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

Packages that use MsScan

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.io.mzdb
io.github.msdk.io.mzml
io.github.msdk.io.mzml.data
io.github.msdk.io.mzxml
io.github.msdk.io.netcdf
io.github.msdk.rawdata.filters
io.github.msdk.spectra.centroiding
io.github.msdk.util

Uses of MsScan in io.github.msdk.datamodel

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

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

Methods in io.github.msdk.datamodel that return types with arguments of type MsScan

Modifier and Type	Method and Description
List<MsScan>	SimpleFeature.getMSMSSpectra() getMSMSSpectra.
List<MsScan>	Feature.getMSMSSpectra() getMSMSSpectra.
List<MsScan>	SimpleRawDataFile.getScans() Returns an immutable list of all scans.
List<MsScan>	RawDataFile.getScans() Returns an immutable list of all scans.

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

Modifier and Type	Method and Description
void	SimpleRawDataFile.addScan(MsScan scan)
void	SimpleRawDataFile.removeScan(MsScan scan)

Method parameters in io.github.msdk.datamodel with type arguments of type MsScan

Modifier and Type	Method and Description
void	SimpleFeature.setMSMSSpectra(List<MsScan> msmsSpectra) setMSMSSpectra.

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

Constructor parameters in io.github.msdk.featuredetection.adap3d with type arguments of type MsScan

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

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

Constructor parameters in io.github.msdk.featuredetection.adap3d.algorithms with type arguments of type MsScan

Constructor and Description
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 MsScan in io.github.msdk.featuredetection.chromatogrambuilder

Constructor parameters in io.github.msdk.featuredetection.chromatogrambuilder with type arguments of type MsScan

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

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

Constructor parameters in io.github.msdk.featuredetection.gridmass with type arguments of type MsScan

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 MsScan in io.github.msdk.featuredetection.msmsdetection

Constructor parameters in io.github.msdk.featuredetection.msmsdetection with type arguments of type MsScan

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

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

Methods in io.github.msdk.io.mzdb that return types with arguments of type MsScan

Modifier and Type	Method and Description
List<MsScan>	MzDBRawDataFile.getScans()

Constructor parameters in io.github.msdk.io.mzdb with type arguments of type MsScan

Constructor and Description
MzDBRawDataFile(File sourceFile, List<String> msFunctions, List<MsScan> msScans, List<Chromatogram> chromatograms)

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

Methods in io.github.msdk.io.mzml that return types with arguments of type MsScan

Modifier and Type	Method and Description
Predicate<MsScan>	MzMLFileImportMethod.getMsScanPredicate() Getter for the field msScanPredicate.

Constructor parameters in io.github.msdk.io.mzml with type arguments of type MsScan

Constructor and Description
MzMLFileImportMethod(File mzMLFile, Predicate<MsScan> msScanPredicate, Predicate<Chromatogram> chromatogramPredicate) Constructor for MzMLFileImportMethod.
MzMLFileImportMethod(InputStream inputStream, Predicate<MsScan> msScanPredicate, Predicate<Chromatogram> chromatogramPredicate) Constructor for MzMLFileImportMethod.
MzMLFileImportMethod(Path mzMLFilePath, Predicate<MsScan> msScanPredicate, Predicate<Chromatogram> chromatogramPredicate) Constructor for MzMLFileImportMethod.
MzMLFileImportMethod(String mzMLFilePath, Predicate<MsScan> msScanPredicate, Predicate<Chromatogram> chromatogramPredicate) Constructor for MzMLFileImportMethod.

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

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

Modifier and Type	Class and Description
class	MzMLMsScan MzMLMsScan class.

Methods in io.github.msdk.io.mzml.data that return types with arguments of type MsScan

Modifier and Type	Method and Description
List<MsScan>	MzMLRawDataFile.getScans() Returns an immutable list of all scans.

Constructor parameters in io.github.msdk.io.mzml.data with type arguments of type MsScan

Constructor and Description
MzMLRawDataFile(File sourceFile, List<String> msFunctions, List<MsScan> msScans, List<Chromatogram> chromatograms) Constructor for MzMLRawDataFile.

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

Methods in io.github.msdk.io.mzxml that return types with arguments of type MsScan

Modifier and Type	Method and Description
List<MsScan>	MzXMLRawDataFile.getScans() Returns an immutable list of all scans.

Methods in io.github.msdk.io.mzxml with parameters of type MsScan

Modifier and Type	Method and Description
void	MzXMLRawDataFile.addScan(MsScan scan)
void	MzXMLRawDataFile.removeScan(MsScan scan)

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

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

Modifier and Type	Class and Description
class	NetCDFMsScan NetCDFMsScan class.

Constructor parameters in io.github.msdk.io.netcdf with type arguments of type MsScan

Constructor and Description
NetCDFFileImportMethod(File sourceFile, Predicate<MsScan> msScanPredicate) Constructor for NetCDFFileImportMethod.

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

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

Modifier and Type	Method and Description
MsScan	SGFilterAlgorithm.performFilter(MsScan scan) performFilter.
MsScan	ResampleFilterAlgorithm.performFilter(MsScan scan) performFilter.
MsScan	MeanFilterAlgorithm.performFilter(MsScan scan) performFilter.
MsScan	MSDKFilteringAlgorithm.performFilter(MsScan input) performFilter.
MsScan	CropFilterAlgorithm.performFilter(MsScan scan) performFilter.

Methods in io.github.msdk.rawdata.filters with parameters of type MsScan

Modifier and Type	Method and Description
MsScan	SGFilterAlgorithm.performFilter(MsScan scan) performFilter.
MsScan	ResampleFilterAlgorithm.performFilter(MsScan scan) performFilter.
MsScan	MeanFilterAlgorithm.performFilter(MsScan scan) performFilter.
MsScan	MSDKFilteringAlgorithm.performFilter(MsScan input) performFilter.
MsScan	CropFilterAlgorithm.performFilter(MsScan scan) performFilter.

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

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

Modifier and Type	Method and Description
MsScan	WaveletCentroidingAlgorithm.centroidScan(MsScan inputScan) centroidScan.
MsScan	RecursiveCentroidingAlgorithm.centroidScan(MsScan inputScan) centroidScan.
MsScan	MSDKCentroidingAlgorithm.centroidScan(MsScan input) centroidScan.
MsScan	LocalMaximaCentroidingAlgorithm.centroidScan(MsScan inputScan) centroidScan.
MsScan	ExactMassCentroidingAlgorithm.centroidScan(MsScan inputScan) centroidScan.
MsScan	BinningCentroidingAlgorithm.centroidScan(MsScan inputScan) centroidScan.

Methods in io.github.msdk.spectra.centroiding with parameters of type MsScan

Modifier and Type	Method and Description
MsScan	WaveletCentroidingAlgorithm.centroidScan(MsScan inputScan) centroidScan.
MsScan	RecursiveCentroidingAlgorithm.centroidScan(MsScan inputScan) centroidScan.
MsScan	MSDKCentroidingAlgorithm.centroidScan(MsScan input) centroidScan.
MsScan	LocalMaximaCentroidingAlgorithm.centroidScan(MsScan inputScan) centroidScan.
MsScan	ExactMassCentroidingAlgorithm.centroidScan(MsScan inputScan) centroidScan.
MsScan	BinningCentroidingAlgorithm.centroidScan(MsScan inputScan) centroidScan.

Uses of MsScan in io.github.msdk.util

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

Modifier and Type	Method and Description
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.

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

Modifier and Type	Method and Description
static SimpleMsScan	MsScanUtil.clone(MsScan scan, Boolean copyDataPoints) clone.
String	MsScanUtil.msScanToString(MsScan scan)