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 experimental settings.
Definition: ExperimentalSettings.h:59
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
void setType(SpectrumType type)
sets the spectrum type
A more convenient string class.
Definition: String.h:58
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
void clear(bool clear_meta_data)
Clears all data and meta data.
static DateTime now()
Returns the current date and time.
void set(UInt month, UInt day, UInt year, UInt hour, UInt minute, UInt second)
sets data from six integers
bool hasSuffix(const String &string) const
true if String ends with string, false otherwise
Positive polarity.
Definition: IonSource.h:143
Description of the applied preprocessing steps.
Definition: DataProcessing.h:51
void load(const String &filename, MSSpectrum &spectrum)
Loads a spectrum from a XMass file.
Definition: XMassFile.h:83
void setPolarity(IonSource::Polarity polarity)
sets the polarity
Description of the settings a MS Instrument was run with.
Definition: InstrumentSettings.h:47
void setSoftware(const Software &software)
sets the software used for processing
void setZoomScan(bool zoom_scan)
sets if this scan is a zoom (enhanced resolution) scan
void setIntensity(IntensityType intensity)
Mutable access to the data point intensity (height)
Definition: Peak1D.h:112
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
void setName(const String &name)
Sets the name of the software.
Baseline reduction.
Definition: DataProcessing.h:66
bool hasPrefix(const String &string) const
true if String begins with string, false otherwise
void setAcquisitionInfo(const AcquisitionInfo &acquisition_info)
sets the acquisition info
void store(const String &, const MSSpectrum &)
Stores a spectrum in a XMass file (not available)
Definition: XMassFile.h:240
Description of a MS instrument.
Definition: Instrument.h:63
void setComment(const String &comment)
sets the free-text comment
const ExperimentalSettings & getExperimentalSettings() const
returns the meta information of this experiment (const access)
void setFileType(const String &file_type)
sets the file type
void setPosition(PositionType const &position)
Mutable access to the position.
Definition: Peak1D.h:151
void setRT(double rt)
Sets the absolute retention time (in seconds)
Description of the software used for processing.
Definition: Software.h:48
Smoothing of the signal to reduce noise.
Definition: DataProcessing.h:63
File not found exception.
Definition: Exception.h:523
void setVersion(const String &version)
Sets the software version.
Matrix-assisted laser desorption ionization.
Definition: IonSource.h:107
void setNameOfFile(const String &name_of_file)
sets the file name
void setInstrumentSettings(const InstrumentSettings &instrument_settings)
sets the instrument settings of the current spectrum
Unknown.
Definition: IonSource.h:142
void setCompletionTime(const DateTime &completion_time)
sets the time of completion taking a DateTime object
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
Unknown.
Definition: MassAnalyzer.h:54
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
profile data
Definition: SpectrumSettings.h:74
Calibration of m/z positions.
Definition: DataProcessing.h:69
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void setScanMode(ScanMode scan_mode)
sets the scan mode
Read-only acqus File handler for XMass Analysis.
Definition: AcqusHandler.h:52
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
DateTime Class.
Definition: DateTime.h:54
File adapter for 'XMass Analysis (fid)' files.
Definition: XMassFile.h:66
void importExperimentalSettings(const String &filename, PeakMap &exp)
Import settings from a XMass file.
Definition: XMassFile.h:180
void setSourceFile(const SourceFile &source_file)
sets the source file
void setModel(const String &model)
sets the instrument model
Read-only fid File handler for XMass Analysis.
Definition: FidHandler.h:51
String prefix(SizeType length) const
returns the prefix of length length
void setProcessingActions(const std::set< ProcessingAction > &actions)
sets the description of the applied processing
String suffix(SizeType length) const
returns the suffix of length length
const std::vector< MassAnalyzer > & getMassAnalyzers() const
returns a const reference to the mass analyzer list
void setName(const String &name)
sets the name of the instrument
void setFileSize(float file_size)
sets the file size in MB
void setMSLevel(UInt ms_level)
Sets the MS level.
Direct.
Definition: IonSource.h:55
void setVendor(const String &vendor)
sets the instrument vendor
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
Not implemented exception.
Definition: Exception.h:436
void setDataProcessing(const std::vector< DataProcessingPtr > &data_processing)
sets the description of the applied processing
void setNativeID(const String &native_id)
sets the native identifier for the spectrum, used by the acquisition software.
Unknown.
Definition: IonSource.h:54
general spectrum type
Definition: InstrumentSettings.h:55
const std::vector< IonSource > & getIonSources() const
returns a const reference to the ion source list
Description of the combination of raw data to a single spectrum.
Definition: AcquisitionInfo.h:52
Negative polarity.
Definition: IonSource.h:144
void setPathToFile(const String &path_path_to_file)
sets the file path
void setMethodOfCombination(const String &method_of_combination)
sets the method of combination
Time-of-flight.
Definition: MassAnalyzer.h:59