OpenMS  2.4.0
MzXMLHandler.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm, Chris Bielow $
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34 
35 #pragma once
36 
43 
44 namespace OpenMS
45 {
46  class MetaInfoInterface;
47  namespace Interfaces
48  {
49  class IMSDataConsumer;
50  }
51 
52  namespace Internal
53  {
54 
55 
63  typedef PeakMap MapType;
64  typedef MSSpectrum SpectrumType;
65 
66  class OPENMS_DLLAPI MzXMLHandler :
67  public XMLHandler
68  {
69 public:
72  MzXMLHandler(MapType& exp, const String& filename, const String& version, ProgressLogger& logger);
74 
76  MzXMLHandler(const MapType& exp, const String& filename, const String& version, const ProgressLogger& logger);
77 
79  ~MzXMLHandler() override {}
81 
83  virtual LOADDETAIL getLoadDetail() const override;
84 
86  virtual void setLoadDetail(const LOADDETAIL d) override;
87 
88  // Docu in base class
89  void endElement(const XMLCh* const uri, const XMLCh* const local_name, const XMLCh* const qname) override;
90 
91  // Docu in base class
92  void startElement(const XMLCh* const uri, const XMLCh* const local_name, const XMLCh* const qname, const xercesc::Attributes& attributes) override;
93 
94  // Docu in base class
95  void characters(const XMLCh* const chars, const XMLSize_t length) override;
96 
98  void writeTo(std::ostream& os) override;
99 
101  void setOptions(const PeakFileOptions& options)
102  {
103  options_ = options;
104  }
105 
108  {
109  return scan_count_;
110  }
111 
114  {
115  consumer_ = consumer;
116  }
117 
118 protected:
119 
124 
128  const MapType* cexp_;
129 
132 
136 
145  {
151  bool skip_data;
152  };
153 
155  std::vector< SpectrumData > spectrum_data_;
157 
160 
163 
166 
169 
172 
173 
175  inline std::ostream& writeAttributeIfExists_(std::ostream& os, const MetaInfoInterface& meta, const String& metakey, const String& attname);
176 
178  inline void writeUserParam_(std::ostream& os, const MetaInfoInterface& meta, int indent = 4, String tag = "nameValue");
179 
186  void doPopulateSpectraWithData_(SpectrumData & spectrum_data);
187 
194  void populateSpectraWithData_();
195 
197  std::vector< boost::shared_ptr< DataProcessing> > data_processing_;
198 
199 
200 private:
202  MzXMLHandler();
203 
205  void init_();
206 
207  // init all the static members, which is necessary because otherwise the undefined order will cause problems
208  void initStaticMembers_();
209 
210  static const XMLCh* s_value_;
211  static const XMLCh* s_count_;
212  static const XMLCh* s_type_;
213  static const XMLCh* s_name_;
214  static const XMLCh* s_version_;
215  static const XMLCh* s_filename_;
216  static const XMLCh* s_filetype_;
217  static const XMLCh* s_filesha1_;
218  static const XMLCh* s_completiontime_;
219  static const XMLCh* s_precision_;
220  static const XMLCh* s_byteorder_;
221  static const XMLCh* s_contentType_;
222  static const XMLCh* s_compressionType_;
223  static const XMLCh* s_precursorintensity_;
224  static const XMLCh* s_precursorcharge_;
225  static const XMLCh* s_windowwideness_;
226  static const XMLCh* s_mslevel_;
227  static const XMLCh* s_peakscount_;
228  static const XMLCh* s_polarity_;
229  static const XMLCh* s_scantype_;
230  static const XMLCh* s_filterline_;
231  static const XMLCh* s_retentiontime_;
232  static const XMLCh* s_startmz_;
233  static const XMLCh* s_endmz_;
234  static const XMLCh* s_first_;
235  static const XMLCh* s_last_;
236  static const XMLCh* s_phone_;
237  static const XMLCh* s_email_;
238  static const XMLCh* s_uri_;
239  static const XMLCh* s_num_;
240  static const XMLCh* s_intensitycutoff_;
241  static const XMLCh* s_centroided_;
242  static const XMLCh* s_deisotoped_;
243  static const XMLCh* s_chargedeconvoluted_;
244  };
245 
246  } // namespace Internal
247 
248 } // namespace OpenMS
249 
static const XMLCh * s_precursorintensity_
Definition: MzXMLHandler.h:223
static const XMLCh * s_uri_
Definition: MzXMLHandler.h:238
A more convenient string class.
Definition: String.h:57
static const XMLCh * s_precision_
Definition: MzXMLHandler.h:219
static const XMLCh * s_peakscount_
Definition: MzXMLHandler.h:227
UInt spec_write_counter_
spectrum counter (spectra without peaks are not written)
Definition: MzXMLHandler.h:162
static const XMLCh * s_value_
Definition: MzXMLHandler.h:210
UInt peak_count_
Definition: MzXMLHandler.h:146
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Definition: MzXMLHandler.h:66
IMSDataConsumer IMSDataConsumer
Definition: IMSDataConsumer.h:125
Base class for XML handlers.
Definition: XMLHandler.h:148
std::vector< boost::shared_ptr< DataProcessing > > data_processing_
data processing auxiliary variable
Definition: MzXMLHandler.h:197
static const XMLCh * s_startmz_
Definition: MzXMLHandler.h:232
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
static const XMLCh * s_deisotoped_
Definition: MzXMLHandler.h:242
static const XMLCh * s_precursorcharge_
Definition: MzXMLHandler.h:224
static const XMLCh * s_retentiontime_
Definition: MzXMLHandler.h:231
const MapType * cexp_
map pointer for writing
Definition: MzXMLHandler.h:128
static const XMLCh * s_intensitycutoff_
Definition: MzXMLHandler.h:240
static const XMLCh * s_contentType_
Definition: MzXMLHandler.h:221
Interfaces::IMSDataConsumer * consumer_
Consumer class to work on spectra.
Definition: MzXMLHandler.h:165
static const XMLCh * s_chargedeconvoluted_
Definition: MzXMLHandler.h:243
static const XMLCh * s_completiontime_
Definition: MzXMLHandler.h:218
static const XMLCh * s_last_
Definition: MzXMLHandler.h:235
String precision_
Definition: MzXMLHandler.h:147
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
static const XMLCh * s_scantype_
Definition: MzXMLHandler.h:229
static const XMLCh * s_byteorder_
Definition: MzXMLHandler.h:220
static const XMLCh * s_polarity_
Definition: MzXMLHandler.h:228
~MzXMLHandler() override
Destructor.
Definition: MzXMLHandler.h:79
static const XMLCh * s_first_
Definition: MzXMLHandler.h:234
UInt getScanCount()
Gets the scan count.
Definition: MzXMLHandler.h:107
MSExperiment PeakMap
Two-dimensional map of raw data points or peaks.
Definition: StandardTypes.h:61
PeakFileOptions options_
Options for loading and storing.
Definition: MzXMLHandler.h:131
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
void setOptions(const PeakFileOptions &options)
Sets the options.
Definition: MzXMLHandler.h:101
static const XMLCh * s_filetype_
Definition: MzXMLHandler.h:216
static const XMLCh * s_filename_
Definition: MzXMLHandler.h:215
static const XMLCh * s_filterline_
Definition: MzXMLHandler.h:230
Int nesting_level_
Definition: MzXMLHandler.h:135
static const XMLCh * s_filesha1_
Definition: MzXMLHandler.h:217
static const XMLCh * s_email_
Definition: MzXMLHandler.h:237
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:55
static const XMLCh * s_version_
Definition: MzXMLHandler.h:214
String compressionType_
Definition: MzXMLHandler.h:148
std::vector< SpectrumData > spectrum_data_
Vector of spectrum data stored for later parallel processing.
Definition: MzXMLHandler.h:155
void setMSDataConsumer(Interfaces::IMSDataConsumer *consumer)
Set the IMSDataConsumer consumer which will consume the read data.
Definition: MzXMLHandler.h:113
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
MapType::PeakType PeakType
Peak type.
Definition: MzXMLHandler.h:121
static const XMLCh * s_endmz_
Definition: MzXMLHandler.h:233
PeakMap MapType
XML handler for MzDataFile.
Definition: MzDataHandler.h:59
SpectrumType spectrum
Definition: MzXMLHandler.h:150
static const XMLCh * s_type_
Definition: MzXMLHandler.h:212
UInt scan_count_
Consumer class to work on spectra.
Definition: MzXMLHandler.h:168
static const XMLCh * s_compressionType_
Definition: MzXMLHandler.h:222
static const XMLCh * s_centroided_
Definition: MzXMLHandler.h:241
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:67
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
MSSpectrum SpectrumType
Spectrum type.
Definition: MzXMLHandler.h:123
String char_rest_
Definition: MzXMLHandler.h:149
bool skip_spectrum_
Flag that indicates whether this spectrum should be skipped (due to options)
Definition: MzXMLHandler.h:159
Data necessary to generate a single spectrum.
Definition: MzXMLHandler.h:144
static const XMLCh * s_mslevel_
Definition: MzXMLHandler.h:226
static const XMLCh * s_windowwideness_
Definition: MzXMLHandler.h:225
static const XMLCh * s_name_
Definition: MzXMLHandler.h:213
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
const ProgressLogger & logger_
Progress logging class.
Definition: MzXMLHandler.h:171
static const XMLCh * s_num_
Definition: MzXMLHandler.h:239
bool skip_data
Definition: MzXMLHandler.h:151
int Int
Signed integer type.
Definition: Types.h:102
MapType * exp_
map pointer for reading
Definition: MzXMLHandler.h:126
static const XMLCh * s_count_
Definition: MzXMLHandler.h:211
static const XMLCh * s_phone_
Definition: MzXMLHandler.h:236
MSSpectrum SpectrumType
Definition: MzDataHandler.h:60