std::vector< std::streampos > chrom_index_
Definition: CachedMzMLHandler.h:222
OpenMS::Internal::CachedMzMLHandler::MapType
PeakMap MapType
Definition: CachedMzMLHandler.h:74
OpenMS::Internal::CachedMzMLHandler::readChromatogramFast
static void readChromatogramFast(OpenSwath::BinaryDataArrayPtr &data1, OpenSwath::BinaryDataArrayPtr &data2, std::ifstream &ifs)
Fast access to a chromatogram.
Definition: CachedMzMLHandler.h:170
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:53
OpenMS::Internal::CachedMzMLHandler::spectra_index_
std::vector< std::streampos > spectra_index_
Members.
Definition: CachedMzMLHandler.h:221
OpenMS::Internal::CachedMzMLHandler::DatumSingleton
double DatumSingleton
Definition: CachedMzMLHandler.h:79
StandardDeclarations.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
StandardTypes.h
OpenMS::Internal::CachedMzMLHandler
An class that uses on-disk caching to read and write spectra and chromatograms.
Definition: CachedMzMLHandler.h:66
OpenMS::Internal::CachedMzMLHandler::ChromatogramType
MSChromatogram ChromatogramType
Definition: CachedMzMLHandler.h:76