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

Packages that use RawDataFile

Package	Description
io.github.msdk.datamodel
io.github.msdk.featuredetection.adap3d
io.github.msdk.featuredetection.adap3d.algorithms
io.github.msdk.featuredetection.chromatogrambuilder
io.github.msdk.featuredetection.gridmass
io.github.msdk.featuredetection.msmsdetection
io.github.msdk.featuredetection.srm
io.github.msdk.featuredetection.targeted
io.github.msdk.io
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.mzxml
io.github.msdk.io.nativeformats
io.github.msdk.io.netcdf
io.github.msdk.rawdata.filters
io.github.msdk.spectra.centroiding
io.github.msdk.spectra.peakinvestigator
io.github.msdk.util

Uses of RawDataFile in io.github.msdk.datamodel

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

Modifier and Type	Class and Description
class	SimpleRawDataFile Implementation of the RawDataFile interface.

Methods in io.github.msdk.datamodel that return RawDataFile

Modifier and Type	Method and Description
RawDataFile	SimpleSample.getRawDataFile() Returns a raw data file or null if this sample has no associated raw data.
RawDataFile	SimpleMsScan.getRawDataFile() Returns the raw data file that contains this scan.
RawDataFile	SimpleChromatogram.getRawDataFile() Returns the raw data file that contains this chromatogram.
RawDataFile	Sample.getRawDataFile() Returns a raw data file or null if this sample has no associated raw data.
RawDataFile	MsScan.getRawDataFile() Returns the raw data file that contains this scan.
RawDataFile	Chromatogram.getRawDataFile() Returns the raw data file that contains this chromatogram.

Methods in io.github.msdk.datamodel with parameters of type RawDataFile

Modifier and Type	Method and Description
void	SimpleSample.setRawDataFile(RawDataFile rawDataFile)
void	SimpleMsScan.setRawDataFile(RawDataFile newRawDataFile)
void	SimpleChromatogram.setRawDataFile(RawDataFile newRawDataFile)

Constructors in io.github.msdk.datamodel with parameters of type RawDataFile

Constructor and Description
SimpleSample(String name, RawDataFile rawDataFile) Constructor for SimpleSample.

Uses of RawDataFile in io.github.msdk.featuredetection.adap3d

Constructors in io.github.msdk.featuredetection.adap3d with parameters of type RawDataFile

Constructor and Description
ADAP3DFeatureDetectionMethod(RawDataFile rawFile) Constructor
ADAP3DFeatureDetectionMethod(RawDataFile rawFile, ADAP3DFeatureDetectionParameters params) Constructor
ADAP3DFeatureDetectionMethod(RawDataFile rawFile, Predicate<MsScan> msScanPredicate) Constructor
ADAP3DFeatureDetectionMethod(RawDataFile rawFile, Predicate<MsScan> msScanPredicate, ADAP3DFeatureDetectionParameters parameters) Constructor

Uses of RawDataFile in io.github.msdk.featuredetection.adap3d.algorithms

Constructors in io.github.msdk.featuredetection.adap3d.algorithms with parameters of type RawDataFile

Constructor and Description
SliceSparseMatrix(RawDataFile rawFile) This constructor takes raw data file and create the triplet map which contains information such as mz,intensity,rt,scan number
SliceSparseMatrix(RawDataFile rawFile, Predicate<MsScan> msScanPredicate) This constructor takes raw data file and create the triplet map which contains information such as mz,intensity,rt,scan number

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

Constructors in io.github.msdk.featuredetection.chromatogrambuilder with parameters of type RawDataFile

Constructor and Description
ChromatogramBuilderMethod(RawDataFile inputFile, double noiseLevel, double minimumTimeSpan, double minimumHeight, MzTolerance mzTolerance) Constructor for ChromatogramBuilderMethod.
ChromatogramBuilderMethod(RawDataFile inputFile, List<MsScan> inputScans, Double noiseLevel, Double minimumTimeSpan, Double minimumHeight, MzTolerance mzTolerance) Constructor for ChromatogramBuilderMethod.

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

Constructors in io.github.msdk.featuredetection.gridmass with parameters of type RawDataFile

Constructor and Description
GridMassMethod(RawDataFile rawDataFile, List<MsScan> scans, MzTolerance mzTol, Double intensitySimilarity, Double minimumTimeSpan, Double maximumTimeSpan, Double smoothTimeSpan, Double smoothTimeMZ, Double smoothMZ, Double additionTimeMaxPeaksPerScan, Double minimumHeight, Double rtPerScan) Constructor for GridMassMethod.

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

Constructors in io.github.msdk.featuredetection.msmsdetection with parameters of type RawDataFile

Constructor and Description
MsMsDetectionMethod(RawDataFile rawDataFile, List<MsScan> msScans, MzTolerance mzTolerance, RTTolerance rtTolerance, Double intensityTolerance) Constructor for MsMsDetectionMethod.

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

Constructors in io.github.msdk.featuredetection.srm with parameters of type RawDataFile

Constructor and Description
SrmDetectionMethod(RawDataFile rawDataFile) Constructor for SrmDetectionMethod.

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

Constructors in io.github.msdk.featuredetection.targeted with parameters of type RawDataFile

Constructor and Description
TargetedDetectionMethod(List<IonAnnotation> ionAnnotations, RawDataFile rawDataFile, MzTolerance mzTolerance, RTTolerance rtTolerance, Double intensityTolerance, Double noiseLevel) Constructor for TargetedDetectionMethod.

Uses of RawDataFile in io.github.msdk.io

Methods in io.github.msdk.io that return RawDataFile

Modifier and Type	Method and Description
RawDataFile	RawDataFileImportMethod.execute() Performs the algorithm.
RawDataFile	RawDataFileImportMethod.getResult() Returns the result of this algorithm, or null.

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

Methods in io.github.msdk.io.mzdata that return RawDataFile

Modifier and Type	Method and Description
RawDataFile	MzDataFileImportMethod.execute() Performs the algorithm.
RawDataFile	MzDataFileImportMethod.getResult() Returns the result of this algorithm, or null.

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

Classes in io.github.msdk.io.mzdb that implement RawDataFile

Modifier and Type	Class and Description
class	MzDBRawDataFile

Methods in io.github.msdk.io.mzdb that return RawDataFile

Modifier and Type	Method and Description
RawDataFile	MzDBFileImportMethod.getResult() Returns the result of this algorithm, or null.

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

Methods in io.github.msdk.io.mzml that return RawDataFile

Modifier and Type	Method and Description
RawDataFile	MzMLFileImportMethod.getResult() Returns the result of this algorithm, or null.

Constructors in io.github.msdk.io.mzml with parameters of type RawDataFile

Constructor and Description
MzMLFileExportMethod(RawDataFile rawDataFile, File target, MzMLCompressionType doubleArrayCompression, MzMLCompressionType floatArrayCompression) Constructor for MzMLFileExportMethod.

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

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

Modifier and Type	Class and Description
class	MzMLRawDataFile MzMLRawDataFile class.

Methods in io.github.msdk.io.mzml.data that return RawDataFile

Modifier and Type	Method and Description
RawDataFile	MzMLMsScan.getRawDataFile() Returns the raw data file that contains this scan.

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

Classes in io.github.msdk.io.mzxml that implement RawDataFile

Modifier and Type	Class and Description
class	MzXMLRawDataFile MzXMLRawDataFile class.

Methods in io.github.msdk.io.mzxml that return RawDataFile

Modifier and Type	Method and Description
RawDataFile	MzXMLFileParser.execute() execute.
RawDataFile	MzXMLFileImportMethod.execute() Performs the algorithm.
RawDataFile	MzXMLFileParser.getResult() Returns the result of this algorithm, or null.
RawDataFile	MzXMLFileImportMethod.getResult() Returns the result of this algorithm, or null.

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

Methods in io.github.msdk.io.nativeformats that return RawDataFile

Modifier and Type	Method and Description
RawDataFile	WatersRawImportMethod.execute() Performs the algorithm.
RawDataFile	ThermoRawImportMethod.execute() Performs the algorithm.
RawDataFile	WatersRawImportMethod.getResult() Returns the result of this algorithm, or null.
RawDataFile	ThermoRawImportMethod.getResult() Returns the result of this algorithm, or null.

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

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

Modifier and Type	Class and Description
class	NetCDFRawDataFile NetCDFRawDataFile class.

Methods in io.github.msdk.io.netcdf that return RawDataFile

Modifier and Type	Method and Description
RawDataFile	NetCDFFileImportMethod.execute() Performs the algorithm.
RawDataFile	NetCDFFileImportMethod.getResult() Returns the result of this algorithm, or null.

Constructors in io.github.msdk.io.netcdf with parameters of type RawDataFile

Constructor and Description
NetCDFFileExportMethod(RawDataFile rawDataFile, File target) Constructor for NetCDFFileExportMethod.
NetCDFFileExportMethod(RawDataFile rawDataFile, File target, double massValueScaleFactor, double intensityValueScaleFactor) Constructor for NetCDFFileExportMethod.

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

Methods in io.github.msdk.rawdata.filters that return RawDataFile

Modifier and Type	Method and Description
RawDataFile	MSDKFilteringMethod.execute() Performs the algorithm.
RawDataFile	MSDKFilteringMethod.getResult() Returns the result of this algorithm, or null.

Constructors in io.github.msdk.rawdata.filters with parameters of type RawDataFile

Constructor and Description
MSDKFilteringMethod(RawDataFile rawDataFile, MSDKFilteringAlgorithm filteringAlgorithm) Constructor for MSDKFilteringMethod.

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

Methods in io.github.msdk.spectra.centroiding that return RawDataFile

Modifier and Type	Method and Description
RawDataFile	MSDKCentroidingMethod.execute() Performs the algorithm.
RawDataFile	MSDKCentroidingMethod.getResult() Returns the result of this algorithm, or null.

Constructors in io.github.msdk.spectra.centroiding with parameters of type RawDataFile

Constructor and Description
MSDKCentroidingMethod(RawDataFile rawDataFile, MSDKCentroidingAlgorithm centroidingAlgorithm) Constructor for MSDKCentroidingMethod.

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

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

Constructor and Description
PeakInvestigatorScanBundlingMethod(RawDataFile rawDataFile) Constructor for PeakInvestigatorScanBundlingMethod.
PeakInvestigatorScanBundlingMethod(RawDataFile rawDataFile, File file) Constructor for PeakInvestigatorScanBundlingMethod.

Uses of RawDataFile in io.github.msdk.util

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

Modifier and Type	Method and Description
static Integer	RawDataFileUtil.getNextChromatogramNumber(RawDataFile rawDataFile) getNextChromatogramNumber.
static List<MsScan>	RawDataFileUtil.getScans(RawDataFile rawDataFile, com.google.common.collect.Range<Float> rtRange) getScans.
static List<MsScan>	RawDataFileUtil.getScans(RawDataFile rawDataFile, String msFunction) getScans.
static List<MsScan>	RawDataFileUtil.getScans(RawDataFile rawDataFile, String msFunction, com.google.common.collect.Range<Float> rtRange) getScans.