- generateConstraint(MolecularFormulaRange) - Static method in class io.github.msdk.id.sirius.ConstraintsGenerator
-
Method for generating FormulaConstraints from user-defined search space
- generateIsotopes(String, Double, Float, Double) - Static method in class io.github.msdk.isotopes.isotopepattern.IsotopePatternGeneratorAlgorithm
-
generateIsotopes.
- generateIsotopes(IMolecularFormula, Integer, Double, Float, Double) - Static method in class io.github.msdk.isotopes.isotopepattern.IsotopePatternGeneratorAlgorithm
-
generateIsotopes.
- generateNewId() - Static method in class fr.profi.mzdb.util.misc.AbstractInMemoryIdGen
-
- getAccession() - Method in enum fr.profi.mzdb.db.model.params.param.CVEntry
-
Gets the accession.
- getAccession() - Method in class fr.profi.mzdb.db.model.params.param.CVParam
-
- getAccession() - Method in class fr.profi.mzdb.db.model.params.param.UserParam
-
- getAccession() - Method in class fr.profi.mzdb.db.model.params.param.UserText
-
- getAccession() - Method in enum io.github.msdk.io.mzml.data.MzMLArrayType
-
Getter for the field accession.
- getAccession() - Method in enum io.github.msdk.io.mzml.data.MzMLCompressionType
-
Getter for the field accession.
- getAccession() - Method in class io.github.msdk.io.mzml.data.MzMLCVParam
-
Getter for the field accession.
- getAccessionURL() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
getAccessionURL.
- getAccessionURL() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
getAccessionURL.
- getAcquisitionMode(SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
Lazy loading of the acquisition mode, parameter
- getAcquisitionMode(String) - Static method in enum fr.profi.mzdb.model.AcquisitionMode
-
- getAcquisitionMode() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Lazy loading of the acquisition mode, parameter
- getAcquisitionMode() - Method in class fr.profi.mzdb.MzDbReader
-
Lazy loading of the acquisition mode, parameter
- getAcquisitionType() - Method in class fr.profi.mzdb.db.model.params.thermo.ThermoScanMetaData
-
- getActivation() - Method in class fr.profi.mzdb.db.model.params.Precursor
-
- getActivation() - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorElement
-
Getter for the field activation.
- getActivationEnergy() - Method in interface io.github.msdk.datamodel.ActivationInfo
-
Returns the activation energy applied for this MS/MS scan.
- getActivationEnergy() - Method in class io.github.msdk.datamodel.SimpleActivationInfo
-
Returns the activation energy applied for this MS/MS scan.
- getActivationInfo() - Method in interface io.github.msdk.datamodel.IsolationInfo
-
Returns the details about the fragmentation that followed this isolation.
- getActivationInfo() - Method in class io.github.msdk.datamodel.SimpleIsolationInfo
-
Returns the details about the fragmentation that followed this isolation.
- getActivationType() - Method in class fr.profi.mzdb.db.model.params.thermo.ThermoFragmentationTarget
-
- getActivationType() - Method in interface io.github.msdk.datamodel.ActivationInfo
-
Returns the type of the fragmentation (MS/MS) experiment.
- getActivationType() - Method in class io.github.msdk.datamodel.SimpleActivationInfo
-
Returns the type of the fragmentation (MS/MS) experiment.
- getAdductFormula() - Method in interface io.github.msdk.datamodel.IonType
-
getAdductFormula.
- getAdductFormula() - Method in class io.github.msdk.datamodel.SimpleIonType
-
getAdductFormula.
- getAllSpectrumIds() - Method in class fr.profi.mzdb.io.reader.bb.AbstractBlobReader
-
- getAllSpectrumIds() - Method in interface fr.profi.mzdb.io.reader.bb.IBlobReader
-
- getAnalyzerType() - Method in class fr.profi.mzdb.db.model.params.thermo.ThermoScanMetaData
-
- getAnnotationId() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
getAnnotationId.
- getAnnotationId() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
getAnnotationId.
- getArea() - Method in interface io.github.msdk.datamodel.Feature
-
getArea.
- getArea() - Method in class io.github.msdk.datamodel.SimpleFeature
-
getArea.
- getArea(float[], float[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns the area of this feature.
- getArrayLength() - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo
-
Getter for the field arrayLength.
- getArrayType() - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo
-
Getter for the field arrayType.
- getArrayType(String) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo
-
Gets the binary data array type for the given accession
- getAsymmetryFactor(float[], float[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns the asymmetry factor of this feature.
- getBasePeakIndex(float[], Integer) - Static method in class io.github.msdk.util.MsSpectrumUtil
-
Returns the index of the highest intensity value.
- getBasePeakIndex(double[], float[], Integer, Range<Double>) - Static method in class io.github.msdk.util.MsSpectrumUtil
-
Returns the index of the highest intensity value.
- getBasePeakIntensity() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
Gets the base peak intensity.
- getBasePeakMz() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
Gets the base peak mz.
- getBBFirstSpectrumId() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
- getBBSizes() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getBeginMz() - Method in class fr.profi.mzdb.model.RunSliceHeader
-
Gets the begin mz.
- getBiGaussianSimilarityThreshold() - Method in class io.github.msdk.featuredetection.adap3d.ADAP3DFeatureDetectionParameters
-
Getter for the field biGaussianSimilarityThreshold.
- getBitLength() - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo
-
Getter for the field bitLength.
- getBitLength(String) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo
-
Gets the bit length for the given accession
- getBlobSize() - Method in class fr.profi.mzdb.io.reader.bb.BytesReader
-
- getBlobSize() - Method in class fr.profi.mzdb.io.reader.bb.SQLiteBlobReader
-
- getBoundingBoxData(int, SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the bounding box data.
- getBoundingBoxData(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the bounding box data.
- getBoundingBoxData(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the bounding box data.
- getBoundingBoxesCount(SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the bounding box count.
- getBoundingBoxesCount(int, SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the bounding box count.
- getBoundingBoxesCount() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the bounding box count.
- getBoundingBoxesCount(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the bounding box count.
- getBoundingBoxesCount() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the bounding box count.
- getBoundingBoxesCount(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the bounding box count.
- getBoundingBoxFirstSpectrumId(long, SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the bounding box first spectrum index.
- getBoundingBoxFirstSpectrumId(long) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the bounding box first spectrum index.
- getBoundingBoxFirstSpectrumId(long) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the bounding box first spectrum index.
- getBoundingBoxIterator(int) - Method in class fr.profi.mzdb.MzDbReader
-
- getBoundingBoxMinMz(int, SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the bounding box min mz.
- getBoundingBoxMinMz(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the bounding box min mz.
- getBoundingBoxMinMz(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the bounding box min mz.
- getBoundingBoxMinTime(int, SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the bounding box min time.
- getBoundingBoxMinTime(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the bounding box min time.
- getBoundingBoxMinTime(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the bounding box min time.
- getBoundingBoxMsLevel(int, SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the bounding box ms level.
- getBoundingBoxMsLevel(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the bounding box ms level.
- getBoundingBoxMsLevel(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the bounding box ms level.
- getBoundingBoxStream(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the bounding box iterator.
- getByteOrder() - Method in class fr.profi.mzdb.model.DataEncoding
-
Gets the byte order.
- getCharge() - Method in interface io.github.msdk.datamodel.FeatureTableRow
-
Return the charge of this row
- getCharge() - Method in interface io.github.msdk.datamodel.GroupedFeature
-
getCharge.
- getCharge() - Method in interface io.github.msdk.datamodel.IonType
-
getCharge.
- getCharge() - Method in class io.github.msdk.datamodel.SimpleFeatureTableRow
-
Return the charge of this row
- getCharge() - Method in class io.github.msdk.datamodel.SimpleIonType
-
getCharge.
- getChemicalStructure() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
getChemicalStructure.
- getChemicalStructure() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
getChemicalStructure.
- getChromatogram() - Method in interface io.github.msdk.datamodel.Feature
-
getChromatogram.
- getChromatogram() - Method in class io.github.msdk.datamodel.SimpleFeature
-
getChromatogram.
- getChromatogram() - Method in class io.github.msdk.featuredetection.adap3d.datamodel.Peak
-
Getter for the field chromatogram.
- getChromatogramNumber() - Method in interface io.github.msdk.datamodel.Chromatogram
-
Returns the number of this chromatogram, represented by an integer, typically positive.
- getChromatogramNumber() - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
Returns the number of this chromatogram, represented by an integer, typically positive.
- getChromatogramPredicate() - Method in class io.github.msdk.io.mzml.MzMLFileImportMethod
-
Getter for the field chromatogramPredicate.
- getChromatograms() - Method in interface io.github.msdk.datamodel.RawDataFile
-
Returns an immutable list of all chromatograms.
- getChromatograms() - Method in class io.github.msdk.datamodel.SimpleRawDataFile
-
Returns an immutable list of all chromatograms.
- getChromatograms() - Method in class io.github.msdk.io.mzdb.MzDBRawDataFile
-
Returns an immutable list of all chromatograms.
- getChromatograms() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
-
Returns an immutable list of all chromatograms.
- getChromatograms() - Method in class io.github.msdk.io.mzxml.MzXMLRawDataFile
-
Returns an immutable list of all chromatograms.
- getChromatogramType() - Method in interface io.github.msdk.datamodel.Chromatogram
-
Returns the type of the chromatogram.
- getChromatogramType() - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
Returns the type of the chromatogram.
- getCoefAreaRatioTolerance() - Method in class io.github.msdk.featuredetection.adap3d.ADAP3DFeatureDetectionParameters
-
Getter for the field coefAreaRatioTolerance.
- getCoefficientsForAllScales() - Method in class io.github.msdk.featuredetection.adap3d.algorithms.ContinuousWaveletTransform
-
getCoefficientsForAllScales.
- getCoefficientsForThisScale(double) - Method in class io.github.msdk.featuredetection.adap3d.algorithms.ContinuousWaveletTransform
-
getCoefficientsForThisScale.
- getColIdxByColName() - Method in class fr.profi.mzdb.util.sqlite.SQLiteResultDescriptor
-
- getCollisionEnergy() - Method in class fr.profi.mzdb.db.model.params.thermo.ThermoFragmentationTarget
-
- getColumnForName(ChromaTofParser.ColumnName) - Method in class io.github.msdk.io.chromatof.TableRow
-
getColumnForName.
- getColumnIndex(String) - Method in class fr.profi.mzdb.util.sqlite.SQLiteQuery
-
- getColumnIndex(String) - Method in class fr.profi.mzdb.util.sqlite.SQLiteResultDescriptor
-
- getColumnName() - Method in class io.github.msdk.io.chromatof.ChromaTofParser.TableColumn
-
- getColumnNames() - Method in class fr.profi.mzdb.util.sqlite.SQLiteQuery
-
- getColumnNames() - Method in class fr.profi.mzdb.util.sqlite.SQLiteResultDescriptor
-
- getComponentList() - Method in class fr.profi.mzdb.db.model.InstrumentConfiguration
-
Gets the param tree.
- getCompression() - Method in class fr.profi.mzdb.model.DataEncoding
-
Gets the compression.
- getCompressionType() - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo
-
Getter for the field compressionType.
- getCompressionType(String) - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo
-
Gets the compression type for the given accession
- getConnection() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the connection.
- getCVParam(CVEntry) - Method in class fr.profi.mzdb.db.model.params.AbstractParamTree
-
- getCVParams() - Method in class fr.profi.mzdb.db.model.AbstractTableModel
-
- getCVParams() - Method in class fr.profi.mzdb.db.model.params.AbstractParamTree
-
- getCVParams(CVEntry[]) - Method in class fr.profi.mzdb.db.model.params.AbstractParamTree
-
- getCVParams() - Method in interface fr.profi.mzdb.db.model.params.IParamContainer
-
Gets the cV params.
- getCVParams() - Method in class fr.profi.mzdb.db.model.params.ParamTree
-
- getCVParams() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
getCVParams.
- getCVParamsList() - Method in class io.github.msdk.io.mzml.data.MzMLCVGroup
-
getCVParamsList.
- getCvRef() - Method in class fr.profi.mzdb.db.model.params.param.CVParam
-
- getCvRef() - Method in class fr.profi.mzdb.db.model.params.param.UserParam
-
- getCvRef() - Method in class fr.profi.mzdb.db.model.params.param.UserText
-
- getCVValue(String) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Search for the CV Parameter value for the given accession in the
MsScan's CV Parameters
- getCVValue(MzMLCVGroup, String) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Search for the CV Parameter value for the given accession in the given
MzMLCVGroup
- getCWTDataPoint(List<SliceSparseMatrix.Triplet>) - Method in class io.github.msdk.featuredetection.adap3d.algorithms.SliceSparseMatrix
-
This method returns sorted list of ContinuousWaveletTransform.DataPoint object.Object contain
retention time and intensity values.
- getCycle() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
Gets the cycle.
- getCyclesCount(SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the cycle count.
- getCyclesCount() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the cycle count.
- getCyclesCount() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the cycle count.
- getData() - Method in class fr.profi.mzdb.model.RunSlice
-
Gets the data.
- getData() - Method in class fr.profi.mzdb.model.Spectrum
-
Gets the data.
- getDatabase() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
getDatabase
- getDatabase() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
getDatabase
- getDataEncoding(int, SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractDataEncodingReader
-
Gets the data encoding.
- getDataEncoding(int) - Method in class fr.profi.mzdb.io.reader.cache.DataEncodingAsyncReader
-
Gets the data encoding.
- getDataEncoding(int) - Method in class fr.profi.mzdb.io.reader.cache.DataEncodingReader
-
Gets the data encoding.
- getDataEncoding(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the data encoding.
- getDataEncoding(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the data encoding.
- getDataEncodingById(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractDataEncodingReader
-
Gets the data encoding by id.
- getDataEncodingById() - Method in class fr.profi.mzdb.io.reader.cache.DataEncodingAsyncReader
-
Gets the data encoding by id.
- getDataEncodingById() - Method in class fr.profi.mzdb.io.reader.cache.DataEncodingReader
-
Gets the data encoding by id.
- getDataEncodingBySpectrumId(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractDataEncodingReader
-
Gets the data encoding by spectrum id.
- getDataEncodingBySpectrumId() - Method in class fr.profi.mzdb.io.reader.cache.DataEncodingAsyncReader
-
Gets the data encoding by spectrum id.
- getDataEncodingBySpectrumId() - Method in class fr.profi.mzdb.io.reader.cache.DataEncodingReader
-
Gets the data encoding by spectrum id.
- getDataEncodingBySpectrumId() - Method in class fr.profi.mzdb.io.reader.cache.MzDbEntityCache
-
- getDataEncodingBySpectrumId() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the data encoding by spectrum id.
- getDataEncodingBySpectrumId() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the data encoding by spectrum id.
- getDataEncodingReader() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getDataEncodingReader() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getDataEncodingReader() - Method in class fr.profi.mzdb.MzDbReader
-
- getDataEncodings(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractDataEncodingReader
-
Gets the data encodings.
- getDataEncodings() - Method in class fr.profi.mzdb.io.reader.cache.DataEncodingAsyncReader
-
Gets the data encodings.
- getDataEncodings() - Method in class fr.profi.mzdb.io.reader.cache.DataEncodingReader
-
Gets the data encodings.
- getDataEncodingsCount(SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the data encoding count.
- getDataEncodingsCount() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the data encoding count.
- getDataEncodingsCount() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the data encoding count.
- getDataPoints() - Method in class fr.profi.mzdb.model.Chromatogram
-
Gets the data points.
- getDataPointsChromatographyRange(float[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns the range of Float of all data points in this feature.
- getDataPointsIntensityRange(Float[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns the range of intensity values of all data points in this chromatogram.
- getDBLinks() - Method in class io.github.msdk.id.sirius.SiriusIonAnnotation
-
- getDbLocation() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getDefaultDataProcessingChromatogram() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
-
- getDefaultDataProcessingScan() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
-
- getDefaultInstrumentConfiguration() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
-
- getDescription() - Method in enum fr.profi.mzdb.model.AcquisitionMode
-
- getDescription() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
getDescription.
- getDescription() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
getDescription.
- getDIAIsolationWindows(SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
Get the DIA IsolationWindows
- getDIAIsolationWindows() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
ImmutablePair can not be wrapped into an array
- getDIAIsolationWindows() - Method in class fr.profi.mzdb.MzDbReader
-
Get the DIA IsolationWindows
- getDuration(float[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns the duration of this feature.
- getElutionTime() - Method in interface fr.profi.mzdb.model.ILcContext
-
Gets the elution time.
- getElutionTime() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
- getEncodedLength() - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo
-
Getter for the field encodedLength.
- getEndMass() - Method in interface io.github.msdk.spectra.peakinvestigator.providers.PeakInvestigatorOptionsProvider
-
getEndMass.
- getEndMz() - Method in class fr.profi.mzdb.model.RunSliceHeader
-
Gets the end mz.
- getEntityCache() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
Gets the entity cache.
- getEntityCache() - Method in class fr.profi.mzdb.io.reader.cache.MzDbEntityCacheContainer
-
- getError(Double) - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorMsSpectrum
-
getError.
- getExpectedMz() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
getExpectedMz.
- getExpectedMz() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
getExpectedMz.
- getExpectedRetentionTime() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
getRetentionTime.
- getExpectedRetentionTime() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
getRetentionTime.
- getExperiment() - Method in class io.github.msdk.id.sirius.SiriusIdentificationMethod
-
- getFeature(Sample) - Method in interface io.github.msdk.datamodel.FeatureTableRow
-
Return feature assigned to this row
- getFeature(Integer) - Method in interface io.github.msdk.datamodel.FeatureTableRow
-
Return feature assigned to this row
- getFeature(Sample) - Method in class io.github.msdk.datamodel.SimpleFeatureTableRow
-
Return feature assigned to this row
- getFeature(Integer) - Method in class io.github.msdk.datamodel.SimpleFeatureTableRow
-
Return feature assigned to this row
- getFeatureDimensions() - Method in enum io.github.msdk.datamodel.SeparationType
-
Return the number of additional features linked to an
MsScan and to
- getFeatureTable() - Method in interface io.github.msdk.datamodel.FeatureTableRow
-
Returns the feature table where this feature table row belongs.
- getFeatureTable() - Method in class io.github.msdk.datamodel.SimpleFeatureTableRow
-
Returns the feature table where this feature table row belongs.
- getFieldSeparator() - Method in class io.github.msdk.io.chromatof.ChromaTofParser
-
Getter for the field fieldSeparator.
- getFilenameToGroupMap(File, String) - Static method in class io.github.msdk.io.chromatof.ParserUtilities
-
getFilenameToGroupMap.
- getFingerIdScore() - Method in class io.github.msdk.id.sirius.SiriusIonAnnotation
-
- getFinishedPercent() - Method in class io.github.msdk.featuredetection.adap3d.algorithms.ADAP3DPeakDetectionAlgorithm
-
This method tracks progress of algorithm
- getFinishedPercent(SliceSparseMatrix.Triplet) - Method in class io.github.msdk.featuredetection.adap3d.algorithms.SliceSparseMatrix
-
This method tracks progress of algorithm
- getFinishedPercentage() - Method in class io.github.msdk.alignment.joinaligner.JoinAlignerMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.alignment.ransac.RansacAlignerMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.featuredetection.adap3d.ADAP3DFeatureDetectionMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.featuredetection.chromatogrambuilder.ChromatogramBuilderMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.featuredetection.gridmass.GridMassMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.featuredetection.msmsdetection.MsMsDetectionMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.featuredetection.srm.SrmDetectionMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.featuredetection.targeted.TargetedDetectionMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.id.localdatabase.LocalDatabaseSearchMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.id.sirius.FingerIdWebMethod
-
- getFinishedPercentage() - Method in class io.github.msdk.id.sirius.SiriusIdentificationMethod
-
- getFinishedPercentage() - Method in class io.github.msdk.io.chromatof.ChromaTofFileImportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.FeatureTableImportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.mgf.MgfFileExportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.mgf.MgfFileImportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.mzdata.MzDataFileImportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.mzdb.MzDBFileImportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.mzml.MzMLFileExportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.mzml.MzMLFileImportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.mztab.MzTabFileExportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.mztab.MzTabFileImportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.mzxml.MzXMLFileImportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.mzxml.MzXMLFileParser
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.nativeformats.ThermoRawImportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.nativeformats.WatersRawImportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.netcdf.NetCDFFileExportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.netcdf.NetCDFFileImportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.io.RawDataFileImportMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.isotopes.isotopegrouper.IsotopeGrouperMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in interface io.github.msdk.MSDKMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.normalization.compound.FeatureNormalizationByCompoundMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.rawdata.filters.MSDKFilteringMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.spectra.centroiding.MSDKCentroidingMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorScanBundlingMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFinishedPercentage() - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorScanExtractingMethod
-
Returns a number in the interval 0 to 1.0, representing the portion of the task that has
completed, or null if the algorithm has not yet started.
- getFirst() - Method in class io.github.msdk.io.chromatof.Pair
-
getFirst.
- getFirstSourceFileName() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getFirstSpectrumId() - Method in class fr.profi.mzdb.model.BoundingBox
-
Gets the first spectrum id.
- getFormula() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
Chemical formula annotation should include charge, e.g.
- getFormula() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
Chemical formula annotation should include charge, e.g.
- getFTree() - Method in class io.github.msdk.id.sirius.SiriusIonAnnotation
-
- getFwhm(float[], float[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns the full width at half maximum (FWHM) of this feature.
- getHeader() - Method in class fr.profi.mzdb.model.RunSlice
-
Gets the header.
- getHeader() - Method in class fr.profi.mzdb.model.Spectrum
-
Gets the header.
- getHeader(File, boolean) - Method in class io.github.msdk.io.chromatof.ChromaTofParser
-
- getHeight() - Method in interface io.github.msdk.datamodel.Feature
-
getHeight.
- getHeight() - Method in class io.github.msdk.datamodel.SimpleFeature
-
getHeight.
- getHorizontalSlice(double, int, int) - Method in class io.github.msdk.featuredetection.adap3d.algorithms.SliceSparseMatrix
-
This method returns the MultiKeyMap slice of data for given mz,lowerScanBound,upperScanBound
- getHorizontalSlice(int, int, int) - Method in class io.github.msdk.featuredetection.adap3d.algorithms.SliceSparseMatrix
-
This method returns the MultiKeyMap slice of data for rounded mz,lowerScanBound,upperScanBound
- getId() - Method in class fr.profi.mzdb.db.model.AbstractTableModel
-
Gets the id.
- getId() - Method in class fr.profi.mzdb.db.model.InstrumentConfiguration
-
Gets the id.
- getId() - Method in class fr.profi.mzdb.model.BoundingBox
-
Gets the id.
- getId() - Method in class fr.profi.mzdb.model.DataEncoding
-
Gets the id.
- getId() - Method in class fr.profi.mzdb.model.RunSliceData
-
Gets the id.
- getId() - Method in class fr.profi.mzdb.model.RunSliceHeader
-
Gets the id.
- getId() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
Gets the id.
- getId() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Getter for the field id.
- getIdentificationMethod() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
getIdentificationMethod.
- getIdentificationMethod() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
getIdentificationMethod.
- getInchiKey() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
getInchiKey
- getInchiKey() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
getInchiKey
- getIndex() - Method in class io.github.msdk.io.chromatof.ChromaTofParser.TableColumn
-
- getIndexOfHeaderColumn(List<ChromaTofParser.TableColumn>, ChromaTofParser.TableColumn) - Method in class io.github.msdk.io.chromatof.ChromaTofParser
-
getIndexOfHeaderColumn.
- getIndividualFeatures() - Method in interface io.github.msdk.datamodel.GroupedFeature
-
getIndividualFeatures.
- getInfo() - Method in class io.github.msdk.featuredetection.adap3d.datamodel.Peak
-
Getter for the field info.
- getInitialId() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
Gets the initial id.
- getInputStream() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
getInputStream.
- getInstrumentConfig(int) - Method in class fr.profi.mzdb.io.reader.table.InstrumentConfigReader
-
Gets the instrument config.
- getInstrumentConfigList() - Method in class fr.profi.mzdb.io.reader.table.InstrumentConfigReader
-
- getInstrumentConfigurations() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getInstrumentConfigurations() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getInstrumentConfigurations() - Method in class fr.profi.mzdb.MzDbReader
-
- getIntensities(ADAP3DPeakDetectionAlgorithm.GoodPeakInfo) - Method in class io.github.msdk.featuredetection.adap3d.algorithms.SliceSparseMatrix
-
This method returns intensity array for detected peak
- getIntensity() - Method in class fr.profi.mzdb.model.Peak
-
Gets the intensity.
- getIntensity() - Method in class io.github.msdk.featuredetection.adap3d.datamodel.Peak
-
getIntensity.
- getIntensityBinaryDataInfo() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Getter for the field intensityBinaryDataInfo.
- getIntensityComp() - Static method in class fr.profi.mzdb.model.Peak
-
Gets the intensity comp.
- getIntensityList() - Method in class fr.profi.mzdb.model.SpectrumData
-
Gets the intensity list.
- getIntensityValues(float[]) - Method in class io.github.msdk.datamodel.AbstractMsSpectrum
-
Returns the intensity values of this spectrum.
- getIntensityValues() - Method in interface io.github.msdk.datamodel.Chromatogram
-
getIntensityValues.
- getIntensityValues(float[]) - Method in interface io.github.msdk.datamodel.Chromatogram
-
getIntensityValues.
- getIntensityValues() - Method in interface io.github.msdk.datamodel.MsSpectrum
-
Returns the intensity values of this spectrum.
- getIntensityValues(float[]) - Method in interface io.github.msdk.datamodel.MsSpectrum
-
Returns the intensity values of this spectrum.
- getIntensityValues() - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
getIntensityValues.
- getIntensityValues(float[]) - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
getIntensityValues.
- getIntensityValues(float[]) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the intensity values of this spectrum.
- getIntensityValues(float[]) - Method in class io.github.msdk.io.netcdf.NetCDFMsScan
-
Returns the intensity values of this spectrum.
- getIntensityValues(float[]) - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorMsSpectrum
-
Returns the intensity values of this spectrum.
- getIonAnnotation() - Method in interface io.github.msdk.datamodel.Chromatogram
-
Returns the ion annotation for this chromatogram.
- getIonAnnotation() - Method in interface io.github.msdk.datamodel.Feature
-
getIonAnnotation.
- getIonAnnotation() - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
Returns the ion annotation for this chromatogram.
- getIonAnnotation() - Method in class io.github.msdk.datamodel.SimpleFeature
-
getIonAnnotation.
- getIonInjectTime() - Method in interface io.github.msdk.datamodel.IsolationInfo
-
Returns the ion injection time in ms, for ion trap experiments.
- getIonInjectTime() - Method in class io.github.msdk.datamodel.SimpleIsolationInfo
-
Returns the ion injection time in ms, for ion trap experiments.
- getIonization() - Method in class io.github.msdk.id.sirius.SiriusIdentificationMethod
-
- getIonType() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
getIonType.
- getIonType() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
getIonType.
- getIsolationMzRange() - Method in interface io.github.msdk.datamodel.IsolationInfo
-
Returns the isolated m/z range.
- getIsolationMzRange() - Method in class io.github.msdk.datamodel.SimpleIsolationInfo
-
Returns the isolated m/z range.
- getIsolations() - Method in interface io.github.msdk.datamodel.Chromatogram
-
Returns a list of isolations performed for this chromatogram.
- getIsolations() - Method in interface io.github.msdk.datamodel.MsScan
-
Returns a list of isolations performed for this scan.
- getIsolations() - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
Returns a list of isolations performed for this chromatogram.
- getIsolations() - Method in class io.github.msdk.datamodel.SimpleMsScan
-
Returns a list of isolations performed for this scan.
- getIsolations() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns a list of isolations performed for this scan.
- getIsolationWindow() - Method in class fr.profi.mzdb.db.model.params.Precursor
-
- getIsolationWindow() - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorElement
-
Getter for the field isolationWindow.
- getIsolationWindow() - Method in class io.github.msdk.io.mzml.data.MzMLProduct
-
Getter for the field isolationWindow.
- getLargeScaleIn() - Method in class io.github.msdk.featuredetection.adap3d.ADAP3DFeatureDetectionParameters
-
Getter for the field largeScaleIn.
- getLastSpectrumId() - Method in class fr.profi.mzdb.model.BoundingBox
-
- getLastTime(SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the last time.
- getLastTime() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the last time.
- getLastTime() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the last time.
- getLcContext() - Method in class fr.profi.mzdb.model.Peak
-
Gets the lc context.
- getLcMsnRunSliceIterator(double, double) - Method in class fr.profi.mzdb.MzDbReader
-
Gets a DIA data RunSlice iterator
- getLcMsnRunSliceIterator(double, double, double, double) - Method in class fr.profi.mzdb.MzDbReader
-
Gets a DIA data RunSlice iterator for a given m/z range
- getLcMsnRunSliceStream(double, double) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets a DIA data RunSlice iterator
- getLcMsnRunSliceStream(double, double, double, double) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets a DIA data RunSlice iterator for a given m/z range
- getLcMsRunSliceIterator() - Method in class fr.profi.mzdb.MzDbReader
-
Gets a RunSlice iterator.
- getLcMsRunSliceIterator(double, double) - Method in class fr.profi.mzdb.MzDbReader
-
Gets a RunSlice iterator for a given m/z range
- getLcMsRunSliceStream() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets a RunSlice iterator.
- getLcMsRunSliceStream(double, double) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets a RunSlice iterator for a given m/z range
- getLeftHwhm() - Method in class fr.profi.mzdb.model.Peak
-
Gets the left hwhm.
- getLeftHwhmList() - Method in class fr.profi.mzdb.model.SpectrumData
-
Gets the left hwhm list.
- getLocale() - Method in class io.github.msdk.io.chromatof.ChromaTofParser
-
Getter for the field locale.
- getLocation() - Method in class fr.profi.mzdb.db.model.SourceFile
-
Gets the location.
- getLossStateParamName() - Method in interface fr.profi.mzdb.db.model.IMzDBParamNameGetter
-
- getLossStateParamName() - Method in class fr.profi.mzdb.db.model.MzDBParamName_0_8
-
- getLossStateParamName() - Method in class fr.profi.mzdb.db.model.MzDBParamName_0_9
-
- getMaxHeight(float[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns the maximum height of this chromatogram, or null if size == 0.
- getMaxIntensity(float[], Integer) - Static method in class io.github.msdk.util.MsSpectrumUtil
-
Returns the highest intensity value.
- getMaxIntensity(double[], float[], Integer, Range<Double>) - Static method in class io.github.msdk.util.MsSpectrumUtil
-
Returns the highest intensity value.
- getMaxMsLevel(SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the max ms level.
- getMaxMsLevel() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the max ms level.
- getMaxMsLevel() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the max ms level.
- getMaxMz() - Method in class fr.profi.mzdb.model.IsolationWindow
-
- getMaxMz() - Method in class fr.profi.mzdb.model.SpectrumData
-
Gets the max mz.
- getMaxPeakWidth() - Method in class io.github.msdk.featuredetection.adap3d.ADAP3DFeatureDetectionParameters
-
Getter for the field maxPeakWidth.
- getMaxSpectrumId() - Method in class fr.profi.mzdb.model.BoundingBox
-
Max id.
- getMedianMz(double[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns median m/z value of the chromatogram
- getMinMz() - Method in class fr.profi.mzdb.model.IsolationWindow
-
- getMinMz() - Method in class fr.profi.mzdb.model.SpectrumData
-
Gets the min mz.
- getMinPeakWidth() - Method in class io.github.msdk.featuredetection.adap3d.ADAP3DFeatureDetectionParameters
-
Getter for the field minPeakWidth.
- getMinSpectrumId() - Method in class fr.profi.mzdb.model.BoundingBox
-
Min id.
- getMode() - Method in class fr.profi.mzdb.model.DataEncoding
-
Gets the mode.
- getMode(List<TableRow>) - Method in class io.github.msdk.io.chromatof.ChromaTofParser
-
getMode.
- getModelVersion(SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
- getModelVersion() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getModelVersion() - Method in class fr.profi.mzdb.MzDbReader
-
- getMs1BBMzWidthParamName() - Method in interface fr.profi.mzdb.db.model.IMzDBParamNameGetter
-
- getMs1BBMzWidthParamName() - Method in class fr.profi.mzdb.db.model.MzDBParamName_0_8
-
- getMs1BBMzWidthParamName() - Method in class fr.profi.mzdb.db.model.MzDBParamName_0_9
-
- getMs1BBTimeWidthParamName() - Method in interface fr.profi.mzdb.db.model.IMzDBParamNameGetter
-
- getMs1BBTimeWidthParamName() - Method in class fr.profi.mzdb.db.model.MzDBParamName_0_8
-
- getMs1BBTimeWidthParamName() - Method in class fr.profi.mzdb.db.model.MzDBParamName_0_9
-
- getMs1SpectrumHeaderById(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader
-
Gets the MS1 spectrum header by id.
- getMs1SpectrumHeaderById() - Method in class fr.profi.mzdb.io.reader.cache.MzDbEntityCache
-
- getMs1SpectrumHeaderById() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderAsyncReader
-
Gets the MS1 spectrum header by id.
- getMs1SpectrumHeaderById() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderReader
-
Gets the MS1 spectrum header by id.
- getMs1SpectrumHeaderById() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the MS1 spectrum header by id.
- getMs1SpectrumHeaderById() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the MS1 spectrum header by id.
- getMs1SpectrumHeaders(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader
-
Gets the MS1 spectrum headers.
- getMs1SpectrumHeaders() - Method in class fr.profi.mzdb.io.reader.cache.MzDbEntityCache
-
- getMs1SpectrumHeaders() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderAsyncReader
-
Gets the MS1 spectrum headers.
- getMs1SpectrumHeaders() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderReader
-
Gets the MS1 spectrum headers.
- getMs1SpectrumHeaders() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the MS1 spectrum headers.
- getMs1SpectrumHeaders() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the MS1 spectrum headers.
- getMs2Spectra() - Method in class io.github.msdk.id.sirius.SiriusIdentificationMethod
-
- getMs2SpectrumHeaderById(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader
-
Gets the MS2 spectrum header by id.
- getMs2SpectrumHeaderById() - Method in class fr.profi.mzdb.io.reader.cache.MzDbEntityCache
-
- getMs2SpectrumHeaderById() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderAsyncReader
-
Gets the MS2 spectrum header by id.
- getMs2SpectrumHeaderById() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderReader
-
Gets the MS2 spectrum header by id.
- getMs2SpectrumHeaderById() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the MS2 spectrum header by id.
- getMs2SpectrumHeaderById() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the MS2 spectrum header by id.
- getMs2SpectrumHeaders(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader
-
Gets the MS2 spectrum headers.
- getMs2SpectrumHeaders() - Method in class fr.profi.mzdb.io.reader.cache.MzDbEntityCache
-
- getMs2SpectrumHeaders() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderAsyncReader
-
Gets the MS2 spectrum headers.
- getMs2SpectrumHeaders() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderReader
-
Gets the MS2 spectrum headers.
- getMs2SpectrumHeaders() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the MS2 spectrum headers.
- getMs2SpectrumHeaders() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the MS2 spectrum headers.
- getMs3SpectrumHeaderById(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader
-
Gets the MS2 spectrum header by id.
- getMs3SpectrumHeaders(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader
-
Gets the MS2 spectrum headers.
- getMSDKVersion() - Static method in class io.github.msdk.MSDKVersion
-
getMSDKVersion.
- getMsFunction() - Method in interface io.github.msdk.datamodel.MsScan
-
Returns the MS function of this scan, e.g.
- getMsFunction() - Method in class io.github.msdk.datamodel.SimpleMsScan
-
Returns the MS function of this scan, e.g.
- getMsFunction() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the MS function of this scan, e.g.
- getMsFunctions() - Method in interface io.github.msdk.datamodel.RawDataFile
-
Returns all MS functions found in this raw data file.
- getMsFunctions() - Method in class io.github.msdk.datamodel.SimpleRawDataFile
-
Returns all MS functions found in this raw data file.
- getMsFunctions() - Method in class io.github.msdk.io.mzdb.MzDBRawDataFile
-
- getMsFunctions() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
-
Returns all MS functions found in this raw data file.
- getMsFunctions() - Method in class io.github.msdk.io.mzxml.MzXMLRawDataFile
-
Returns all MS functions found in this raw data file.
- getMsLevel() - Method in class fr.profi.mzdb.db.model.params.thermo.ThermoFragmentationTarget
-
- getMsLevel() - Method in class fr.profi.mzdb.db.model.params.thermo.ThermoScanMetaData
-
- getMsLevel() - Method in class fr.profi.mzdb.model.RunSliceHeader
-
Gets the ms level.
- getMsLevel() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
Gets the ms level.
- getMsLevel() - Method in interface io.github.msdk.datamodel.MsScan
-
Returns MS level (1 = default, 2 = MS/MS, 3 = MS3 etc.).
- getMsLevel() - Method in class io.github.msdk.datamodel.SimpleMsScan
-
Returns MS level (1 = default, 2 = MS/MS, 3 = MS3 etc.).
- getMsLevel() - Method in class io.github.msdk.io.mgf.MgfMsSpectrum
-
Getter for MS level of spectrum
- getMsLevel() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns MS level (1 = default, 2 = MS/MS, 3 = MS3 etc.).
- getMSMSSpectra() - Method in interface io.github.msdk.datamodel.Feature
-
getMSMSSpectra.
- getMSMSSpectra() - Method in class io.github.msdk.datamodel.SimpleFeature
-
getMSMSSpectra.
- getMsnBBMzWidthParamName() - Method in interface fr.profi.mzdb.db.model.IMzDBParamNameGetter
-
- getMsnBBMzWidthParamName() - Method in class fr.profi.mzdb.db.model.MzDBParamName_0_8
-
- getMsnBBMzWidthParamName() - Method in class fr.profi.mzdb.db.model.MzDBParamName_0_9
-
- getMsnBBTimeWidthParamName() - Method in interface fr.profi.mzdb.db.model.IMzDBParamNameGetter
-
- getMsnBBTimeWidthParamName() - Method in class fr.profi.mzdb.db.model.MzDBParamName_0_8
-
- getMsnBBTimeWidthParamName() - Method in class fr.profi.mzdb.db.model.MzDBParamName_0_9
-
- getMsnPeaksInMzRtRanges(double, double, double, float, float, SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getMsnPeaksInMzRtRanges(double, double, double, float, float) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getMsnPeaksInMzRtRanges(double, double, double, float, float) - Method in class fr.profi.mzdb.MzDbReader
-
- getMsnSpectrumSlices(double, double, double, float, float, SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getMsnSpectrumSlices(double, double, double, float, float) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getMsnSpectrumSlices(double, double, double, float, float) - Method in class fr.profi.mzdb.MzDbReader
-
- getMsnXic(double, double, double, float, float, XicMethod, SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getMsnXic(double, double, double, float, float, XicMethod) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getMsnXIC(double, double, double, float, float, XicMethod) - Method in class fr.profi.mzdb.MzDbReader
-
- getMsPeaksInMzRtRanges(double, double, float, float, SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
Gets the peaks.
- getMsPeaksInMzRtRanges(double, double, float, float) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getMsPeaksInMzRtRanges(double, double, float, float) - Method in class fr.profi.mzdb.MzDbReader
-
- getMsScanPredicate() - Method in class io.github.msdk.io.mzml.MzMLFileImportMethod
-
Getter for the field msScanPredicate.
- getMsScanType() - Method in interface io.github.msdk.datamodel.MsScan
-
Returns the type of the MS scan.
- getMsScanType() - Method in class io.github.msdk.datamodel.SimpleMsScan
-
Returns the type of the MS scan.
- getMsScanType() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the type of the MS scan.
- getMsSpectra() - Method in class io.github.msdk.id.sirius.SiriusIdentificationMethod
-
- getMsSpectrumSlices(double, double, float, float, SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
Gets the spectrum slices.
- getMsSpectrumSlices(double, double, float, float) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the spectrum slices.
- getMsSpectrumSlices(double, double, float, float) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the spectrum slices.
- getMsXic(double, double, float, float, XicMethod, SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getMsXic(double, double, float, float, XicMethod) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getMsXic(double, double, float, float, int, XicMethod) - Method in class fr.profi.mzdb.MzDbReader
-
- getMsXicInMzRange(double, double, XicMethod, SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
Gets the xic.
- getMsXicInMzRange(double, double, XicMethod) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getMsXicInMzRange(double, double, XicMethod) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the xic.
- getMsXicInMzRtRanges(double, double, float, float, XicMethod, SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getMsXicInMzRtRanges(double, double, float, float, XicMethod) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getMsXicInMzRtRanges(double, double, float, float, XicMethod) - Method in class fr.profi.mzdb.MzDbReader
-
- getMultiplier() - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorMsSpectrum
-
Getter for the field multiplier.
- getMz() - Method in class fr.profi.mzdb.db.model.params.thermo.ThermoFragmentationTarget
-
- getMz() - Method in class fr.profi.mzdb.model.Peak
-
Gets the mz.
- getMz() - Method in interface io.github.msdk.datamodel.Chromatogram
-
Returns the m/z value of this chromatogram, or null if no m/z value is set for the
chromatogram.
- getMz() - Method in interface io.github.msdk.datamodel.Feature
-
getMz.
- getMz() - Method in interface io.github.msdk.datamodel.FeatureTableRow
-
Shortcut to return the m/z column value of this row
- getMz() - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
Returns the m/z value of this chromatogram, or null if no m/z value is set for the
chromatogram.
- getMz() - Method in class io.github.msdk.datamodel.SimpleFeature
-
getMz.
- getMz() - Method in class io.github.msdk.datamodel.SimpleFeatureTableRow
-
Shortcut to return the m/z column value of this row
- getMZ() - Method in class io.github.msdk.featuredetection.adap3d.datamodel.Peak
-
getMZ.
- getMzBinaryDataInfo() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Getter for the field mzBinaryDataInfo.
- getmzDBFile() - Method in class io.github.msdk.io.mzdb.MzDBFileImportMethod
-
Getter for the field mzDBFile.
- getMzDbHeader() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getMzDbHeader() - Method in class fr.profi.mzdb.io.reader.table.MzDbHeaderReader
-
Gets the mz db header.
- getMzDbReader() - Method in class fr.profi.mzdb.io.reader.cache.DataEncodingAsyncReader
-
specialized getter
- getMzDbReader() - Method in class fr.profi.mzdb.io.reader.cache.DataEncodingReader
-
specialized getter
- getMzDbReader() - Method in class fr.profi.mzdb.io.reader.cache.MzDbEntityCacheContainer
-
- getMzDbReader() - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderAsyncReader
-
specialized getter
- getMzDbReader() - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderReader
-
specialized getter
- getMzDbReader() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderAsyncReader
-
specialized getter
- getMzDbReader() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderReader
-
specialized getter
- getMzDbReader() - Method in class fr.profi.mzdb.io.writer.mgf.MgfWriter
-
- getMzList() - Method in class fr.profi.mzdb.model.SpectrumData
-
Gets the mz list.
- getMzMLFile() - Method in class io.github.msdk.io.mzml.MzMLFileImportMethod
-
Getter for the field mzMLFile.
- getMzMLRawFile() - Method in class io.github.msdk.io.mzml.data.MzMLParser
-
getMzMLRawFile.
- getMzRange() - Method in class fr.profi.mzdb.db.model.params.thermo.ThermoScanMetaData
-
- getMzRange(int, SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the mz range.
- getMzRange(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the mz range.
- getMzRange(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the mz range.
- getMzRange() - Method in class io.github.msdk.datamodel.AbstractMsSpectrum
-
Returns the range of m/z values for the current spectrum.
- getMzRange() - Method in interface io.github.msdk.datamodel.MsSpectrum
-
Returns the range of m/z values for the current spectrum.
- getMzRange() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the range of m/z values for the current spectrum.
- getMzRange() - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorMsSpectrum
-
Returns the range of m/z values for the current spectrum.
- getMzRange(double[], Integer) - Static method in class io.github.msdk.util.MsSpectrumUtil
-
Returns the m/z range of given data points.
- getMzTolerance() - Method in class io.github.msdk.datamodel.AbstractMsSpectrum
-
Returns an object that implements the MzTolerance interface.
- getMzTolerance() - Method in interface io.github.msdk.datamodel.MsSpectrum
-
Returns an object that implements the MzTolerance interface.
- getMzTolerance() - Method in class io.github.msdk.datamodel.SimpleMsScan
-
Returns an object that implements the MzTolerance interface.
- getMzTolerance() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns an object that implements the MzTolerance interface.
- getMzTolerance() - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorMsSpectrum
-
Returns an object that implements the MzTolerance interface.
- getMzTolerance() - Method in class io.github.msdk.util.tolerances.ConstantDaTolerance
-
Getter for the field mzTolerance.
- getMzTolerance() - Method in class io.github.msdk.util.tolerances.MaximumMzTolerance
-
Getter for the field mzTolerance.
- getMzValues(double[]) - Method in class io.github.msdk.datamodel.AbstractMsSpectrum
-
Returns the m/z values of this spectrum.
- getMzValues() - Method in interface io.github.msdk.datamodel.Chromatogram
-
getMzValues.
- getMzValues(double[]) - Method in interface io.github.msdk.datamodel.Chromatogram
-
- getMzValues() - Method in interface io.github.msdk.datamodel.MsSpectrum
-
Returns the m/z values of this spectrum.
- getMzValues(double[]) - Method in interface io.github.msdk.datamodel.MsSpectrum
-
Returns the m/z values of this spectrum.
- getMzValues() - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
getMzValues.
- getMzValues(double[]) - Method in class io.github.msdk.datamodel.SimpleChromatogram
- getMzValues(double[]) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the m/z values of this spectrum.
- getMzValues(double[]) - Method in class io.github.msdk.io.netcdf.NetCDFMsScan
-
Returns the m/z values of this spectrum.
- getMzValues(double[]) - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorMsSpectrum
-
Returns the m/z values of this spectrum.
- getName() - Method in class fr.profi.mzdb.db.model.InstrumentConfiguration
-
Gets the name.
- getName() - Method in class fr.profi.mzdb.db.model.params.param.CVParam
-
- getName() - Method in class fr.profi.mzdb.db.model.params.param.UserParam
-
- getName() - Method in class fr.profi.mzdb.db.model.params.param.UserText
-
- getName() - Method in class fr.profi.mzdb.db.model.Run
-
Gets the name.
- getName() - Method in class fr.profi.mzdb.db.model.Sample
-
Gets the name.
- getName() - Method in class fr.profi.mzdb.db.model.Software
-
Gets the name.
- getName() - Method in class fr.profi.mzdb.db.model.SourceFile
-
Gets the name.
- getName() - Method in interface io.github.msdk.datamodel.IonType
-
getName.
- getName() - Method in interface io.github.msdk.datamodel.RawDataFile
-
Returns the name of this raw data file.
- getName() - Method in interface io.github.msdk.datamodel.Sample
-
getName.
- getName() - Method in class io.github.msdk.datamodel.SimpleIonType
-
getName.
- getName() - Method in class io.github.msdk.datamodel.SimpleRawDataFile
-
Returns the name of this raw data file.
- getName() - Method in class io.github.msdk.datamodel.SimpleSample
-
getName.
- getName() - Method in class io.github.msdk.io.chromatof.ChromaTofParser.TableColumn
-
- getName() - Method in class io.github.msdk.io.mzdb.MzDBRawDataFile
-
- getName() - Method in enum io.github.msdk.io.mzml.data.MzMLCompressionType
-
Getter for the field name.
- getName() - Method in class io.github.msdk.io.mzml.data.MzMLCVParam
-
Getter for the field name.
- getName() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
-
Returns the name of this raw data file.
- getName() - Method in class io.github.msdk.io.mzxml.MzXMLRawDataFile
-
Returns the name of this raw data file.
- getNearestPeak(double, double) - Method in class fr.profi.mzdb.model.Spectrum
-
- getNearestPeak(double, double, ILcContext) - Method in class fr.profi.mzdb.model.SpectrumData
-
assuming mzList is sorted
- getNearestPeakIndex(double) - Method in class fr.profi.mzdb.model.SpectrumData
-
- getNextChromatogramNumber(RawDataFile) - Static method in class io.github.msdk.util.RawDataFileUtil
-
getNextChromatogramNumber.
- getNorm() - Method in class io.github.msdk.featuredetection.adap3d.datamodel.Peak
-
Getter for the field norm.
- getNumber() - Method in class fr.profi.mzdb.model.RunSliceHeader
-
Gets the number.
- getNumberOfCandidates() - Method in class io.github.msdk.id.sirius.SiriusIdentificationMethod
-
- getNumberOfDataPoints() - Method in class io.github.msdk.datamodel.AbstractMsSpectrum
-
getNumberOfDataPoints.
- getNumberOfDataPoints() - Method in interface io.github.msdk.datamodel.Chromatogram
-
getNumberOfDataPoints.
- getNumberOfDataPoints() - Method in interface io.github.msdk.datamodel.MsSpectrum
-
getNumberOfDataPoints.
- getNumberOfDataPoints() - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
getNumberOfDataPoints.
- getNumberOfDataPoints() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
getNumberOfDataPoints.
- getNumberOfDataPoints() - Method in class io.github.msdk.io.netcdf.NetCDFMsScan
-
getNumberOfDataPoints.
- getNumberOfDataPoints() - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorMsSpectrum
-
getNumberOfDataPoints.
- getNumberOfMolecules() - Method in interface io.github.msdk.datamodel.IonType
-
getNumberOfMolecules.
- getNumberOfMolecules() - Method in class io.github.msdk.datamodel.SimpleIonType
-
getNumberOfMolecules.
- getOrder() - Method in class fr.profi.mzdb.db.model.params.Component
-
Gets the order.
- getOriginalFile() - Method in interface io.github.msdk.datamodel.RawDataFile
-
Returns the original file (i.e.
- getOriginalFile() - Method in interface io.github.msdk.datamodel.Sample
-
Returns the original file name and path where the file was loaded from, or null if this file
was created by MSDK.
- getOriginalFile() - Method in class io.github.msdk.datamodel.SimpleRawDataFile
-
Returns the original file (i.e.
- getOriginalFile() - Method in class io.github.msdk.datamodel.SimpleSample
-
Returns the original file name and path where the file was loaded from, or null if this file
was created by MSDK.
- getOriginalFile() - Method in class io.github.msdk.io.mzdb.MzDBRawDataFile
-
- getOriginalFile() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
-
Returns the original file (i.e.
- getOriginalFile() - Method in class io.github.msdk.io.mzxml.MzXMLRawDataFile
-
Returns the original file (i.e.
- getOriginalFilename() - Method in interface io.github.msdk.datamodel.RawDataFile
-
Returns the filename of the original filename.
- getOriginalFilename() - Method in class io.github.msdk.datamodel.SimpleRawDataFile
-
Returns the filename of the original filename.
- getOsName() - Static method in class io.github.msdk.id.sirius.NativeLibraryLoader
-
Method returns formatted OS name
- getParamGroupName() - Method in class io.github.msdk.io.mzml.data.MzMLReferenceableParamGroup
-
Getter for the field paramGroupName.
- getParamName() - Method in class fr.profi.mzdb.io.writer.mgf.DefaultPrecursorComputer
-
- getParamName() - Method in interface fr.profi.mzdb.io.writer.mgf.IPrecursorComputation
-
- getParamTree(SQLiteConnection) - Method in class fr.profi.mzdb.db.model.AbstractTableModel
-
Gets the param tree.
- getParamTree() - Method in class fr.profi.mzdb.db.model.InstrumentConfiguration
-
- getParentMass() - Method in class io.github.msdk.id.sirius.SiriusIdentificationMethod
-
- getParserUtils() - Method in class io.github.msdk.io.chromatof.ChromaTofParser
-
Getter for the field parserUtils.
- getPassword() - Method in interface io.github.msdk.spectra.peakinvestigator.providers.PeakInvestigatorProjectProvider
-
getPassword.
- getPeakEncoding() - Method in class fr.profi.mzdb.model.DataEncoding
-
Gets the peak encoding.
- getPeakIndex(double, double) - Method in class fr.profi.mzdb.model.SpectrumData
-
- getPeaksCount() - Method in class fr.profi.mzdb.model.SpectrumData
-
Gets the peaks count.
- getPeaksCount() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
Gets the peaks count.
- getPeakSimilarityThreshold() - Method in class io.github.msdk.featuredetection.adap3d.ADAP3DFeatureDetectionParameters
-
Getter for the field peakSimilarityThreshold.
- getPeakStructSize() - Method in class fr.profi.mzdb.model.DataEncoding
-
- getPolarity() - Method in interface io.github.msdk.datamodel.IonType
-
getPolarity.
- getPolarity() - Method in interface io.github.msdk.datamodel.MsScan
-
Returns the polarity of this scan.
- getPolarity() - Method in class io.github.msdk.datamodel.SimpleIonType
-
getPolarity.
- getPolarity() - Method in class io.github.msdk.datamodel.SimpleMsScan
-
Returns the polarity of this scan.
- getPolarity() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the polarity of this scan.
- getPosition() - Method in class io.github.msdk.io.mzml.data.MzMLBinaryDataInfo
-
Getter for the field position.
- getPpmTolerance() - Method in class io.github.msdk.util.tolerances.ConstantPpmTolerance
-
Getter for the field ppmTolerance.
- getPpmTolerance() - Method in class io.github.msdk.util.tolerances.MaximumMzTolerance
-
Getter for the field ppmTolerance.
- getPrecursor() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
- getPrecursorCharge(MzDbReader, SpectrumHeader) - Method in class fr.profi.mzdb.io.writer.mgf.DefaultPrecursorComputer
-
- getPrecursorCharge(MzDbReader, SpectrumHeader) - Method in interface fr.profi.mzdb.io.writer.mgf.IPrecursorComputation
-
Returns the precursor m/z value of the specified SpectrumHeader.
- getPrecursorCharge() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
Gets the precursor charge.
- getPrecursorCharge() - Method in interface io.github.msdk.datamodel.IsolationInfo
-
Returns the precursor charge.
- getPrecursorCharge() - Method in class io.github.msdk.datamodel.SimpleIsolationInfo
-
Returns the precursor charge.
- getPrecursorCharge() - Method in class io.github.msdk.io.mgf.MgfMsSpectrum
-
Getter of the precursor ion charge
- getPrecursorElements() - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorList
-
Getter for the field precursorElements.
- getPrecursorList() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
getPrecursorList.
- getPrecursorMass() - Method in class io.github.msdk.io.mgf.MgfMsSpectrum
-
Getter of the precursor ion mass
- getPrecursorMz(MzDbReader, SpectrumHeader) - Method in class fr.profi.mzdb.io.writer.mgf.DefaultPrecursorComputer
-
- getPrecursorMz(MzDbReader, SpectrumHeader) - Method in interface fr.profi.mzdb.io.writer.mgf.IPrecursorComputation
-
Returns the precursor m/z value of the specified SpectrumHeader.
- getPrecursorMz() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
Gets the precursor mz.
- getPrecursorMz() - Method in interface io.github.msdk.datamodel.IsolationInfo
-
Returns the precursor m/z.
- getPrecursorMz() - Method in class io.github.msdk.datamodel.SimpleIsolationInfo
-
Returns the precursor m/z.
- getPrecursorScanNumber() - Method in interface io.github.msdk.datamodel.IsolationInfo
-
Returns the precursor scan number.
- getPrecursorScanNumber() - Method in class io.github.msdk.datamodel.SimpleIsolationInfo
-
Returns the precursor scan number.
- getProductList() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
getProductList.
- getProducts() - Method in class io.github.msdk.io.mzml.data.MzMLProductList
-
Getter for the field products.
- getProjectId() - Method in interface io.github.msdk.spectra.peakinvestigator.providers.PeakInvestigatorProjectProvider
-
getProjectId.
- getProperty(String) - Method in class io.github.msdk.io.msp.MspSpectrum
-
getProperty.
- getPwizMzDbVersion(SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
- getPwizMzDbVersion() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getPwizMzDbVersion() - Method in class fr.profi.mzdb.MzDbReader
-
- getQuantile(List<Double>, double) - Static method in class io.github.msdk.featuredetection.adap3d.algorithms.SignalToNoise
-
Estimate quantile of the list of values
Estimation is equivalent to the default quantile estimate in R: if x[j] and x[j+1] are two
values adjacent to the quantile, than Q[p] = (gamma - 1) * x[j] + gamma * x[j+1] where gamma =
(size - 1) * p + 1 - j and j starts from 1
- getQuotationCharacter() - Method in class io.github.msdk.io.chromatof.ChromaTofParser
-
Getter for the field quotationCharacter.
- getRawDataFile() - Method in interface io.github.msdk.datamodel.Chromatogram
-
Returns the raw data file that contains this chromatogram.
- getRawDataFile() - Method in interface io.github.msdk.datamodel.MsScan
-
Returns the raw data file that contains this scan.
- getRawDataFile() - Method in interface io.github.msdk.datamodel.Sample
-
Returns a raw data file or null if this sample has no associated raw data.
- getRawDataFile() - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
Returns the raw data file that contains this chromatogram.
- getRawDataFile() - Method in class io.github.msdk.datamodel.SimpleMsScan
-
Returns the raw data file that contains this scan.
- getRawDataFile() - Method in class io.github.msdk.datamodel.SimpleSample
-
Returns a raw data file or null if this sample has no associated raw data.
- getRawDataFile() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the raw data file that contains this scan.
- getRawDataFileType() - Method in interface io.github.msdk.datamodel.RawDataFile
-
Returns the file type of this raw data file.
- getRawDataFileType() - Method in class io.github.msdk.datamodel.SimpleRawDataFile
-
Returns the file type of this raw data file.
- getRawDataFileType() - Method in class io.github.msdk.io.mzdb.MzDBRawDataFile
-
- getRawDataFileType() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
-
Returns the file type of this raw data file.
- getRawDataFileType() - Method in class io.github.msdk.io.mzxml.MzXMLRawDataFile
-
Returns the file type of this raw data file.
- getReader() - Method in class fr.profi.mzdb.model.BoundingBox
-
Gets the reader.
- getRecord(String, int) - Method in class fr.profi.mzdb.io.reader.table.AbstractTableModelReader
-
- getRecordIterator() - Method in class fr.profi.mzdb.util.sqlite.SQLiteQuery
-
- getRecordList(String) - Method in class fr.profi.mzdb.io.reader.table.AbstractTableModelReader
-
- getReliability() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
Returns the reliability of the identification.
- getReliability() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
Returns the reliability of the identification.
- getRequiredAttribute(XMLStreamReader, String) - Method in class io.github.msdk.io.mzml.data.MzMLParser
-
Gets the required attribute from xmlStreamReader, throws an exception if the attribute is not
found
- getRequiredAttribute(XMLStreamReader, String) - Method in class io.github.msdk.io.mzxml.MzXMLFileParser
-
Gets the required attribute from xmlStreamReader, throws an exception of the attribute is not
found
- getResult() - Method in class io.github.msdk.alignment.joinaligner.JoinAlignerMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.alignment.ransac.RansacAlignerMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.featuredetection.adap3d.ADAP3DFeatureDetectionMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.featuredetection.chromatogrambuilder.ChromatogramBuilderMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.featuredetection.gridmass.GridMassMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.featuredetection.msmsdetection.MsMsDetectionMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.featuredetection.srm.SrmDetectionMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.featuredetection.targeted.TargetedDetectionMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.id.localdatabase.LocalDatabaseSearchMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.id.sirius.FingerIdWebMethod
-
- getResult() - Method in class io.github.msdk.id.sirius.SiriusIdentificationMethod
-
- getResult() - Method in class io.github.msdk.io.chromatof.ChromaTofFileImportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.FeatureTableImportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.mgf.MgfFileExportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.mgf.MgfFileImportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.mzdata.MzDataFileImportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.mzdb.MzDBFileImportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.mzml.MzMLFileExportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.mzml.MzMLFileImportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.mztab.MzTabFileExportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.mztab.MzTabFileImportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.mzxml.MzXMLFileImportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.mzxml.MzXMLFileParser
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.nativeformats.ThermoRawImportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.nativeformats.WatersRawImportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.netcdf.NetCDFFileExportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.netcdf.NetCDFFileImportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.io.RawDataFileImportMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.isotopes.isotopegrouper.IsotopeGrouperMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in interface io.github.msdk.MSDKMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.normalization.compound.FeatureNormalizationByCompoundMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.rawdata.filters.MSDKFilteringMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.spectra.centroiding.MSDKCentroidingMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorScanBundlingMethod
-
Returns the result of this algorithm, or null.
- getResult() - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorScanExtractingMethod
-
Returns the result of this algorithm, or null.
- getResults() - Method in class fr.profi.mzdb.util.threading.Executor
-
- getRetentionTime() - Method in interface io.github.msdk.datamodel.Feature
-
getRetentionTime.
- getRetentionTime() - Method in interface io.github.msdk.datamodel.MsScan
-
Returns the retention time in seconds
- getRetentionTime() - Method in class io.github.msdk.datamodel.SimpleFeature
-
getRetentionTime.
- getRetentionTime() - Method in class io.github.msdk.datamodel.SimpleMsScan
-
Returns the retention time in seconds
- getRetentionTime(int) - Method in class io.github.msdk.featuredetection.adap3d.algorithms.SliceSparseMatrix
-
This method returns retention time for given scan number.
- getRetentionTime() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the retention time in seconds
- getRetentionTime() - Method in class io.github.msdk.io.netcdf.NetCDFMsScan
-
Returns the retention time in seconds
- getRetentionTimeArray(int, int) - Method in class io.github.msdk.featuredetection.adap3d.algorithms.SliceSparseMatrix
-
This method returns retention time array for given upper and lower scan bounds.
- getRetentionTimes() - Method in interface io.github.msdk.datamodel.Chromatogram
-
Returns the info of this chromatogram.
- getRetentionTimes(float[]) - Method in interface io.github.msdk.datamodel.Chromatogram
-
- getRetentionTimes() - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
Returns the info of this chromatogram.
- getRetentionTimes(float[]) - Method in class io.github.msdk.datamodel.SimpleChromatogram
- getRetTime() - Method in class io.github.msdk.featuredetection.adap3d.datamodel.Peak
-
getRetTime.
- getRidgeEndScale() - Method in class io.github.msdk.featuredetection.adap3d.datamodel.Ridgeline
-
getRidgeEndScale.
- getRidgeLength() - Method in class io.github.msdk.featuredetection.adap3d.datamodel.Ridgeline
-
getRidgeLength.
- getRidgeStartScale() - Method in class io.github.msdk.featuredetection.adap3d.datamodel.Ridgeline
-
getRidgeStartScale.
- getRightHwhm() - Method in class fr.profi.mzdb.model.Peak
-
Gets the right hwhm.
- getRightHwhmList() - Method in class fr.profi.mzdb.model.SpectrumData
-
Gets the right hwhm list.
- getRows() - Method in interface io.github.msdk.datamodel.FeatureTable
-
Returns an immutable list of rows
- getRows() - Method in class io.github.msdk.datamodel.SimpleFeatureTable
-
Returns an immutable list of rows
- getRowsInsideRange(FeatureTable, Range<Float>, Range<Double>) - Static method in class io.github.msdk.util.FeatureTableUtil
-
getRowsInsideRange.
- getRT() - Method in interface io.github.msdk.datamodel.FeatureTableRow
-
Shortcut to return the m/z column value of this row
- getRT() - Method in class io.github.msdk.datamodel.SimpleFeatureTableRow
-
Shortcut to return the m/z column value of this row
- getRt(float[], float[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns the retention time of this feature.
- getRtEnd(float[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns the end retention time of this feature.
- getRto() - Method in interface io.github.msdk.spectra.peakinvestigator.providers.PeakInvestigatorInitProvider
-
getRto.
- getRtRange() - Method in interface io.github.msdk.datamodel.Chromatogram
-
Returns the range of retention times.
- getRtRange() - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
Returns the range of retention times.
- getRtRange(float[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns the RT range
- getRtStart(float[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns the start retention time of this feature.
- getRun(int) - Method in class fr.profi.mzdb.io.reader.table.RunReader
-
- getRunId() - Method in class fr.profi.mzdb.model.RunSliceHeader
-
Gets the run id.
- getRunList() - Method in class fr.profi.mzdb.io.reader.table.RunReader
-
- getRunningGapNum() - Method in class io.github.msdk.featuredetection.adap3d.datamodel.Ridgeline
-
getRunningGapNum.
- getRuns() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getRuns() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getRuns() - Method in class fr.profi.mzdb.MzDbReader
-
- getRunSliceData(int, SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
Gets the run slice data.
- getRunSliceData(int) - Method in class fr.profi.mzdb.io.reader.provider.RunSliceDataProvider
-
Gets the run slice data.
- getRunSliceData(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the run slice data.
- getRunSliceData(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the run slice data.
- getRunSliceForMz(double, int, SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractRunSliceHeaderReader
-
Gets the run slice for mz.
- getRunSliceForMz(double, int) - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderAsyncReader
-
Gets the run slice for mz.
- getRunSliceForMz(double, int) - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderReader
-
Gets the run slice for mz.
- getRunSliceHeader(int, SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractRunSliceHeaderReader
-
Gets the run slice header.
- getRunSliceHeader(int) - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderAsyncReader
-
Gets the run slice header.
- getRunSliceHeader(int) - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderReader
-
Gets the run slice header.
- getRunSliceHeaderById(int, SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractRunSliceHeaderReader
-
Gets the run slice by id.
- getRunSliceHeaderById(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractRunSliceHeaderReader
-
Gets the run slice header by id.
- getRunSliceHeaderById() - Method in class fr.profi.mzdb.io.reader.cache.MzDbEntityCache
-
- getRunSliceHeaderById(int) - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderAsyncReader
-
Gets the run slice by id.
- getRunSliceHeaderById() - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderAsyncReader
-
Gets the run slice header by id.
- getRunSliceHeaderById(int) - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderReader
-
Gets the run slice by id.
- getRunSliceHeaderById() - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderReader
-
Gets the run slice header by id.
- getRunSliceHeaderById(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the run slice header by id.
- getRunSliceHeaderById(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the run slice header by id.
- getRunSliceHeaderReader() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getRunSliceHeaderReader() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getRunSliceHeaderReader() - Method in class fr.profi.mzdb.MzDbReader
-
- getRunSliceHeaders(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractRunSliceHeaderReader
-
Gets the run slices.
- getRunSliceHeaders(int, SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractRunSliceHeaderReader
-
Gets the run slices.
- getRunSliceHeaders() - Method in class fr.profi.mzdb.io.reader.cache.MzDbEntityCache
-
- getRunSliceHeaders() - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderAsyncReader
-
Gets the run slices.
- getRunSliceHeaders(int) - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderAsyncReader
-
Gets the run slices.
- getRunSliceHeaders() - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderReader
-
Gets the run slices.
- getRunSliceHeaders(int) - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderReader
-
Gets the run slices.
- getRunSliceHeaders(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the run slices.
- getRunSliceHeaders(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the run slices.
- getRunSliceId() - Method in class fr.profi.mzdb.model.BoundingBox
-
Gets the run slice id.
- getRunSliceId() - Method in class fr.profi.mzdb.model.SpectrumSlice
-
Gets the run slice id.
- getRunSliceIdsForMzRange(double, double, int, SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractRunSliceHeaderReader
-
Gets the run slice ids for mz range.
- getRunSliceIdsForMzRange(double, double, int) - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderAsyncReader
-
Gets the run slice ids for mz range.
- getRunSliceIdsForMzRange(double, double, int) - Method in class fr.profi.mzdb.io.reader.cache.RunSliceHeaderReader
-
Gets the run slice ids for mz range.
- getRunSlicesCount(SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the run slice count.
- getRunSlicesCount() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the run slice count.
- getRunSlicesCount() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the run slice count.
- getSample(int) - Method in class fr.profi.mzdb.io.reader.table.SampleReader
-
- getSampleList() - Method in class fr.profi.mzdb.io.reader.table.SampleReader
-
- getSamples() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getSamples() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getSamples() - Method in class fr.profi.mzdb.MzDbReader
-
- getSamples() - Method in interface io.github.msdk.datamodel.FeatureTable
-
Shortcut to return an immutable list of
Samples found in this feature table.
- getSamples() - Method in class io.github.msdk.datamodel.SimpleFeatureTable
-
Shortcut to return an immutable list of
Samples found in this feature table.
- getSAXSource(String) - Static method in class fr.profi.mzdb.util.jaxb.XercesSAXParser
-
- getScanDefinition() - Method in interface io.github.msdk.datamodel.MsScan
-
Returns the instrument-specific textual definition of the scan parameters.
- getScanDefinition() - Method in class io.github.msdk.datamodel.SimpleMsScan
-
Returns the instrument-specific textual definition of the scan parameters.
- getScanDefinition() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the instrument-specific textual definition of the scan parameters.
- getScanIndex() - Method in class io.github.msdk.io.netcdf.NetCDFMsScan
-
The Scan Index is the inde of the scan in the array
- getScanList() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
- getScanList() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
getScanList.
- getScanningRange() - Method in interface io.github.msdk.datamodel.MsScan
-
Returns the scanning range of the instrument.
- getScanningRange() - Method in class io.github.msdk.datamodel.SimpleMsScan
-
Returns the scanning range of the instrument.
- getScanningRange() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the scanning range of the instrument.
- getScanNumber() - Method in interface io.github.msdk.datamodel.MsScan
-
Returns the number of this scan, represented by an integer, typically positive.
- getScanNumber() - Method in class io.github.msdk.datamodel.SimpleMsScan
-
Returns the number of this scan, represented by an integer, typically positive.
- getScanNumber() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the number of this scan, represented by an integer, typically positive.
- getScanNumber(String) - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
getScanNumber.
- getScanNumber(String) - Method in class io.github.msdk.io.mzml.data.MzMLParser
-
getScanNumber.
- getScans() - Method in class fr.profi.mzdb.db.model.params.ScanList
-
- getScans() - Method in interface io.github.msdk.datamodel.RawDataFile
-
Returns an immutable list of all scans.
- getScans() - Method in class io.github.msdk.datamodel.SimpleRawDataFile
-
Returns an immutable list of all scans.
- getScans() - Method in class io.github.msdk.io.mzdb.MzDBRawDataFile
-
- getScans() - Method in class io.github.msdk.io.mzml.data.MzMLRawDataFile
-
Returns an immutable list of all scans.
- getScans() - Method in class io.github.msdk.io.mzml.data.MzMLScanList
-
Getter for the field scans.
- getScans() - Method in class io.github.msdk.io.mzxml.MzXMLRawDataFile
-
Returns an immutable list of all scans.
- getScans(RawDataFile, String) - Static method in class io.github.msdk.util.RawDataFileUtil
-
getScans.
- getScans(RawDataFile, Range<Float>) - Static method in class io.github.msdk.util.RawDataFileUtil
-
getScans.
- getScans(RawDataFile, String, Range<Float>) - Static method in class io.github.msdk.util.RawDataFileUtil
-
getScans.
- getScanWindowList() - Method in class fr.profi.mzdb.db.model.params.ScanParamTree
-
- getScanWindowList() - Method in class io.github.msdk.io.mzml.data.MzMLScan
-
Getter for the field scanWindowList.
- getScanWindows() - Method in class io.github.msdk.io.mzml.data.MzMLScanWindowList
-
Getter for the field scanWindows.
- getScore() - Method in interface io.github.msdk.datamodel.Feature
-
Returns arbitrary, dimension-less quality score for the feature
- getScore() - Method in class io.github.msdk.datamodel.SimpleFeature
-
Returns arbitrary, dimension-less quality score for the feature
- getSecond() - Method in class io.github.msdk.io.chromatof.Pair
-
getSecond.
- getSelectedIonList() - Method in class fr.profi.mzdb.db.model.params.Precursor
-
- getSelectedIonList() - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorElement
-
Getter for the field selectedIonList.
- getSelectedIonList() - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorSelectedIonList
-
Getter for the field selectedIonList.
- getSelectedIons() - Method in class fr.profi.mzdb.db.model.params.SelectedIonList
-
- getSeparationType() - Method in interface io.github.msdk.datamodel.Chromatogram
-
Returns the separation type used for separation of molecules.
- getSeparationType() - Method in class io.github.msdk.datamodel.SimpleChromatogram
-
Returns the separation type used for separation of molecules.
- getSiriusScore() - Method in class io.github.msdk.id.sirius.SiriusIonAnnotation
-
- getSizeOfRawDataFile() - Method in class io.github.msdk.featuredetection.adap3d.algorithms.SliceSparseMatrix
-
This method returns size of raw data file in terms of total scans.
- getSMILES() - Method in class io.github.msdk.id.sirius.SiriusIonAnnotation
-
- getSNRatio() - Method in interface io.github.msdk.datamodel.Feature
-
Returns signal to noise ratio.
- getSNRatio() - Method in class io.github.msdk.datamodel.SimpleFeature
-
Returns signal to noise ratio.
- getSoftware(int) - Method in class fr.profi.mzdb.io.reader.table.SoftwareReader
-
Gets the software.
- getSoftwareId() - Method in class fr.profi.mzdb.db.model.InstrumentConfiguration
-
Gets the software id.
- getSoftwareList() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getSoftwareList() - Method in class fr.profi.mzdb.io.reader.table.SoftwareReader
-
- getSoftwareList() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getSoftwareList() - Method in class fr.profi.mzdb.MzDbReader
-
- getSourceFile(int) - Method in class fr.profi.mzdb.io.reader.table.SourceFileReader
-
- getSourceFileList() - Method in class fr.profi.mzdb.io.reader.table.SourceFileReader
-
- getSourceFiles() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getSourceFiles() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getSourceFiles() - Method in class fr.profi.mzdb.MzDbReader
-
- getSourceInducedFragmentation() - Method in interface io.github.msdk.datamodel.MsScan
-
Returns the fragmentation parameters of ion source-induced fragmentation, or null if no such
information is known.
- getSourceInducedFragmentation() - Method in class io.github.msdk.datamodel.SimpleMsScan
-
Returns the fragmentation parameters of ion source-induced fragmentation, or null if no such
information is known.
- getSourceInducedFragmentation() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the fragmentation parameters of ion source-induced fragmentation, or null if no such
information is known.
- getSpectraCount() - Method in class fr.profi.mzdb.io.reader.bb.BytesReader
-
- getSpectraCount() - Method in interface fr.profi.mzdb.io.reader.bb.IBlobReader
-
- getSpectraCount() - Method in class fr.profi.mzdb.io.reader.bb.SQLiteBlobReader
-
- getSpectraCount() - Method in class fr.profi.mzdb.io.reader.bb.StreamReader
-
- getSpectraCount(SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the spectra count.
- getSpectraCount(int, SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the spectra count for a given MS level.
- getSpectraCount() - Method in class fr.profi.mzdb.model.BoundingBox
-
Spectra count.
- getSpectraCount() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the spectrum count.
- getSpectraCount(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the spectrum count.
- getSpectraCount() - Method in class fr.profi.mzdb.MzDbReader
-
Gets the spectrum count.
- getSpectraCount(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the spectrum count.
- getSpectraRef() - Method in interface io.github.msdk.datamodel.IonAnnotation
-
getSpectraRef
- getSpectraRef() - Method in class io.github.msdk.datamodel.SimpleIonAnnotation
-
getSpectraRef
- getSpectrum(long, SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
Gets the spectrum.
- getSpectrum(long) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the spectrum.
- getSpectrum(long) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the spectrum.
- getSpectrumData(long, SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
Gets the spectrum data.
- getSpectrumData(long) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the spectrum data.
- getSpectrumData(long) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the spectrum data.
- getSpectrumDataEncoding(long, SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractDataEncodingReader
-
Gets the spectrum data encoding.
- getSpectrumDataEncoding(long) - Method in class fr.profi.mzdb.io.reader.cache.DataEncodingAsyncReader
-
Gets the spectrum data encoding.
- getSpectrumDataEncoding(long) - Method in class fr.profi.mzdb.io.reader.cache.DataEncodingReader
-
Gets the spectrum data encoding.
- getSpectrumDataEncoding(long) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the spectrum data encoding.
- getSpectrumDataEncoding(long) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the spectrum data encoding.
- getSpectrumHeader(long, SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader
-
/** Gets the spectrum header.
- getSpectrumHeader(long) - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderAsyncReader
-
/**
Gets the spectrum header.
- getSpectrumHeader(long) - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderReader
-
/**
Gets the spectrum header.
- getSpectrumHeader() - Method in class fr.profi.mzdb.model.Peak
-
Gets the SpectrumHeader.
- getSpectrumHeader(long) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the spectrum header.
- getSpectrumHeader(long) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the spectrum header.
- getSpectrumHeaderById(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader
-
Gets the spectrum headers by id.
- getSpectrumHeaderById() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderAsyncReader
-
Gets the spectrum headers by id.
- getSpectrumHeaderById() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderReader
-
Gets the spectrum headers by id.
- getSpectrumHeaderById() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets each spectrum header mapped by its id.
- getSpectrumHeaderById() - Method in class fr.profi.mzdb.MzDbReader
-
Gets each spectrum header mapped by its id.
- getSpectrumHeaderForTime(float, int, SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader
-
Gets the spectrum header for time.
- getSpectrumHeaderForTime(float, int) - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderAsyncReader
-
Gets the spectrum header for time.
- getSpectrumHeaderForTime(float, int) - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderReader
-
Gets the spectrum header for time.
- getSpectrumHeaderForTime(float, int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the spectrum header for time.
- getSpectrumHeaderForTime(float, int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the spectrum header for time.
- getSpectrumHeaderReader() - Method in class fr.profi.mzdb.AbstractMzDbReader
-
- getSpectrumHeaderReader() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getSpectrumHeaderReader() - Method in class fr.profi.mzdb.MzDbReader
-
- getSpectrumHeaders(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader
-
Gets the spectrum headers.
- getSpectrumHeaders() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderAsyncReader
-
Gets the spectrum headers.
- getSpectrumHeaders() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderReader
-
Gets the spectrum headers.
- getSpectrumHeaders() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets all spectrum headers.
- getSpectrumHeaders() - Method in class fr.profi.mzdb.MzDbReader
-
Gets all spectrum headers.
- getSpectrumId() - Method in interface fr.profi.mzdb.model.ILcContext
-
Gets the spectrum id.
- getSpectrumId() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
- getSpectrumId() - Method in class fr.profi.mzdb.model.SpectrumSlice
-
Gets the spectrum id.
- getSpectrumIdAt(int) - Method in class fr.profi.mzdb.io.reader.bb.BytesReader
-
- getSpectrumIdAt(int) - Method in interface fr.profi.mzdb.io.reader.bb.IBlobReader
-
- getSpectrumIdAt(int) - Method in class fr.profi.mzdb.io.reader.bb.SQLiteBlobReader
-
- getSpectrumIdAt(int) - Method in class fr.profi.mzdb.io.reader.bb.StreamReader
-
- getSpectrumIdsForTimeRange(float, float, int, SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader
-
Gets the spectrum ids for time range.
- getSpectrumIdsForTimeRange(float, float, int) - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderAsyncReader
-
Gets the spectrum ids for time range.
- getSpectrumIdsForTimeRange(float, float, int) - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderReader
-
Gets the spectrum ids for time range.
- getSpectrumIterator() - Method in class fr.profi.mzdb.MzDbReader
-
- getSpectrumIterator(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the ms spectrum iterator.
- getSpectrumPeaks(int, SQLiteConnection) - Method in class fr.profi.mzdb.AbstractMzDbReader
-
Gets the spectrum peaks.
- getSpectrumPeaks(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the spectrum peaks.
- getSpectrumPeaks(int) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the spectrum peaks.
- getSpectrumRef() - Method in class fr.profi.mzdb.db.model.params.Precursor
-
- getSpectrumRef() - Method in class io.github.msdk.io.mzml.data.MzMLPrecursorElement
-
Getter for the field spectrumRef.
- getSpectrumSliceList() - Method in class fr.profi.mzdb.model.RunSliceData
-
Gets the spectrum slice list.
- getSpectrumSlicesInRanges(double, double, float, float, File, MzDbEntityCache, Callback<SpectrumSlice[]>) - Static method in class fr.profi.mzdb.MzDbReaderHelper
-
get an async
- getSpectrumStream() - Method in class fr.profi.mzdb.MzDbAsyncReader
-
- getSpectrumStream(int) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the ms spectrum iterator.
- getSpectrumTimeById(SQLiteConnection) - Method in class fr.profi.mzdb.io.reader.cache.AbstractSpectrumHeaderReader
-
Gets the spectrum time by id.
- getSpectrumTimeById() - Method in class fr.profi.mzdb.io.reader.cache.MzDbEntityCache
-
- getSpectrumTimeById() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderAsyncReader
-
Gets the spectrum time by id.
- getSpectrumTimeById() - Method in class fr.profi.mzdb.io.reader.cache.SpectrumHeaderReader
-
Gets the spectrum time by id.
- getSpectrumType() - Method in class io.github.msdk.datamodel.AbstractMsSpectrum
-
Returns the type of this mass spectrum.
- getSpectrumType() - Method in interface io.github.msdk.datamodel.MsSpectrum
-
Returns the type of this mass spectrum.
- getSpectrumType() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the type of this mass spectrum.
- getSpectrumType() - Method in class io.github.msdk.io.netcdf.NetCDFMsScan
-
Returns the type of this mass spectrum.
- getSpectrumType() - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorMsSpectrum
-
Returns the type of this mass spectrum.
- getSQLiteJob() - Method in class fr.profi.mzdb.util.sqlite.SQLiteJobWrapper
-
- getSQLiteJobWrapper() - Method in class fr.profi.mzdb.util.sqlite.SQLiteObservableJob
-
- getStartMass() - Method in interface io.github.msdk.spectra.peakinvestigator.providers.PeakInvestigatorOptionsProvider
-
getStartMass.
- getStartTimestamp() - Method in class fr.profi.mzdb.db.model.Run
-
Gets the location.
- getStatement() - Method in class fr.profi.mzdb.io.reader.iterator.AbstractSpectrumSliceIterator
-
- getStatement() - Method in class fr.profi.mzdb.util.sqlite.SQLiteQuery
-
- getStatement() - Method in class fr.profi.mzdb.util.sqlite.SQLiteRecord
-
- getTableRecordsCount(String, SQLiteConnection) - Static method in class fr.profi.mzdb.io.reader.MzDbReaderQueries
-
Gets the table records count.
- getTableRecordsCount(String) - Method in class fr.profi.mzdb.MzDbAsyncReader
-
Gets the table records count.
- getTableRecordsCount(String) - Method in class fr.profi.mzdb.MzDbReader
-
Gets the table records count.
- getTailingFactor(float[], float[], Integer) - Static method in class io.github.msdk.util.ChromatogramUtil
-
Returns the tailing factor of this feature.
- getTargets() - Method in class fr.profi.mzdb.db.model.params.thermo.ThermoScanMetaData
-
- getText() - Method in class fr.profi.mzdb.db.model.params.param.UserText
-
- getThermoMetaData() - Method in class fr.profi.mzdb.db.model.params.ScanParamTree
-
- getTIC() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
- getTIC() - Method in class io.github.msdk.datamodel.AbstractMsSpectrum
-
getTIC.
- getTIC() - Method in interface io.github.msdk.datamodel.MsSpectrum
-
Returns the sum of intensities of all data points (total ion current or TIC).
- getTIC() - Method in class io.github.msdk.io.mzml.data.MzMLMsScan
-
Returns the sum of intensities of all data points (total ion current or TIC).
- getTIC() - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorMsSpectrum
-
Returns the sum of intensities of all data points (total ion current or TIC).
- getTIC(float[], Integer) - Static method in class io.github.msdk.util.MsSpectrumUtil
-
Calculates the total ion current (=sum of all intensity values)
- getTIC(double[], float[], Integer, Range<Double>) - Static method in class io.github.msdk.util.MsSpectrumUtil
-
Calculates the total ion current (=sum of all intensity values)
- getTime() - Method in class fr.profi.mzdb.model.SpectrumHeader
-
Gets the time.
- getTitle() - Method in class io.github.msdk.io.mgf.MgfMsSpectrum
-
Getter of the MgfMsSpectrum title
- getTolerance() - Method in class io.github.msdk.util.tolerances.RTTolerance
-
getTolerance.
- getToleranceRange(Double) - Method in class io.github.msdk.spectra.peakinvestigator.PeakInvestigatorMsSpectrum
-
getToleranceRange.
- getToleranceRange(Double) - Method in class io.github.msdk.util.tolerances.ConstantDaTolerance
-
Get a m/z tolerance range for a given m/z.
- getToleranceRange(Double) - Method in class io.github.msdk.util.tolerances.ConstantPpmTolerance
-
Get a m/z tolerance range for a given m/z.
- getToleranceRange(Double) - Method in class io.github.msdk.util.tolerances.MaximumMzTolerance
-
Get a m/z tolerance range for a given m/z.
- getToleranceRange(Double) - Method in interface io.github.msdk.util.tolerances.MzTolerance
-
Get a m/z tolerance range for a given m/z.
- getToleranceRange(float) - Method in class io.github.msdk.util.tolerances.RTTolerance
-
getToleranceRange.
- getType() - Method in class fr.profi.mzdb.db.model.params.param.UserParam
-
- getType() - Method in class fr.profi.mzdb.db.model.params.param.UserText
-
- getUnitAccession() - Method in class fr.profi.mzdb.db.model.params.param.CVParam
-
- getUnitAccession() - Method in class io.github.msdk.io.mzml.data.MzMLCVParam
-
Getter for the field unitAccession.
- getUnitCvRef() - Method in class fr.profi.mzdb.db.model.params.param.CVParam
-
- getUnitName() - Method in class fr.profi.mzdb.db.model.params.param.CVParam
-
- getUsername() - Method in interface io.github.msdk.spectra.peakinvestigator.providers.PeakInvestigatorProjectProvider
-
getUsername.
- getUserParam(String) - Method in class fr.profi.mzdb.db.model.AbstractTableModel
-
- getUserParam(String) - Method in class fr.profi.mzdb.db.model.params.AbstractParamTree
-
- getUserParam(String) - Method in interface fr.profi.mzdb.db.model.params.IParamContainer
-
Gets the user param.
- getUserParamName() - Method in enum fr.profi.mzdb.io.writer.mgf.PrecursorMzComputationEnum
-
- getUserParams() - Method in class fr.profi.mzdb.db.model.AbstractTableModel
-
- getUserParams() - Method in class fr.profi.mzdb.db.model.params.AbstractParamTree
-
- getUserParams() - Method in interface fr.profi.mzdb.db.model.params.IParamContainer
-
Gets the user params.
- getUserParams() - Method in class fr.profi.mzdb.db.model.params.ParamTree
-
- getUserTexts() - Method in class fr.profi.mzdb.db.model.AbstractTableModel
-
- getUserTexts() - Method in class fr.profi.mzdb.db.model.params.AbstractParamTree
-
- getUserTexts() - Method in interface fr.profi.mzdb.db.model.params.IParamContainer
-
Gets the user texts.
- getUserTexts() - Method in class fr.profi.mzdb.db.model.params.ParamTree
-
- getValue() - Method in class fr.profi.mzdb.db.model.params.param.CVParam
-
- getValue() - Method in class fr.profi.mzdb.db.model.params.param.UserParam
-
- getValue() - Method in enum fr.profi.mzdb.db.table.BoundingBoxMsnRtreeTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.BoundingBoxRtreeTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.BoundingBoxTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.ChromatogramTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.ControlledVocabularyTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.CvTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.DataEncodingTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.DataProcessingTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.InstrumentConfigurationTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.MzdbTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.ParamTreeSchemaTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.ProcessingMethodTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.RunSliceTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.RunTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.SampleTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.ScanSettingsTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.SharedParamTreeTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.SoftwareTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.SourceFileScanSettingsMapTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.SourceFileTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.SpectrumTable
-
- getValue() - Method in enum fr.profi.mzdb.db.table.TableParamTreeSchemaTable
-
- getValue() - Method in enum fr.profi.mzdb.model.DataMode
-
Gets the value.
- getValue() - Method in enum fr.profi.mzdb.model.PeakEncoding
-
- getValue(int) - Method in class io.github.msdk.featuredetection.adap3d.algorithms.BiGaussian
-
This method is used calculating BiGaussian values for EIC.
- getValue() - Method in enum io.github.msdk.io.mzml.data.MzMLBitLength
-
getValue.
- getValue() - Method in class io.github.msdk.io.mzml.data.MzMLCVParam
-
Getter for the field value.
- getValueForName(ChromaTofParser.ColumnName) - Method in class io.github.msdk.io.chromatof.TableRow
-
getValueForName.
- getVersion() - Method in class fr.profi.mzdb.db.model.MzDbHeader
-
- getVersion() - Method in class fr.profi.mzdb.db.model.Software
-
Gets the version.
- getVersion() - Method in interface io.github.msdk.spectra.peakinvestigator.providers.PeakInvestigatorOptionsProvider
-
getVersion.
- getVerticalSlice(int) - Method in class io.github.msdk.featuredetection.adap3d.algorithms.SliceSparseMatrix
-
This method returns the List of type VerticalSliceDataPoint for given Scan Number.
- getX() - Method in class fr.profi.mzdb.model.DataPoint
-
Gets the x.
- getXMLReaderInstance() - Static method in class fr.profi.mzdb.util.jaxb.XercesSAXParser
-
- getY() - Method in class fr.profi.mzdb.model.DataPoint
-
Gets the y.
- GoodPeakInfo() - Constructor for class io.github.msdk.featuredetection.adap3d.algorithms.ADAP3DPeakDetectionAlgorithm.GoodPeakInfo
-
- GridMassMethod - Class in io.github.msdk.featuredetection.gridmass
-
GridMassMethod class.
- GridMassMethod(RawDataFile, List<MsScan>, MzTolerance, Double, Double, Double, Double, Double, Double, Double, Double, Double) - Constructor for class io.github.msdk.featuredetection.gridmass.GridMassMethod
-
Constructor for GridMassMethod.
- GroupedFeature - Interface in io.github.msdk.datamodel
-
A grouped MS feature that consists of several individual features (m/z and RT pairs).
- value - Variable in class fr.profi.mzdb.db.model.params.param.CVParam
-
- value - Variable in class fr.profi.mzdb.db.model.params.param.UserParam
-
- value - Variable in class fr.profi.mzdb.util.primitives.MutableInt
-
- valueOf(String) - Static method in enum fr.profi.mzdb.db.model.params.param.CVEntry
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.BoundingBoxMsnRtreeTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.BoundingBoxRtreeTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.BoundingBoxTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.ChromatogramTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.ControlledVocabularyTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.CvTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.DataEncodingTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.DataProcessingTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.InstrumentConfigurationTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.MzdbTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.ParamTreeSchemaTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.ProcessingMethodTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.RunSliceTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.RunTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.SampleTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.ScanSettingsTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.SharedParamTreeTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.SoftwareTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.SourceFileScanSettingsMapTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.SourceFileTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.SpectrumTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.db.table.TableParamTreeSchemaTable
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.io.writer.mgf.MgfField
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.io.writer.mgf.PrecursorMzComputationEnum
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.model.AcquisitionMode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.model.DataMode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.model.PeakEncoding
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum fr.profi.mzdb.XicMethod
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.datamodel.ActivationType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.datamodel.ChromatogramType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.datamodel.FileType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.datamodel.MsScanType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.datamodel.MsSpectrumType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.datamodel.PolarityType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.datamodel.SeparationType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.io.chromatof.ChromaTofParser.ColumnName
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.io.chromatof.ChromaTofParser.Mode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.io.mzml.data.MzMLArrayType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.io.mzml.data.MzMLBitLength
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.io.mzml.data.MzMLCompressionType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.normalization.compound.NormalizationType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.spectra.peakinvestigator.providers.PeakInvestigatorProvider.Status
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.util.ChromatogramUtil.CalculationMethod
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.util.DataPointSorter.SortingDirection
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum io.github.msdk.util.DataPointSorter.SortingProperty
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum fr.profi.mzdb.db.model.params.param.CVEntry
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.BoundingBoxMsnRtreeTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.BoundingBoxRtreeTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.BoundingBoxTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.ChromatogramTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.ControlledVocabularyTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.CvTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.DataEncodingTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.DataProcessingTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.InstrumentConfigurationTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.MzdbTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.ParamTreeSchemaTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.ProcessingMethodTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.RunSliceTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.RunTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.SampleTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.ScanSettingsTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.SharedParamTreeTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.SoftwareTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.SourceFileScanSettingsMapTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.SourceFileTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.SpectrumTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.db.table.TableParamTreeSchemaTable
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.io.writer.mgf.MgfField
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.io.writer.mgf.PrecursorMzComputationEnum
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.model.AcquisitionMode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.model.DataMode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.model.PeakEncoding
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum fr.profi.mzdb.XicMethod
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.datamodel.ActivationType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.datamodel.ChromatogramType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.datamodel.FileType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.datamodel.MsScanType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.datamodel.MsSpectrumType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.datamodel.PolarityType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.datamodel.SeparationType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.io.chromatof.ChromaTofParser.ColumnName
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.io.chromatof.ChromaTofParser.Mode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.io.mzml.data.MzMLArrayType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.io.mzml.data.MzMLBitLength
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.io.mzml.data.MzMLCompressionType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.normalization.compound.NormalizationType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.spectra.peakinvestigator.providers.PeakInvestigatorProvider.Status
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.util.ChromatogramUtil.CalculationMethod
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.util.DataPointSorter.SortingDirection
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum io.github.msdk.util.DataPointSorter.SortingProperty
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- version - Variable in class fr.profi.mzdb.db.model.MzDbHeader
-
The version.
- version - Variable in class fr.profi.mzdb.db.model.Software
-
The version.
- VerticalSliceDataPoint() - Constructor for class io.github.msdk.featuredetection.adap3d.algorithms.SliceSparseMatrix.VerticalSliceDataPoint
-