Uses of Class io.github.msdk.MSDKException (MSDK - Mass Spectrometry Development Kit 0.0.20 API)

Packages that use MSDKException
Package	Description
io.github.msdk
io.github.msdk.alignment.joinaligner
io.github.msdk.alignment.ransac
io.github.msdk.featuredetection.chromatogrambuilder
io.github.msdk.featuredetection.gridmass
io.github.msdk.featuredetection.msmsdetection
io.github.msdk.featuredetection.openms
io.github.msdk.featuredetection.srm
io.github.msdk.featuredetection.targeted
io.github.msdk.id.localdatabase
io.github.msdk.id.sirius
io.github.msdk.io
io.github.msdk.io.chromatof
io.github.msdk.io.mgf
io.github.msdk.io.msp
io.github.msdk.io.mzdata
io.github.msdk.io.mzdb
io.github.msdk.io.mzml
io.github.msdk.io.mzml.data
io.github.msdk.io.mztab
io.github.msdk.io.mzxml
io.github.msdk.io.nativeformats
io.github.msdk.io.netcdf
io.github.msdk.isotopes.isotopegrouper
io.github.msdk.normalization.compound
io.github.msdk.rawdata.filters
io.github.msdk.spectra.centroiding
io.github.msdk.spectra.peakinvestigator

Uses of MSDKException in io.github.msdk

Methods in io.github.msdk that throw MSDKException
Modifier and Type Method and Description

ResultType MSDKMethod.execute()
Performs the algorithm.
Uses of MSDKException in io.github.msdk.alignment.joinaligner

Methods in io.github.msdk.alignment.joinaligner that throw MSDKException
Modifier and Type Method and Description

FeatureTable JoinAlignerMethod.execute()
Performs the algorithm.
Uses of MSDKException in io.github.msdk.alignment.ransac

Methods in io.github.msdk.alignment.ransac that throw MSDKException
Modifier and Type Method and Description

FeatureTable RansacAlignerMethod.execute()
Performs the algorithm.

Methods in io.github.msdk that throw MSDKException
Modifier and Type	Method and Description
`ResultType`	MSDKMethod.`execute()` Performs the algorithm.

Methods in io.github.msdk.alignment.joinaligner that throw MSDKException
Modifier and Type	Method and Description
`FeatureTable`	JoinAlignerMethod.`execute()` Performs the algorithm.

Methods in io.github.msdk.alignment.ransac that throw MSDKException
Modifier and Type	Method and Description
`FeatureTable`	RansacAlignerMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.featuredetection.chromatogrambuilder

Methods in io.github.msdk.featuredetection.chromatogrambuilder that throw MSDKException
Modifier and Type	Method and Description
`List<Chromatogram>`	ChromatogramBuilderMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.featuredetection.gridmass

Methods in io.github.msdk.featuredetection.gridmass that throw MSDKException
Modifier and Type Method and Description

FeatureTable GridMassMethod.execute()
Performs the algorithm.

Methods in io.github.msdk.featuredetection.gridmass that throw MSDKException
Modifier and Type	Method and Description
`FeatureTable`	GridMassMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.featuredetection.msmsdetection

Methods in io.github.msdk.featuredetection.msmsdetection that throw MSDKException
Modifier and Type	Method and Description
`List<IonAnnotation>`	MsMsDetectionMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.featuredetection.openms

Methods in io.github.msdk.featuredetection.openms that throw MSDKException
Modifier and Type	Method and Description
`List<Double>`	FeatureFinderMetaboDetector.`execute()` Runs FeatureFinderMetabo on the output file, processes the output file for mz values data.
`static String`	FeatureFinderMetaboLocator.`findFeatureFinderMetabo()` Check for FeatureFinderMetabo in PATH & default Installation directory on various platforms.

Constructors in io.github.msdk.featuredetection.openms that throw MSDKException
Constructor and Description
`FeatureFinderMetaboDetector(File mzMLFile)` Constructor for FeatureFinderMetaboDetector.
`FeatureFinderMetaboDetector(String mzMLFilePath)` Constructor for FeatureFinderMetaboDetector.

Uses of MSDKException in io.github.msdk.featuredetection.srm

Methods in io.github.msdk.featuredetection.srm that throw MSDKException
Modifier and Type Method and Description

List<Chromatogram> SrmDetectionMethod.execute()
Performs the algorithm.

Methods in io.github.msdk.featuredetection.srm that throw MSDKException
Modifier and Type	Method and Description
`List<Chromatogram>`	SrmDetectionMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.featuredetection.targeted

Methods in io.github.msdk.featuredetection.targeted that throw MSDKException
Modifier and Type	Method and Description
`List<Chromatogram>`	TargetedDetectionMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.id.localdatabase

Methods in io.github.msdk.id.localdatabase that throw MSDKException
Modifier and Type Method and Description

Void LocalDatabaseSearchMethod.execute()
Performs the algorithm.

Methods in io.github.msdk.id.localdatabase that throw MSDKException
Modifier and Type	Method and Description
`Void`	LocalDatabaseSearchMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.id.sirius

Methods in io.github.msdk.id.sirius that throw MSDKException
Modifier and Type	Method and Description
`List<IonAnnotation>`	SiriusIdentificationMethod.`execute()`
`List<IonAnnotation>`	FingerIdWebMethod.`execute()`
`static String`	NativeLibraryLoader.`getOsName()` Method returns formatted OS name
`static void`	NativeLibraryLoader.`loadLibraryFromJar(String folder, String[] libs)` Public method for external usage, copies all files from `folder`
`protected List<de.unijena.bioinf.sirius.IdentificationResult>`	SiriusIdentificationMethod.`siriusProcessSpectra()` Method for processing spectra by Sirius module

Constructors in io.github.msdk.id.sirius that throw MSDKException
Constructor and Description
`FingerIdWebMethod(de.unijena.bioinf.ChemistryBase.ms.Ms2Experiment experiment, SiriusIonAnnotation ionAnnotation)` Simplified FingerIdWebMethod constructor
`FingerIdWebMethod(de.unijena.bioinf.ChemistryBase.ms.Ms2Experiment experiment, SiriusIonAnnotation ionAnnotation, Integer candidatesAmount)` Constructor for a FingerIdWebMethod

Uses of MSDKException in io.github.msdk.io

Methods in io.github.msdk.io that throw MSDKException
Modifier and Type	Method and Description
`RawDataFile`	RawDataFileImportMethod.`execute()` Performs the algorithm.
`FeatureTable`	FeatureTableImportMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.io.chromatof

Methods in io.github.msdk.io.chromatof that throw MSDKException
Modifier and Type Method and Description

FeatureTable ChromaTofFileImportMethod.execute()
Performs the algorithm.

Methods in io.github.msdk.io.chromatof that throw MSDKException
Modifier and Type	Method and Description
`FeatureTable`	ChromaTofFileImportMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.io.mgf

Methods in io.github.msdk.io.mgf that throw MSDKException
Modifier and Type	Method and Description
`List<MgfMsSpectrum>`	MgfFileImportMethod.`execute()` Overloaded method, processes the .mgf file (loaded in the costructor) and returns a list of MgfMsSpectrums
`Void`	MgfFileExportMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.io.msp

Methods in io.github.msdk.io.msp that throw MSDKException
Modifier and Type	Method and Description
`static void`	MspExportAlgorithm.`exportSpectra(File exportFile, Collection<MsSpectrum> spectra)` exportSpectra.
`static void`	MspExportAlgorithm.`exportSpectrum(File exportFile, MsSpectrum spectrum)` exportSpectrum.
`static MspSpectrum`	MspImportAlgorithm.`parseMspFromFile(File mspFile)` parseMspFromFile.
`static MspSpectrum`	MspImportAlgorithm.`parseMspFromString(String mspText)` parseMspFromString.

Uses of MSDKException in io.github.msdk.io.mzdata

Methods in io.github.msdk.io.mzdata that throw MSDKException
Modifier and Type Method and Description

RawDataFile MzDataFileImportMethod.execute()
Performs the algorithm.
Uses of MSDKException in io.github.msdk.io.mzdb

Methods in io.github.msdk.io.mzdb that throw MSDKException
Modifier and Type Method and Description

MzDBRawDataFile MzDBFileImportMethod.execute()
Performs the algorithm.

Methods in io.github.msdk.io.mzdata that throw MSDKException
Modifier and Type	Method and Description
`RawDataFile`	MzDataFileImportMethod.`execute()` Performs the algorithm.

Methods in io.github.msdk.io.mzdb that throw MSDKException
Modifier and Type	Method and Description
`MzDBRawDataFile`	MzDBFileImportMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.io.mzml

Methods in io.github.msdk.io.mzml that throw MSDKException
Modifier and Type	Method and Description
`MzMLRawDataFile`	MzMLFileImportMethod.`execute()` Performs the algorithm.
`Void`	MzMLFileExportMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.io.mzml.data

Methods in io.github.msdk.io.mzml.data that throw MSDKException
Modifier and Type	Method and Description
`static double[]`	MzMLPeaksDecoder.`decodeToDouble(InputStream inputStream, MzMLBinaryDataInfo binaryDataInfo, double[] data)` Converts a base64 encoded mz or intensity string used in mzML files to an array of doubles.
`static float[]`	MzMLPeaksDecoder.`decodeToFloat(InputStream inputStream, MzMLBinaryDataInfo binaryDataInfo, float[] data)` Converts a base64 encoded mz or intensity string used in mzML files to an array of floats.
`static byte[]`	MzMLPeaksEncoder.`encodeDouble(double[] data, MzMLCompressionType compression)` encodeDouble.
`static byte[]`	MzMLPeaksEncoder.`encodeFloat(float[] data, MzMLCompressionType compression)` encodeFloat.

Uses of MSDKException in io.github.msdk.io.mztab

Methods in io.github.msdk.io.mztab that throw MSDKException
Modifier and Type	Method and Description
`FeatureTable`	MzTabFileImportMethod.`execute()` Performs the algorithm.
`File`	MzTabFileExportMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.io.mzxml

Methods in io.github.msdk.io.mzxml that throw MSDKException
Modifier and Type	Method and Description
`RawDataFile`	MzXMLFileParser.`execute()` execute.
`RawDataFile`	MzXMLFileImportMethod.`execute()` Performs the algorithm.
`it.unimi.dsi.io.ByteBufferInputStream`	MzXMLFileMemoryMapper.`mapToMemory(File mzMLFile)` mapToMemory.

Uses of MSDKException in io.github.msdk.io.nativeformats

Methods in io.github.msdk.io.nativeformats that throw MSDKException
Modifier and Type	Method and Description
`RawDataFile`	WatersRawImportMethod.`execute()` Performs the algorithm.
`RawDataFile`	ThermoRawImportMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.io.netcdf

Methods in io.github.msdk.io.netcdf that throw MSDKException
Modifier and Type	Method and Description
`RawDataFile`	NetCDFFileImportMethod.`execute()` Performs the algorithm.
`Void`	NetCDFFileExportMethod.`execute()` Execute the process of writing the data from the the input `RawDataFile` to the target `File`

Uses of MSDKException in io.github.msdk.isotopes.isotopegrouper

Methods in io.github.msdk.isotopes.isotopegrouper that throw MSDKException
Modifier and Type Method and Description

FeatureTable IsotopeGrouperMethod.execute()
Performs the algorithm.

Methods in io.github.msdk.isotopes.isotopegrouper that throw MSDKException
Modifier and Type	Method and Description
`FeatureTable`	IsotopeGrouperMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.normalization.compound

Methods in io.github.msdk.normalization.compound that throw MSDKException
Modifier and Type	Method and Description
`FeatureTable`	FeatureNormalizationByCompoundMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.rawdata.filters

Methods in io.github.msdk.rawdata.filters that throw MSDKException
Modifier and Type Method and Description

RawDataFile MSDKFilteringMethod.execute()
Performs the algorithm.
Uses of MSDKException in io.github.msdk.spectra.centroiding

Methods in io.github.msdk.spectra.centroiding that throw MSDKException
Modifier and Type Method and Description

RawDataFile MSDKCentroidingMethod.execute()
Performs the algorithm.

Methods in io.github.msdk.rawdata.filters that throw MSDKException
Modifier and Type	Method and Description
`RawDataFile`	MSDKFilteringMethod.`execute()` Performs the algorithm.

Methods in io.github.msdk.spectra.centroiding that throw MSDKException
Modifier and Type	Method and Description
`RawDataFile`	MSDKCentroidingMethod.`execute()` Performs the algorithm.

Uses of MSDKException in io.github.msdk.spectra.peakinvestigator

Methods in io.github.msdk.spectra.peakinvestigator that throw MSDKException
Modifier and Type	Method and Description
`List<MsSpectrum>`	PeakInvestigatorScanExtractingMethod.`execute()` Performs the algorithm.
`File`	PeakInvestigatorScanBundlingMethod.`execute()` Performs the algorithm.

Uses of Classio.github.msdk.MSDKException

Uses of MSDKException in io.github.msdk

Uses of MSDKException in io.github.msdk.alignment.joinaligner

Uses of MSDKException in io.github.msdk.alignment.ransac

Uses of MSDKException in io.github.msdk.featuredetection.chromatogrambuilder

Uses of MSDKException in io.github.msdk.featuredetection.gridmass

Uses of MSDKException in io.github.msdk.featuredetection.msmsdetection

Uses of MSDKException in io.github.msdk.featuredetection.openms

Uses of MSDKException in io.github.msdk.featuredetection.srm

Uses of MSDKException in io.github.msdk.featuredetection.targeted

Uses of MSDKException in io.github.msdk.id.localdatabase

Uses of MSDKException in io.github.msdk.id.sirius

Uses of MSDKException in io.github.msdk.io

Uses of MSDKException in io.github.msdk.io.chromatof

Uses of MSDKException in io.github.msdk.io.mgf

Uses of MSDKException in io.github.msdk.io.msp

Uses of MSDKException in io.github.msdk.io.mzdata

Uses of MSDKException in io.github.msdk.io.mzdb

Uses of MSDKException in io.github.msdk.io.mzml

Uses of MSDKException in io.github.msdk.io.mzml.data

Uses of MSDKException in io.github.msdk.io.mztab

Uses of MSDKException in io.github.msdk.io.mzxml

Uses of MSDKException in io.github.msdk.io.nativeformats

Uses of MSDKException in io.github.msdk.io.netcdf

Uses of MSDKException in io.github.msdk.isotopes.isotopegrouper

Uses of MSDKException in io.github.msdk.normalization.compound

Uses of MSDKException in io.github.msdk.rawdata.filters

Uses of MSDKException in io.github.msdk.spectra.centroiding

Uses of MSDKException in io.github.msdk.spectra.peakinvestigator

Uses of Class
io.github.msdk.MSDKException