| OpenMS 2.5.0

Public Member Functions | List of all members
XMassFile Class Reference
Format » File IO

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

`#include <OpenMS/FORMAT/XMassFile.h>`

Inheritance 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...
| ~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(), 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.

## ◆ 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(), String::hasPrefix(), String::hasSuffix(), InstrumentSettings::MASSSPECTRUM, IonSource::NEGATIVE, DateTime::now(), IonSource::POLNULL, IonSource::POSITIVE, String::prefix(), SpectrumSettings::PROFILE, SpectrumSettings::setAcquisitionInfo(), SpectrumSettings::setComment(), DataProcessing::setCompletionTime(), SpectrumSettings::setDataProcessing(), SourceFile::setFileSize(), SourceFile::setFileType(), SpectrumSettings::setInstrumentSettings(), Peak1D::setIntensity(), MetaInfoInterface::setMetaValue(), AcquisitionInfo::setMethodOfCombination(), MSSpectrum::setMSLevel(), Software::setName(), MSSpectrum::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