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XMassFile.h
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34 
35 #ifndef OPENMS_FORMAT_XMASSFILE_H
36 #define OPENMS_FORMAT_XMASSFILE_H
37 
43 
44 namespace OpenMS
45 {
67  class OPENMS_DLLAPI XMassFile :
68  public ProgressLogger
69  {
70 public:
72  XMassFile();
74  virtual ~XMassFile();
75 
84  void load(const String & filename, MSSpectrum & spectrum)
85  {
86  Internal::AcqusHandler acqus(filename.prefix(filename.length() - 3) + String("acqus"));
87 
88  Internal::FidHandler fid(filename);
89  if (!fid)
90  {
91  throw Exception::FileNotFound(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, filename);
92  }
93 
94  // Delete old spectrum
95  spectrum.clear(true);
96 
97  //temporary variables
98  Peak1D p;
99 
100  while (spectrum.size() < acqus.getSize())
101  {
102  //fill peak
103  p.setPosition((Peak1D::PositionType)acqus.getPosition(fid.getIndex()));
104  p.setIntensity((Peak1D::IntensityType)fid.getIntensity());
105  spectrum.push_back(p);
106  }
107  fid.close();
108 
109  // import metadata
110  spectrum.setRT(0.0);
111  spectrum.setMSLevel(1);
112  spectrum.setName("Xmass analysis file " + acqus.getParam("$ID_raw"));
114  spectrum.setNativeID("spectrum=xsd:" + acqus.getParam("$ID_raw").remove('<').remove('>'));
115  spectrum.setComment("no comment");
116 
117  InstrumentSettings instrument_settings;
118  instrument_settings.setScanMode(InstrumentSettings::MASSSPECTRUM);
119  instrument_settings.setZoomScan(false);
120 
121  if (acqus.getParam(".IONIZATION MODE") == "LD+")
122  {
123  instrument_settings.setPolarity(IonSource::POSITIVE);
124  }
125  else if (acqus.getParam(".IONIZATION MODE") == "LD-")
126  {
127  instrument_settings.setPolarity(IonSource::NEGATIVE);
128  }
129  else
130  {
131  instrument_settings.setPolarity(IonSource::POLNULL);
132  }
133  spectrum.setInstrumentSettings(instrument_settings);
134 
135  AcquisitionInfo acquisition_info;
136  acquisition_info.setMethodOfCombination("Sum of " + acqus.getParam("$NoSHOTS") + " raw spectrum");
137  spectrum.setAcquisitionInfo(acquisition_info);
138 
139  SourceFile source_file;
140  source_file.setNameOfFile("fid");
141  source_file.setPathToFile(filename.prefix(filename.length() - 3));
142  source_file.setFileSize(4.0 * acqus.getSize() / 1024 / 1024); // 4 bytes / point
143  source_file.setFileType("Xmass analysis file (fid)");
144  spectrum.setSourceFile(source_file);
145 
146  DataProcessing data_processing;
147  Software software;
148  software.setName("FlexControl");
149  String fc_ver = acqus.getParam("$FCVer"); // FlexControlVersion
150  if (fc_ver.hasPrefix("<flexControl "))
151  {
152  fc_ver = fc_ver.suffix(' ');
153  }
154  if (fc_ver.hasSuffix(">"))
155  {
156  fc_ver = fc_ver.prefix('>');
157  }
158  software.setVersion(fc_ver);
159  software.setMetaValue("Acquisition method", DataValue(acqus.getParam("$ACQMETH").remove('<').remove('>')));
160  data_processing.setSoftware(software);
161  std::set<DataProcessing::ProcessingAction> actions;
162  actions.insert(DataProcessing::SMOOTHING);
163  actions.insert(DataProcessing::BASELINE_REDUCTION);
164  actions.insert(DataProcessing::CALIBRATION);
165  data_processing.setProcessingActions(actions);
166  data_processing.setCompletionTime(DateTime::now());
167 
168  std::vector< boost::shared_ptr< DataProcessing> > data_processing_vector;
169  data_processing_vector.push_back( boost::shared_ptr< DataProcessing>(new DataProcessing(data_processing)) );
170  spectrum.setDataProcessing(data_processing_vector);
171  }
172 
181  void importExperimentalSettings(const String & filename, PeakMap & exp)
182  {
183  Internal::AcqusHandler acqus(filename.prefix(filename.length() - 3) + String("acqus"));
184 
185  ExperimentalSettings & experimental_settings = exp.getExperimentalSettings();
186 
187  Instrument & instrument = experimental_settings.getInstrument();
188  instrument.setName(acqus.getParam("SPECTROMETER/DATASYSTEM"));
189  instrument.setVendor(acqus.getParam("ORIGIN"));
190  instrument.setModel(acqus.getParam("$InstrID").remove('<').remove('>'));
191 
192  std::vector<IonSource> & ionSourceList = instrument.getIonSources();
193  ionSourceList.clear();
194  ionSourceList.resize(1);
195  if (acqus.getParam(".INLET") == "DIRECT")
196  {
197  ionSourceList[0].setInletType(IonSource::DIRECT);
198  }
199  else
200  {
201  ionSourceList[0].setInletType(IonSource::INLETNULL);
202  ionSourceList[0].setIonizationMethod(IonSource::MALDI);
203  }
204  if (acqus.getParam(".IONIZATION MODE") == "LD+")
205  {
206  ionSourceList[0].setPolarity(IonSource::POSITIVE);
207  }
208  else if (acqus.getParam(".IONIZATION MODE") == "LD-")
209  {
210  ionSourceList[0].setPolarity(IonSource::NEGATIVE);
211  }
212  else
213  {
214  ionSourceList[0].setPolarity(IonSource::POLNULL);
215  }
216  ionSourceList[0].setMetaValue("MALDI target reference", DataValue(acqus.getParam("$TgIDS").remove('<').remove('>')));
217  ionSourceList[0].setOrder(0);
218 
219  std::vector<MassAnalyzer> & massAnalyzerList = instrument.getMassAnalyzers();
220  massAnalyzerList.clear();
221  massAnalyzerList.resize(1);
222  if (acqus.getParam(".SPECTROMETER TYPE") == "TOF")
223  {
224  massAnalyzerList[0].setType(MassAnalyzer::TOF);
225  }
226  else
227  {
228  massAnalyzerList[0].setType(MassAnalyzer::ANALYZERNULL);
229  }
230 
231  DateTime date;
232  date.set(acqus.getParam("$AQ_DATE").remove('<').remove('>'));
233  experimental_settings.setDateTime(date);
234  }
235 
241  void store(const String & /*filename*/, const MSSpectrum & /*spectrum*/)
242  {
243  throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
244  }
245 
246  };
247 } // namespace OpenMS
248 
249 #endif // OPENMS_FORMAT_XMASSFILE_H
Description of the applied preprocessing steps.
Definition: DataProcessing.h:52
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
Description of a MS instrument.
Definition: Instrument.h:64
void setAcquisitionInfo(const AcquisitionInfo &acquisition_info)
sets the acquisition info
Description of the settings a MS Instrument was run with.
Definition: InstrumentSettings.h:48
A more convenient string class.
Definition: String.h:57
Unknown.
Definition: IonSource.h:54
void setDataProcessing(const std::vector< DataProcessingPtr > &data_processing)
sets the description of the applied processing
void setZoomScan(bool zoom_scan)
sets if this scan is a zoom (enhanced resolution) scan
void set(UInt month, UInt day, UInt year, UInt hour, UInt minute, UInt second)
sets data from six integers
void setInstrumentSettings(const InstrumentSettings &instrument_settings)
sets the instrument settings of the current spectrum
Description of the combination of raw data to a single spectrum.
Definition: AcquisitionInfo.h:53
void setVendor(const String &vendor)
sets the instrument vendor
Negative polarity.
Definition: IonSource.h:144
void setFileType(const String &file_type)
sets the file type
void setScanMode(ScanMode scan_mode)
sets the scan mode
Positive polarity.
Definition: IonSource.h:143
void setComment(const String &comment)
sets the free-text comment
void setProcessingActions(const std::set< ProcessingAction > &actions)
sets the description of the applied processing
void setPolarity(IonSource::Polarity polarity)
sets the polarity
void setName(const String &name)
sets the name of the instrument
Baseline reduction.
Definition: DataProcessing.h:67
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:47
void setName(const String &name)
Sets the name.
Raw data (also called profile data)
Definition: SpectrumSettings.h:75
File not found exception.
Definition: Exception.h:524
Description of the software used for processing.
Definition: Software.h:49
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
File adapter for &#39;XMass Analysis (fid)&#39; files.
Definition: XMassFile.h:67
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:111
const std::vector< IonSource > & getIonSources() const
returns a const reference to the ion source list
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:57
Time-of-flight.
Definition: MassAnalyzer.h:60
Unknown.
Definition: MassAnalyzer.h:55
void load(const String &filename, MSSpectrum &spectrum)
Loads a spectrum from a XMass file.
Definition: XMassFile.h:84
const std::vector< MassAnalyzer > & getMassAnalyzers() const
returns a const reference to the mass analyzer list
void setCompletionTime(const DateTime &completion_time)
sets the time of completion taking a DateTime object
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
void store(const String &, const MSSpectrum &)
Stores a spectrum in a XMass file (not available)
Definition: XMassFile.h:241
String suffix(SizeType length) const
returns the suffix of length length
Read-only fid File handler for XMass Analysis.
Definition: FidHandler.h:52
void setFileSize(float file_size)
sets the file size in MB
Calibration of m/z positions.
Definition: DataProcessing.h:70
void setSoftware(const Software &software)
sets the software used for processing
void setPosition(PositionType const &position)
Mutable access to the position.
Definition: Peak1D.h:150
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:55
void setMSLevel(UInt ms_level)
Sets the MS level.
void clear(bool clear_meta_data)
Clears all data and meta data.
void setRT(double rt)
Sets the absolute retention time (in seconds)
void setNameOfFile(const String &name_of_file)
sets the file name
void setVersion(const String &version)
sets the software version
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
void setSourceFile(const SourceFile &source_file)
sets the source file
void setType(SpectrumType type)
sets the spectrum type
void setMethodOfCombination(const String &method_of_combination)
sets the method of combination
Smoothing of the signal to reduce noise.
Definition: DataProcessing.h:64
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
DateTime Class.
Definition: DateTime.h:55
const ExperimentalSettings & getExperimentalSettings() const
returns the meta information of this experiment (const access)
Definition: MSExperiment.h:738
String prefix(SizeType length) const
returns the prefix of length length
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
void setNativeID(const String &native_id)
sets the native identifier for the spectrum, used by the acquisition software.
Read-only acqus File handler for XMass Analysis.
Definition: AcqusHandler.h:53
general spectrum type
Definition: InstrumentSettings.h:56
static DateTime now()
Returns the current date and time.
void setName(const String &name)
sets the name of the software
void setModel(const String &model)
sets the instrument model
void setPathToFile(const String &path_path_to_file)
sets the file path
void importExperimentalSettings(const String &filename, PeakMap &exp)
Import settings from a XMass file.
Definition: XMassFile.h:181
Matrix-assisted laser desorption ionization.
Definition: IonSource.h:107
Not implemented exception.
Definition: Exception.h:437
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
Unknown.
Definition: IonSource.h:142
bool hasSuffix(const String &string) const
true if String ends with string, false otherwise
Direct.
Definition: IonSource.h:55

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:04 using doxygen 1.8.13