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OpenMS
2.6.0
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Go to the documentation of this file.
99 while (spectrum.size() < acqus.getSize())
104 spectrum.push_back(p);
111 spectrum.
setName(
"Xmass analysis file " + acqus.getParam(
"$ID_raw"));
113 spectrum.
setNativeID(
"spectrum=xsd:" + acqus.getParam(
"$ID_raw").remove(
'<').remove(
'>'));
120 if (acqus.getParam(
".IONIZATION MODE") ==
"LD+")
124 else if (acqus.getParam(
".IONIZATION MODE") ==
"LD-")
141 source_file.
setFileSize(4.0 * acqus.getSize() / 1024 / 1024);
142 source_file.
setFileType(
"Xmass analysis file (fid)");
147 software.
setName(
"FlexControl");
148 String fc_ver = acqus.getParam(
"$FCVer");
151 fc_ver = fc_ver.
suffix(
' ');
155 fc_ver = fc_ver.
prefix(
'>');
158 software.
setMetaValue(
"Acquisition method",
DataValue(acqus.getParam(
"$ACQMETH").remove(
'<').remove(
'>')));
160 std::set<DataProcessing::ProcessingAction> actions;
167 std::vector< boost::shared_ptr< DataProcessing> > data_processing_vector;
168 data_processing_vector.push_back( boost::shared_ptr< DataProcessing>(
new DataProcessing(data_processing)) );
186 Instrument & instrument = experimental_settings.getInstrument();
187 instrument.
setName(acqus.getParam(
"SPECTROMETER/DATASYSTEM"));
188 instrument.
setVendor(acqus.getParam(
"ORIGIN"));
189 instrument.
setModel(acqus.getParam(
"$InstrID").remove(
'<').remove(
'>'));
191 std::vector<IonSource> & ionSourceList = instrument.
getIonSources();
192 ionSourceList.clear();
193 ionSourceList.resize(1);
194 if (acqus.getParam(
".INLET") ==
"DIRECT")
203 if (acqus.getParam(
".IONIZATION MODE") ==
"LD+")
207 else if (acqus.getParam(
".IONIZATION MODE") ==
"LD-")
215 ionSourceList[0].setMetaValue(
"MALDI target reference",
DataValue(acqus.getParam(
"$TgIDS").remove(
'<').remove(
'>')));
216 ionSourceList[0].setOrder(0);
218 std::vector<MassAnalyzer> & massAnalyzerList = instrument.
getMassAnalyzers();
219 massAnalyzerList.clear();
220 massAnalyzerList.resize(1);
221 if (acqus.getParam(
".SPECTROMETER TYPE") ==
"TOF")
231 date.
set(acqus.getParam(
"$AQ_DATE").remove(
'<').remove(
'>'));
232 experimental_settings.setDateTime(date);
Description of the software used for processing.
Definition: Software.h:48
general spectrum type
Definition: InstrumentSettings.h:55
Description of the settings a MS Instrument was run with.
Definition: InstrumentSettings.h:47
const ExperimentalSettings & getExperimentalSettings() const
returns the meta information of this experiment (const access)
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
Description of the combination of raw data to a single spectrum.
Definition: AcquisitionInfo.h:52
Time-of-flight.
Definition: MassAnalyzer.h:59
void setPolarity(IonSource::Polarity polarity)
sets the polarity
void setVendor(const String &vendor)
sets the instrument vendor
void setNameOfFile(const String &name_of_file)
sets the file name
const std::vector< MassAnalyzer > & getMassAnalyzers() const
returns a const reference to the mass analyzer list
const std::vector< IonSource > & getIonSources() const
returns a const reference to the ion source list
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
A more convenient string class.
Definition: String.h:59
File not found exception.
Definition: Exception.h:523
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
void setType(SpectrumType type)
sets the spectrum type
String prefix(SizeType length) const
returns the prefix of length length
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
void load(const String &filename, MSSpectrum &spectrum)
Loads a spectrum from a XMass file.
Definition: XMassFile.h:83
void setDataProcessing(const std::vector< DataProcessingPtr > &data_processing)
sets the description of the applied processing
void setCompletionTime(const DateTime &completion_time)
sets the time of completion taking a DateTime object
profile data
Definition: SpectrumSettings.h:74
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
void setVersion(const String &version)
Sets the software version.
static DateTime now()
Returns the current date and time.
Description of a MS instrument.
Definition: Instrument.h:63
void setFileSize(float file_size)
sets the file size in MB
void setComment(const String &comment)
sets the free-text comment
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void setSourceFile(const SourceFile &source_file)
sets the source file
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
Direct.
Definition: IonSource.h:55
void setScanMode(ScanMode scan_mode)
sets the scan mode
void setPosition(PositionType const &position)
Mutable access to the position.
Definition: Peak1D.h:151
File adapter for 'XMass Analysis (fid)' files.
Definition: XMassFile.h:66
void clear(bool clear_meta_data)
Clears all data and meta data.
void setMSLevel(UInt ms_level)
Sets the MS level.
bool hasSuffix(const String &string) const
true if String ends with string, false otherwise
Not implemented exception.
Definition: Exception.h:436
void set(UInt month, UInt day, UInt year, UInt hour, UInt minute, UInt second)
sets data from six integers
Calibration of m/z positions.
Definition: DataProcessing.h:69
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
void setMethodOfCombination(const String &method_of_combination)
sets the method of combination
void setSoftware(const Software &software)
sets the software used for processing
void setProcessingActions(const std::set< ProcessingAction > &actions)
sets the description of the applied processing
Positive polarity.
Definition: IonSource.h:143
Smoothing of the signal to reduce noise.
Definition: DataProcessing.h:63
void setZoomScan(bool zoom_scan)
sets if this scan is a zoom (enhanced resolution) scan
void setName(const String &name)
sets the name of the instrument
Description of the applied preprocessing steps.
Definition: DataProcessing.h:51
Read-only fid File handler for XMass Analysis.
Definition: FidHandler.h:51
Matrix-assisted laser desorption ionization.
Definition: IonSource.h:107
void setName(const String &name)
Sets the name.
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:46
Unknown.
Definition: IonSource.h:142
Negative polarity.
Definition: IonSource.h:144
void setAcquisitionInfo(const AcquisitionInfo &acquisition_info)
sets the acquisition info
void setFileType(const String &file_type)
sets the file type
Unknown.
Definition: MassAnalyzer.h:54
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:240
String suffix(SizeType length) const
returns the suffix of length length
void setRT(double rt)
Sets the absolute retention time (in seconds)
void setInstrumentSettings(const InstrumentSettings &instrument_settings)
sets the instrument settings of the current spectrum
Unknown.
Definition: IonSource.h:54
DateTime Class.
Definition: DateTime.h:54
Read-only acqus File handler for XMass Analysis.
Definition: AcqusHandler.h:52
void setNativeID(const String &native_id)
sets the native identifier for the spectrum, used by the acquisition software.
void importExperimentalSettings(const String &filename, PeakMap &exp)
Import settings from a XMass file.
Definition: XMassFile.h:180
Baseline reduction.
Definition: DataProcessing.h:66