OpenMS
MzDataHandler.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
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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:
70  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 
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 
Definition: MzDataHandler.h:65
void writeCVS_(std::ostream &os, double value, const String &acc, const String &name, UInt indent=4) const
write cvParam containing strings to stream
std::vector< String > data_to_decode_
encoded data which is read and has to be decoded
Definition: MzDataHandler.h:128
std::vector< std::vector< double > > decoded_double_list_
Definition: MzDataHandler.h:132
UInt peak_count_
The number of peaks in the current spectrum.
Definition: MzDataHandler.h:122
std::vector< String > endians_
Definition: MzDataHandler.h:134
~MzDataHandler() override
Destructor.
Definition: MzDataHandler.h:76
boost::shared_ptr< DataProcessing > data_processing_
Definition: MzDataHandler.h:210
MzDataHandler(MapType &exp, const String &filename, const String &version, ProgressLogger &logger)
Constructor for a write-only handler.
MapType * exp_
map pointer for reading
Definition: MzDataHandler.h:112
void cvParam_(const String &name, const String &value)
read attributes of MzData's cvParamType
void setOptions(const PeakFileOptions &options)
Sets the options.
Definition: MzDataHandler.h:96
void writeTo(std::ostream &os) override
Writes the contents to a stream.
MzDataHandler(const MapType &exp, const String &filename, const String &version, const ProgressLogger &logger)
Constructor for a read-only handler.
const ProgressLogger & logger_
Progress logger.
Definition: MzDataHandler.h:141
std::vector< float > data_to_encode_
floating point numbers which have to be encoded and written
Definition: MzDataHandler.h:130
SpectrumType spec_
The current spectrum.
Definition: MzDataHandler.h:124
MSSpectrum SpectrumType
Spectrum type.
Definition: MzDataHandler.h:109
PeakFileOptions options_
Options that can be set for loading/storing.
Definition: MzDataHandler.h:117
MapType::PeakType PeakType
Peak type.
Definition: MzDataHandler.h:107
bool skip_spectrum_
Flag that indicates whether this spectrum should be skipped (due to options)
Definition: MzDataHandler.h:138
std::vector< std::vector< float > > decoded_list_
Definition: MzDataHandler.h:131
void writeCVS_(std::ostream &os, const String &value, const String &acc, const String &name, UInt indent=4) const
write cvParam containing strings to stream
void writeCVS_(std::ostream &os, UInt value, UInt map, const String &acc, const String &name, UInt indent=4)
write cvParam element to stream
void writeBinary_(std::ostream &os, Size size, const String &tag, const String &name="", SignedSize id=-1)
write binary data to stream (first one)
void startElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname, const xercesc::Attributes &attributes) override
std::vector< std::pair< String, MetaInfoDescription > > meta_id_descs_
An array of pairs MetaInfodescriptions and their ids.
Definition: MzDataHandler.h:126
std::vector< String > precisions_
Definition: MzDataHandler.h:133
void characters(const XMLCh *const chars, const XMLSize_t length) override
void endElement(const XMLCh *const, const XMLCh *const, const XMLCh *const qname) override
void writeUserParam_(std::ostream &os, const MetaInfoInterface &meta, UInt indent=4)
Writing the MetaInfo as UserParam to the file.
void fillData_()
fills the current spectrum with peaks and meta data
const MapType * cexp_
map pointer for writing
Definition: MzDataHandler.h:114
Base class for XML handlers.
Definition: XMLHandler.h:326
The representation of a chromatogram.
Definition: MSChromatogram.h:57
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:61
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
Options for loading files containing peak data.
Definition: PeakFileOptions.h:48
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
A more convenient string class.
Definition: String.h:60
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
MSChromatogram ChromatogramType
Definition: MzDataHandler.h:61
MSSpectrum SpectrumType
Definition: MzDataHandler.h:60
PeakMap MapType
XML handler for MzDataFile.
Definition: MzDataHandler.h:59
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48