OpenMS  3.0.0
MzDataHandler.h
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34 
35 #pragma once
36 
43 
44 #include <sstream>
45 
46 namespace OpenMS
47 {
48  namespace Internal
49  {
59  typedef PeakMap MapType;
62 
63  class OPENMS_DLLAPI MzDataHandler :
64  public XMLHandler
65  {
66 public:
69  MzDataHandler(MapType & exp, const String & filename, const String & version, ProgressLogger & logger);
71 
73  MzDataHandler(const MapType & exp, const String & filename, const String & version, const ProgressLogger & logger);
74 
76  ~MzDataHandler() override
77  {
78  }
79 
81 
82 
83  // Docu in base class
84  void endElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname) override;
85 
86  // Docu in base class
87  void startElement(const XMLCh * const /*uri*/, const XMLCh * const /*local_name*/, const XMLCh * const qname, const xercesc::Attributes & attributes) override;
88 
89  // Docu in base class
90  void characters(const XMLCh * const chars, const XMLSize_t length) override;
91 
93  void writeTo(std::ostream & os) override;
94 
96  void setOptions(const PeakFileOptions & options)
97  {
98  options_ = options;
99  }
100 
101 private:
102  void init_();
103 
104 protected:
105 
110 
114  const MapType * cexp_;
115 
118 
121  UInt peak_count_;
126  std::vector<std::pair<String, MetaInfoDescription> > meta_id_descs_;
128  std::vector<String> data_to_decode_;
130  std::vector<float> data_to_encode_;
131  std::vector<std::vector<float> > decoded_list_;
132  std::vector<std::vector<double> > decoded_double_list_;
133  std::vector<String> precisions_;
134  std::vector<String> endians_;
136 
139 
142 
144  void fillData_();
145 
147 
148 
159  inline void writeCVS_(std::ostream & os, double value, const String & acc, const String & name, UInt indent = 4) const;
160 
172  inline void writeCVS_(std::ostream & os, const String & value, const String & acc, const String & name, UInt indent = 4) const;
173 
187  inline void writeCVS_(std::ostream & os, UInt value, UInt map, const String & acc, const String & name, UInt indent = 4);
188 
190  inline void writeUserParam_(std::ostream & os, const MetaInfoInterface & meta, UInt indent = 4);
191 
199  void cvParam_(const String & name, const String & value);
201 
207  inline void writeBinary_(std::ostream & os, Size size, const String & tag, const String & name = "", SignedSize id = -1);
208 
209  //Data processing auxiliary variable
210  boost::shared_ptr< DataProcessing > data_processing_;
211 
212  };
213 
214  //--------------------------------------------------------------------------------
215  } // namespace Internal
216 
217 } // namespace OpenMS
218 
OpenMS::Internal::MzDataHandler::~MzDataHandler
~MzDataHandler() override
Destructor.
Definition: MzDataHandler.h:76
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:323
OpenMS::Internal::MzDataHandler
Definition: MzDataHandler.h:63
OpenMS::Internal::MzDataHandler::options_
PeakFileOptions options_
Options that can be set for loading/storing.
Definition: MzDataHandler.h:117
OpenMS::Internal::MapType
PeakMap MapType
XML handler for MzDataFile.
Definition: MzDataHandler.h:59
OpenMS::String
A more convenient string class.
Definition: String.h:58
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
OpenMS::Internal::MzDataHandler::logger_
const ProgressLogger & logger_
Progress logger.
Definition: MzDataHandler.h:141
XMLHandler.h
OpenMS::Internal::MzDataHandler::meta_id_descs_
std::vector< std::pair< String, MetaInfoDescription > > meta_id_descs_
An array of pairs MetaInfodescriptions and their ids.
Definition: MzDataHandler.h:126
OpenMS::Internal::MzDataHandler::PeakType
MapType::PeakType PeakType
Peak type.
Definition: MzDataHandler.h:107
OpenMS::Internal::MzDataHandler::data_to_decode_
std::vector< String > data_to_decode_
encoded data which is read and has to be decoded
Definition: MzDataHandler.h:128
OpenMS::Internal::MzDataHandler::data_processing_
boost::shared_ptr< DataProcessing > data_processing_
Definition: MzDataHandler.h:210
OpenMS::Internal::MzDataHandler::exp_
MapType * exp_
map pointer for reading
Definition: MzDataHandler.h:112
OpenMS::Internal::MzDataHandler::setOptions
void setOptions(const PeakFileOptions &options)
Sets the options.
Definition: MzDataHandler.h:96
OpenMS::Internal::MzDataHandler::skip_spectrum_
bool skip_spectrum_
Flag that indicates whether this spectrum should be skipped (due to options)
Definition: MzDataHandler.h:138
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
OpenMS::Internal::MzDataHandler::cexp_
const MapType * cexp_
map pointer for writing
Definition: MzDataHandler.h:114
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::Internal::SpectrumType
MSSpectrum SpectrumType
Definition: MzDataHandler.h:60
OpenMS::Internal::MzDataHandler::decoded_double_list_
std::vector< std::vector< double > > decoded_double_list_
Definition: MzDataHandler.h:132
OpenMS::Internal::MzDataHandler::spec_
SpectrumType spec_
The current spectrum.
Definition: MzDataHandler.h:124
OpenMS::Internal::MzDataHandler::data_to_encode_
std::vector< float > data_to_encode_
floating point numbers which have to be encoded and written
Definition: MzDataHandler.h:130
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:53
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
PeakFileOptions.h
MSExperiment.h
OpenMS::Internal::MzDataHandler::decoded_list_
std::vector< std::vector< float > > decoded_list_
Definition: MzDataHandler.h:131
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::Internal::MzDataHandler::SpectrumType
MSSpectrum SpectrumType
Spectrum type.
Definition: MzDataHandler.h:109
OpenMS::Internal::MzDataHandler::precisions_
std::vector< String > precisions_
Definition: MzDataHandler.h:133
OpenMS::Internal::ChromatogramType
MSChromatogram ChromatogramType
Definition: MzDataHandler.h:61
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:53
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
StandardTypes.h
OpenMS::Internal::MzDataHandler::endians_
std::vector< String > endians_
Definition: MzDataHandler.h:134