Uses of Interface
io.github.msdk.datamodel.MsSpectrum

Packages that use MsSpectrum

Package	Description
io.github.msdk.datamodel
io.github.msdk.id.sirius
io.github.msdk.io.mgf
io.github.msdk.io.msp
io.github.msdk.io.mzml.data
io.github.msdk.io.netcdf
io.github.msdk.io.txt
io.github.msdk.isotopes.isotopepattern
io.github.msdk.spectra.centroidprofiledetection
io.github.msdk.spectra.peakinvestigator
io.github.msdk.spectra.splash
io.github.msdk.util

Uses of MsSpectrum in io.github.msdk.datamodel

Subinterfaces of MsSpectrum in io.github.msdk.datamodel

Modifier and Type	Interface and Description
interface	MsScan Represents a single MS scan in a raw data file.

Classes in io.github.msdk.datamodel that implement MsSpectrum

Modifier and Type	Class and Description
class	AbstractMsSpectrum Simple implementation of the MsSpectrum interface
class	SimpleMsScan Simple implementation of the Scan interface.
class	SimpleMsSpectrum Simple implementation of the MsSpectrum interface.

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

Methods in io.github.msdk.id.sirius that return types with arguments of type MsSpectrum

Modifier and Type	Method and Description
List<MsSpectrum>	SiriusIdentificationMethod.getMs2Spectra()
List<MsSpectrum>	SiriusIdentificationMethod.getMsSpectra()

Constructor parameters in io.github.msdk.id.sirius with type arguments of type MsSpectrum

Constructor and Description
SiriusIdentificationMethod(List<MsSpectrum> ms1, List<MsSpectrum> ms2, Double parentMass, IonType ion, Integer numberOfCandidates, de.unijena.bioinf.ChemistryBase.chem.FormulaConstraints constraints, Double deviation) Constructor for SiriusIdentificationMethod class.
SiriusIdentificationMethod(List<MsSpectrum> ms1, List<MsSpectrum> ms2, Double parentMass, IonType ion, Integer numberOfCandidates, de.unijena.bioinf.ChemistryBase.chem.FormulaConstraints constraints, Double deviation) Constructor for SiriusIdentificationMethod class.

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

Classes in io.github.msdk.io.mgf that implement MsSpectrum

Modifier and Type	Class and Description
class	MgfMsSpectrum MgfMsSpectrum class.

Constructors in io.github.msdk.io.mgf with parameters of type MsSpectrum

Constructor and Description
MgfFileExportMethod(MsSpectrum spectrum, File target) Constructor for MgfFileExportMethod.

Constructor parameters in io.github.msdk.io.mgf with type arguments of type MsSpectrum

Constructor and Description
MgfFileExportMethod(Collection<MsSpectrum> spectra, File target) Constructor for MgfFileExportMethod.

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

Classes in io.github.msdk.io.msp that implement MsSpectrum

Modifier and Type	Class and Description
class	MspSpectrum MspSpectrum class.

Methods in io.github.msdk.io.msp with parameters of type MsSpectrum

Modifier and Type	Method and Description
static void	MspExportAlgorithm.exportSpectrum(File exportFile, MsSpectrum spectrum) exportSpectrum.

Method parameters in io.github.msdk.io.msp with type arguments of type MsSpectrum

Modifier and Type	Method and Description
static void	MspExportAlgorithm.exportSpectra(File exportFile, Collection<MsSpectrum> spectra) exportSpectra.

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

Classes in io.github.msdk.io.mzml.data that implement MsSpectrum

Modifier and Type	Class and Description
class	MzMLMsScan MzMLMsScan class.

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

Classes in io.github.msdk.io.netcdf that implement MsSpectrum

Modifier and Type	Class and Description
class	NetCDFMsScan NetCDFMsScan class.

Uses of MsSpectrum in io.github.msdk.io.txt

Methods in io.github.msdk.io.txt with parameters of type MsSpectrum

Modifier and Type	Method and Description
static void	TxtExportAlgorithm.exportSpectrum(File exportFile, MsSpectrum spectrum) Export a single spectrum to a file.
static String	TxtExportAlgorithm.spectrumToString(MsSpectrum spectrum) Export a spectrum to a string.
static String	TxtExportAlgorithm.spectrumToString(MsSpectrum spectrum, String delimiter) Export a spectrum to a string.
static void	TxtExportAlgorithm.spectrumToWriter(MsSpectrum spectrum, Writer writer) Export a spectrum to a writer.
static void	TxtExportAlgorithm.spectrumToWriter(MsSpectrum spectrum, Writer writer, String delimiter) Export a spectrum to a writer.

Method parameters in io.github.msdk.io.txt with type arguments of type MsSpectrum

Modifier and Type	Method and Description
static void	TxtExportAlgorithm.exportSpectra(File exportFile, Collection<MsSpectrum> spectra) Export one or more spectra to a file.
static void	TxtExportAlgorithm.exportSpectra(File exportFile, Collection<MsSpectrum> spectra, String delimiter) Export one or more spectra to a file.

Uses of MsSpectrum in io.github.msdk.isotopes.isotopepattern

Methods in io.github.msdk.isotopes.isotopepattern that return MsSpectrum

Modifier and Type	Method and Description
static MsSpectrum	IsotopePatternGeneratorAlgorithm.generateIsotopes(org.openscience.cdk.interfaces.IMolecularFormula cdkFormula, Integer charge, Double minAbundance, Float intensityScale, Double mzTolerance) generateIsotopes.
static MsSpectrum	IsotopePatternGeneratorAlgorithm.generateIsotopes(String chemicalFormula, Double minAbundance, Float intensityScale, Double mzTolerance) generateIsotopes.

Uses of MsSpectrum in io.github.msdk.spectra.centroidprofiledetection

Methods in io.github.msdk.spectra.centroidprofiledetection with parameters of type MsSpectrum

Modifier and Type	Method and Description
static MsSpectrumType	SpectrumTypeDetectionAlgorithm.detectSpectrumType(MsSpectrum msSpectrum) detectSpectrumType.

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

Classes in io.github.msdk.spectra.peakinvestigator that implement MsSpectrum

Modifier and Type	Class and Description
class	PeakInvestigatorMsSpectrum This class is used provide m/z-dependent mass tolerances from PeakInvestigator by decorating an existing instance of MsSpectrum.

Methods in io.github.msdk.spectra.peakinvestigator that return MsSpectrum

Modifier and Type	Method and Description
protected MsSpectrum	PeakInvestigatorScanExtractingMethod.parseMsSpectrum(BufferedReader reader) This function assumes that the data is either formatted as two columns or five columns, separated by whitespace.

Methods in io.github.msdk.spectra.peakinvestigator that return types with arguments of type MsSpectrum

Modifier and Type	Method and Description
List<MsSpectrum>	PeakInvestigatorScanExtractingMethod.execute() Performs the algorithm.
List<MsSpectrum>	PeakInvestigatorScanExtractingMethod.getResult() Returns the result of this algorithm, or null.

Constructors in io.github.msdk.spectra.peakinvestigator with parameters of type MsSpectrum

Constructor and Description
PeakInvestigatorMsSpectrum(MsSpectrum spectrum, TreeMap<Double,PeakInvestigatorMsSpectrum.Error> errors) Constructor for PeakInvestigatorMsSpectrum.

Uses of MsSpectrum in io.github.msdk.spectra.splash

Methods in io.github.msdk.spectra.splash with parameters of type MsSpectrum

Modifier and Type	Method and Description
static String	SplashCalculationAlgorithm.calculateSplash(MsSpectrum spectrum) calculates our spectral hash

Uses of MsSpectrum in io.github.msdk.util

Methods in io.github.msdk.util that return MsSpectrum

Modifier and Type	Method and Description
static MsSpectrum	MsSpectrumUtil.filterMsSpectrum(MsSpectrum ms, Integer pairsLimit) Filters with only N most intense elements.

Methods in io.github.msdk.util that return types with arguments of type MsSpectrum

Modifier and Type	Method and Description
static List<MsSpectrum>	MsSpectrumUtil.filterMsSpectra(List<MsSpectrum> spectra, int listLimit) Method preprocesses list of spectra, limits its amount Filtering of Spectrum objects is done by retrieving top N Spectrum objects with largest intensity values

Methods in io.github.msdk.util with parameters of type MsSpectrum

Modifier and Type	Method and Description
static MsSpectrum	MsSpectrumUtil.filterMsSpectrum(MsSpectrum ms, Integer pairsLimit) Filters with only N most intense elements.
static String	MsSpectrumUtil.msSpectrumToString(MsSpectrum spectrum) msSpectrumToString.

Method parameters in io.github.msdk.util with type arguments of type MsSpectrum

Modifier and Type	Method and Description
static List<MsSpectrum>	MsSpectrumUtil.filterMsSpectra(List<MsSpectrum> spectra, int listLimit) Method preprocesses list of spectra, limits its amount Filtering of Spectrum objects is done by retrieving top N Spectrum objects with largest intensity values