XMassFile Class Reference

File adapter for 'XMass Analysis (fid)' files. More...

#include <OpenMS/FORMAT/XMassFile.h>

Inheritance diagram for XMassFile:
Collaboration diagram for XMassFile:

Public Member Functions

 XMassFile ()
 Default constructor. More...
 ~XMassFile () override
 Destructor. More...
void load (const String &filename, MSSpectrum &spectrum)
 Loads a spectrum from a XMass file. More...
void importExperimentalSettings (const String &filename, PeakMap &exp)
 Import settings from a XMass file. More...
void store (const String &, const MSSpectrum &)
 Stores a spectrum in a XMass file (not available) More...
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
virtual ~ProgressLogger ()
 Destructor. More...
 ProgressLogger (const ProgressLogger &other)
 Copy constructor. More...
ProgressLoggeroperator= (const ProgressLogger &other)
 Assignment Operator. More...
void setLogType (LogType type) const
 Sets the progress log that should be used. The default type is NONE! More...
LogType getLogType () const
 Returns the type of progress log being used. More...
void startProgress (SignedSize begin, SignedSize end, const String &label) const
 Initializes the progress display. More...
void setProgress (SignedSize value) const
 Sets the current progress. More...
void endProgress (UInt64 bytes_processed=0) const
void nextProgress () const
 increment progress by 1 (according to range begin-end) More...

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD , GUI , NONE }
 Possible log types. More...
- Static Protected Member Functions inherited from ProgressLogger
static String logTypeToFactoryName_ (LogType type)
 Return the name of the factory product used for this log type. More...
- Protected Attributes inherited from ProgressLogger
LogType type_
time_t last_invoke_
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_

Detailed Description

File adapter for 'XMass Analysis (fid)' files.

XMass Analysis files is native format for Bruker spectrometer Flex Series.
Each spectrum are saved in one directory. Each directory contains several files. We use 2 files for import in OpenMS :
acqus : contains meta data about calibration (conversion for time to mz ratio), instrument specification and acquisition method.
fid : contains intensity array. Intensity for each point are coded in 4 bytes integer.

MZ ratio are calculated with formula based on article :
A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls
Mark K Titulaer, Ivar Siccama, Lennard J Dekker, Angelique LCT van Rijswijk, Ron MA Heeren, Peter A Sillevis Smitt, and Theo M Luider
BMC Bioinformatics. 2006; 7: 403

Constructor & Destructor Documentation

◆ XMassFile()

XMassFile ( )

Default constructor.

◆ ~XMassFile()

~XMassFile ( )


Member Function Documentation

◆ importExperimentalSettings()

void importExperimentalSettings ( const String filename,
PeakMap exp 

◆ load()

void load ( const String filename,
MSSpectrum spectrum 

Loads a spectrum from a XMass file.

filenameName of the XMass file which should be loaded.
spectrumSpectrum in which the data loaded from the file should be stored.
Exception::FileNotFoundis thrown if the file could not be read

References DataProcessing::BASELINE_REDUCTION, DataProcessing::CALIBRATION, MSSpectrum::clear(), FidHandler::getIndex(), FidHandler::getIntensity(), AcqusHandler::getParam(), AcqusHandler::getPosition(), AcqusHandler::getSize(), String::hasPrefix(), String::hasSuffix(), InstrumentSettings::MASSSPECTRUM, IonSource::NEGATIVE, DateTime::now(), IonSource::POLNULL, IonSource::POSITIVE, String::prefix(), SpectrumSettings::PROFILE, String::remove(), SpectrumSettings::setAcquisitionInfo(), SpectrumSettings::setComment(), DataProcessing::setCompletionTime(), SpectrumSettings::setDataProcessing(), SourceFile::setFileSize(), SourceFile::setFileType(), SpectrumSettings::setInstrumentSettings(), Peak1D::setIntensity(), MetaInfoInterface::setMetaValue(), AcquisitionInfo::setMethodOfCombination(), MSSpectrum::setMSLevel(), MSSpectrum::setName(), Software::setName(), SourceFile::setNameOfFile(), SpectrumSettings::setNativeID(), SourceFile::setPathToFile(), InstrumentSettings::setPolarity(), Peak1D::setPosition(), DataProcessing::setProcessingActions(), MSSpectrum::setRT(), InstrumentSettings::setScanMode(), DataProcessing::setSoftware(), SpectrumSettings::setSourceFile(), SpectrumSettings::setType(), Software::setVersion(), InstrumentSettings::setZoomScan(), DataProcessing::SMOOTHING, and String::suffix().

◆ store()

void store ( const String ,
const MSSpectrum  

Stores a spectrum in a XMass file (not available)

Exception::FileNotWritableis thrown