35 #ifndef OPENMS_FORMAT_XMASSFILE_H 
   36 #define OPENMS_FORMAT_XMASSFILE_H 
   83     template <
class PeakType>
 
  100       while (spectrum.size() < acqus.getSize())
 
  105         spectrum.push_back(p);
 
  112       spectrum.
setName(
"Xmass analysis file " + acqus.getParam(
"$ID_raw"));
 
  114       spectrum.
setNativeID(
"spectrum=xsd:" + acqus.getParam(
"$ID_raw").remove(
'<').remove(
'>'));
 
  121       if (acqus.getParam(
".IONIZATION MODE") == 
"LD+")
 
  125       else if (acqus.getParam(
".IONIZATION MODE") == 
"LD-")
 
  142       source_file.
setFileSize(4.0 * acqus.getSize() / 1024 / 1024);   
 
  143       source_file.
setFileType(
"Xmass analysis file (fid)");
 
  148       software.
setName(
"FlexControl");
 
  149       String fc_ver = acqus.getParam(
"$FCVer");   
 
  152         fc_ver = fc_ver.
suffix(
' ');
 
  156         fc_ver = fc_ver.
prefix(
'>');
 
  159       software.
setMetaValue(
"Acquisition method", 
DataValue(acqus.getParam(
"$ACQMETH").remove(
'<').remove(
'>')));
 
  161       std::set<DataProcessing::ProcessingAction> actions;
 
  168       std::vector<DataProcessing> data_processing_vector;
 
  169       data_processing_vector.push_back(data_processing);
 
  181     template <
class PeakType>
 
  188       Instrument & instrument = experimental_settings.getInstrument();
 
  189       instrument.
setName(acqus.getParam(
"SPECTROMETER/DATASYSTEM"));
 
  190       instrument.
setVendor(acqus.getParam(
"ORIGIN"));
 
  191       instrument.
setModel(acqus.getParam(
"$InstrID").remove(
'<').remove(
'>'));
 
  193       std::vector<IonSource> & ionSourceList = instrument.
getIonSources();
 
  194       ionSourceList.clear();
 
  195       ionSourceList.resize(1);
 
  196       if (acqus.getParam(
".INLET") == 
"DIRECT")
 
  205       if (acqus.getParam(
".IONIZATION MODE") == 
"LD+")
 
  209       else if (acqus.getParam(
".IONIZATION MODE") == 
"LD-")
 
  217       ionSourceList[0].setMetaValue(
"MALDI target reference", 
DataValue(acqus.getParam(
"$TgIDS").remove(
'<').remove(
'>')));
 
  218       ionSourceList[0].setOrder(0);
 
  220       std::vector<MassAnalyzer> & massAnalyzerList = instrument.
getMassAnalyzers();
 
  221       massAnalyzerList.clear();
 
  222       massAnalyzerList.resize(1);
 
  223       if (acqus.getParam(
".SPECTROMETER TYPE") == 
"TOF")
 
  233       date.
set(acqus.getParam(
"$AQ_DATE").remove(
'<').remove(
'>'));
 
  234       experimental_settings.setDateTime(date);
 
  242     template <
typename SpectrumType>
 
  251 #endif // OPENMS_FORMAT_XMASSFILE_H 
Descripton of the applied preprocessing steps. 
Definition: DataProcessing.h:51
void load(const String &filename, MSSpectrum< PeakType > &spectrum)
Loads a spectrum from a XMass file. 
Definition: XMassFile.h:84
Description of a MS instrument. 
Definition: Instrument.h:64
Real IntensityType
Intensity type. 
Definition: Peak2D.h:63
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:56
const std::vector< IonSource > & getIonSources() const 
returns a const reference to the ion source list 
A 2-dimensional raw data point or peak. 
Definition: Peak2D.h:55
Unknown. 
Definition: IonSource.h:54
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:54
bool hasSuffix(const String &string) const 
true if String ends with string, false otherwise 
void setVendor(const String &vendor)
sets the instrument vendor 
Negative polarity. 
Definition: IonSource.h:144
const std::vector< MassAnalyzer > & getMassAnalyzers() const 
returns a const reference to the mass analyer list 
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:66
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. 
Definition: MSSpectrum.h:249
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
File adapter for 'XMass Analysis (fid)' files. 
Definition: XMassFile.h:66
void setIntensity(IntensityType intensity)
Non-mutable access to the data point intensity (height) 
Definition: Peak2D.h:167
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 setCompletionTime(const DateTime &completion_time)
sets the time of completition taking a DateTime object 
Read-only fid File handler for XMass Analysis. 
Definition: FidHandler.h:52
Calibration of m/z positions. 
Definition: DataProcessing.h:69
const ExperimentalSettings & getExperimentalSettings() const 
returns the meta information of this experiment (const access) 
Definition: MSExperiment.h:664
void setSoftware(const Software &software)
sets the software used for processing 
void setMSLevel(UInt ms_level)
Sets the MS level. 
Definition: MSSpectrum.h:237
void setPosition(const PositionType &position)
Mutable access to the position. 
Definition: Peak2D.h:185
void clear(bool clear_meta_data)
Clears all data and meta data. 
Definition: MSSpectrum.h:605
void setNameOfFile(const String &name_of_file)
sets the file name 
void setVersion(const String &version)
sets the software version 
Representation of a mass spectrometry experiment. 
Definition: MSExperiment.h:68
void setSourceFile(const SourceFile &source_file)
sets the source file 
void setType(SpectrumType type)
sets the spectrum type 
void store(const String &, const SpectrumType &)
Stores a spectrum in a XMass file (not avaible) 
Definition: XMassFile.h:243
void setMethodOfCombination(const String &method_of_combination)
sets the method of combination 
void setFileSize(Real file_size)
sets the file size in MB 
Smoothing of the signal to reduce noise. 
Definition: DataProcessing.h:63
void setRT(DoubleReal rt)
Sets the absolute retention time (is seconds) 
Definition: MSSpectrum.h:221
String prefix(SizeType length) const 
returns the prefix of length length 
void setDataProcessing(const std::vector< DataProcessing > &data_processing)
sets the description of the applied processing 
DateTime Class. 
Definition: DateTime.h:55
Base class for all classes that want to report their progess. 
Definition: ProgressLogger.h:56
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
void importExperimentalSettings(const String &filename, MSExperiment< PeakType > &exp)
Import settings from a XMass file. 
Definition: XMassFile.h:182
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 
String suffix(SizeType length) const 
returns the suffix of length length 
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
Direct. 
Definition: IonSource.h:55
bool hasPrefix(const String &string) const 
true if String begins with string, false otherwise