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...
virtual	~XMassFile ()
	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...
ProgressLogger &	operator= (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 () const
	Ends the progress display. More...
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_
ProgressLoggerImpl *	current_logger_
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.

Note

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
http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1594579&blobtype=pdf

Constructor & Destructor Documentation

XMassFile()

XMassFile

(

)

Default constructor.

~XMassFile()

virtual ~XMassFile ( )

virtual

Destructor.

Member Function Documentation

importExperimentalSettings()

void importExperimentalSettings ( const String &  filename, PeakMap &  exp  )

inline

Import settings from a XMass file.

Parameters

filename	File from which the experimental settings should be loaded.
exp	MSExperiment where the experimental settings will be stored.

Exceptions

Exception::FileNotFound

is thrown if the file could not be opened.

References MassAnalyzer::ANALYZERNULL, IonSource::DIRECT, MSExperiment::getExperimentalSettings(), ExperimentalSettings::getInstrument(), Instrument::getIonSources(), Instrument::getMassAnalyzers(), AcqusHandler::getParam(), IonSource::INLETNULL, IonSource::MALDI, IonSource::NEGATIVE, IonSource::POLNULL, IonSource::POSITIVE, String::prefix(), String::remove(), DateTime::set(), ExperimentalSettings::setDateTime(), Instrument::setModel(), Instrument::setName(), Instrument::setVendor(), and MassAnalyzer::TOF.

load()

void load ( const String &  filename, MSSpectrum &  spectrum  )

inline

Loads a spectrum from a XMass file.

Parameters

filename	Name of the XMass file which should be loaded.
spectrum	Spectrum in which the data loaded from the file should be stored.

Exceptions

Exception::FileNotFound

is 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 &    )

inline

Stores a spectrum in a XMass file (not available)

Exceptions

Exception::FileNotWritable

is thrown