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XMassFile Class Reference
[File IO]

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

#include <OpenMS/FORMAT/XMassFile.h>

Inheritance diagram for XMassFile:
ProgressLogger

List of all members.

Public Member Functions

 XMassFile ()
 Default constructor.
virtual ~XMassFile ()
 Destructor.
template<class PeakType >
void load (const String &filename, MSSpectrum< PeakType > &spectrum)
 Loads a spectrum from a XMass file.
template<class PeakType >
void importExperimentalSettings (const String &filename, MSExperiment< PeakType > &exp)
 Import settings from a XMass file.
template<typename SpectrumType >
void store (const String &, const SpectrumType &)
 Stores a spectrum in a XMass file (not avaible).

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 calculed with forumla 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 (  ) 

Default constructor.

virtual ~XMassFile (  )  [virtual]

Destructor.

Member Function Documentation

void importExperimentalSettings ( const String &  filename,
MSExperiment< PeakType > &  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< PeakT, ChromatogramPeakT >::getExperimentalSettings(), ExperimentalSettings::getInstrument(), Instrument::getIonSources(), Instrument::getMassAnalyzers(), IonSource::INLETNULL, IonSource::MALDI, IonSource::NEGATIVE, IonSource::POLNULL, IonSource::POSITIVE, String::prefix(), DateTime::set(), Instrument::setModel(), Instrument::setName(), Instrument::setVendor(), and MassAnalyzer::TOF.

void load ( const String &  filename,
MSSpectrum< PeakType > &  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< PeakT >::clear(), String::hasPrefix(), String::hasSuffix(), InstrumentSettings::MASSSPECTRUM, IonSource::NEGATIVE, DateTime::now(), IonSource::POLNULL, IonSource::POSITIVE, String::prefix(), SpectrumSettings::RAWDATA, SpectrumSettings::setAcquisitionInfo(), SpectrumSettings::setComment(), DataProcessing::setCompletionTime(), SpectrumSettings::setDataProcessing(), SourceFile::setFileSize(), SourceFile::setFileType(), SpectrumSettings::setInstrumentSettings(), Peak2D::setIntensity(), MetaInfoInterface::setMetaValue(), AcquisitionInfo::setMethodOfCombination(), MSSpectrum< PeakT >::setMSLevel(), Software::setName(), MSSpectrum< PeakT >::setName(), SourceFile::setNameOfFile(), SpectrumSettings::setNativeID(), SourceFile::setPathToFile(), InstrumentSettings::setPolarity(), Peak2D::setPosition(), DataProcessing::setProcessingActions(), MSSpectrum< PeakT >::setRT(), InstrumentSettings::setScanMode(), DataProcessing::setSoftware(), SpectrumSettings::setSourceFile(), SpectrumSettings::setType(), Software::setVersion(), InstrumentSettings::setZoomScan(), DataProcessing::SMOOTHING, and String::suffix().

void store ( const String &  ,
const SpectrumType &   
) [inline]

Stores a spectrum in a XMass file (not avaible).

Exceptions:
Exception::FileNotWritable is thrown
OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:54 using doxygen 1.7.1