OpenMS
2.4.0
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File adapter for 'XMass Analysis (fid)' files. More...
#include <OpenMS/FORMAT/XMassFile.h>
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_ |
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.
XMassFile | ( | ) |
Default constructor.
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virtual |
Destructor.
Import settings from a XMass file.
filename | File from which the experimental settings should be loaded. |
exp | MSExperiment where the experimental settings will be stored. |
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.
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inline |
Loads a spectrum from a XMass file.
filename | Name of the XMass file which should be loaded. |
spectrum | Spectrum in which the data loaded from the file should be stored. |
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().
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inline |
Stores a spectrum in a XMass file (not available)
Exception::FileNotWritable | is thrown |