A B C D E F G H I J K L M N O P Q R S T U V W Z

G

gammaln(double) - Static method in class peakml.math.Statistical

The gamma function interpolates the factorial function.

geomean(double[]) - Static method in class peakml.math.Statistical

The geometric mean, in mathematics, is a type of mean or average, which indicates the central tendency or typical value of a set of numbers.

get(int) - Method in class peakml.IPeakSet

Returns the peak at the given position.

get(double) - Method in class peakml.math.BinArray

get(int, int) - Method in class peakml.math.DataFrame.Double

Returns the value at the given row and column.

get(String, int) - Method in class peakml.math.DataFrame.Double

Returns the value at the given row and column.

get(int, String) - Method in class peakml.math.DataFrame.Double

Returns the value at the given row and column.

get(String, String) - Method in class peakml.math.DataFrame.Double

Returns the value at the given row and column.

getAbundance() - Method in class peakml.chemistry.PeriodicTable.Element

Returns the abundance (in percentage) at which the most abundant isotope occurs naturally.

getAbundance(int) - Method in class peakml.chemistry.PeriodicTable.Element

Returns the natural abundance of the isotope at the given index.

getAccurateMass() - Method in class peakml.io.dac.DACExScanStats

getAccurateMass() - Method in class peakml.io.dac.DACScanStats

getAccurateMassFlags() - Method in class peakml.io.dac.DACExScanStats

getAccVoltage() - Method in class peakml.io.dac.DACExScanStats

getAcquDate() - Method in class peakml.io.dac.DACHeader

getAcquisitionFile() - Method in class peakml.io.dac.DACCalibrationInfo.DynamicParams

getAcquisitionFile() - Method in class peakml.io.dac.DACCalibrationInfo.FastParams

getAcquisitionFile() - Method in class peakml.io.dac.DACCalibrationInfo.StaticParams

getAcquName() - Method in class peakml.io.dac.DACHeader

getAcquTime() - Method in class peakml.io.dac.DACHeader

getAllMeasurementIDs() - Method in class peakml.io.SetInfo

Returns a list of all the measurement id's associated with this set (including all the child sets).

getAllPeaks() - Method in class peakml.ChromatographyMS

This method makes a collection of all the peaks in this class.

getAnalogOffset() - Method in class peakml.io.dac.DACHeader

getAnnotation(String) - Method in class peakml.Annotatable

Returns the annotation with the given name, stored in this peak.

getAnnotation(int, String) - Method in class peakml.util.rjava.Project

getAnnotationLabels(int) - Method in class peakml.util.rjava.Project

getAnnotations() - Method in class peakml.Annotatable

Returns the hashmap containing all the annotations.

getApplicationInfo(int) - Method in class peakml.io.Header

Returns the application information with the given id.

getApplicationInfos() - Method in class peakml.io.Header

Returns the vector with all the application information instances.

getAtomicMass() - Method in class peakml.chemistry.PeriodicTable.Element

Returns the atomic mass of the most abundant isotope.

getAtomicMass(int) - Method in class peakml.chemistry.PeriodicTable.Element

Returns the atomic mass of the given isotope.

getAutosamplerType() - Method in class peakml.io.dac.DACHeader

getBaseline() - Method in class peakml.io.xrawfile.IXRawfile.Label

Returns the baseline.

getBaseline() - Method in class peakml.io.xrawfile.IXRawfile.Noise

Returns the detected baseline for this mass.

getBasePeakIntensity() - Method in class peakml.io.xrawfile.IXRawfile.ScanHeaderInfo

Returns the intensity of the most intense peak.

getBasePeakMass() - Method in class peakml.io.xrawfile.IXRawfile.ScanHeaderInfo

Returns the mass of the most intense peak.

getBestPeakOnMass(Vector<IPeak>, double) - Static method in class peakml.IPeak

Locates the closest matching peak on the given mass from the list of peaks.

getBestPeakOnRT(Vector<IPeak>, double) - Static method in class peakml.IPeak

Locates the closest matching peak on the given retention time from the list of peaks.

getBottleNumber() - Method in class peakml.io.dac.DACHeader

getBPI() - Method in class peakml.io.dac.DACScanStats

getBPM() - Method in class peakml.io.dac.DACScanStats

getCalDate() - Method in class peakml.io.dac.DACCalibrationInfo

getCalFunctions() - Method in class peakml.io.dac.DACCalibrationInfo

getCalibrated() - Method in class peakml.io.dac.DACScanStats

getCalTime() - Method in class peakml.io.dac.DACCalibrationInfo

getCategoriesForAxis(CategoryAxis) - Method in class peakml.util.jfreechart.FastErrorBarPlot

getCharge() - Method in class peakml.chemistry.MolecularFormula

Returns the charge on the molecule.

getCharge() - Method in class peakml.chemistry.MolecularFormula.SubFormula

getCharge() - Method in class peakml.chemistry.PeriodicTable.Derivative

Returns the charge needed for the basepeak of the adduct.

getCharge() - Method in class peakml.io.xrawfile.IXRawfile.Label

Returns the detected charge.

getChargeState() - Method in class peakml.io.xrawfile.IXRawfile.PrecursorInfo

Returns the charge state as determined by the instrument firmware.

getChart() - Method in class peakml.util.swt.widget.IPeakGraph

getChart() - Method in class peakml.util.swt.widget.TimePlot

getChild(int) - Method in class peakml.io.SetInfo

Returns the child at the given index.

getChildren() - Method in class peakml.io.SetInfo

Returns the list with all the children.

getCoarseLaserControl() - Method in class peakml.io.dac.DACExScanStats

getCoefficients() - Method in class peakml.io.dac.DACCalibrationInfo.StaticFunction

getCoFactors() - Method in class peakml.chemistry.Protein

getCol(String) - Method in class peakml.math.DataFrame.Double

Returns the complete column with the given name.

getCol(int) - Method in class peakml.math.DataFrame.Double

Returns the complete column with the given name.

getColIndexOf(String) - Method in class peakml.math.DataFrame

Returns the index of the column with the given name.

getCollisionEnergy() - Method in class peakml.io.dac.DACExScanStats

getCollisionRF() - Method in class peakml.io.dac.DACExScanStats

getColName(int) - Method in class peakml.math.DataFrame

Returns the name of the column at the given index.

getColNames() - Method in class peakml.math.DataFrame

Returns a list with all the column-names.

getColor(int) - Method in class peakml.graphics.Colormap

Returns an integer representation of the color at the given index.

getConditions() - Method in class peakml.io.dac.DACHeader

getContainerClass() - Method in class peakml.IPeakSet

Returns the type of peaks stored in the peakset.

getContinuum() - Method in class peakml.io.dac.DACScanStats

getControllerNumber() - Method in class peakml.io.xrawfile.IXRawfile.Controller

Returns the controller number.

getControllerType() - Method in class peakml.io.xrawfile.IXRawfile.Controller

Returns the controller type.

getControllerType(int) - Method in class peakml.io.xrawfile.IXRawfile

Returns the type of the device controller registered at the specified index position in the raw file.

getCounterElectrodeVoltage() - Method in class peakml.io.dac.DACExScanStats

getCreationDate() - Method in class peakml.io.xrawfile.IXRawfile

Returns the file creation date in DATE format.

getCreatorID() - Method in class peakml.io.xrawfile.IXRawfile

Returns the creator ID.

getCurrentController() - Method in class peakml.io.xrawfile.IXRawfile

Gets the current controller type and number for the raw file.

getDatabaseID() - Method in class peakml.chemistry.Molecule

Returns the unique id of the molecule.

getDataFormat() - Method in class peakml.io.dac.DACExperimentInfo.ExFunctionInfo

getDate() - Method in class peakml.io.ApplicationInfo

Returns the date of running the application.

getDate() - Method in class peakml.io.Header

Returns the date at which the file was created.

getDateAsString() - Method in class peakml.io.Header

Returns the date at which the file was created in string format.

getDefaultN() - Method in class peakml.chemistry.MolecularFormula.SubFormula

getDefaultNamespace() - Method in class peakml.io.Vocabulary

Returns the default namespace of this vocabulary.

getDescription() - Method in class peakml.chemistry.Molecule

Returns the optional description for the molecule.

getDescription() - Method in class peakml.io.Header

Returns an optional description for the information stored in the file.

getDwellTime() - Method in class peakml.io.dac.DACCalibrationInfo.StaticParams

getElement(String) - Static method in class peakml.chemistry.PeriodicTable

Returns the element with the given identifier (e.g.

getEncrypted() - Method in class peakml.io.dac.DACHeader

getEndRT() - Method in class peakml.io.dac.DACFunctionInfo

getEndTime() - Method in class peakml.ChromatographyMS

getEndTime() - Method in class peakml.io.xrawfile.IXRawfile

Gets the start time of the last scan or reading for the current controller.

getEntrance() - Method in class peakml.io.dac.DACExScanStats

getErrorLogItem(int) - Method in class peakml.io.xrawfile.IXRawfile

Returns the specified error log item information and the retention time at which the error occurred.

getErrorMessage() - Method in class peakml.io.xrawfile.IXRawfile

Returns the last error message that was recorded by the Thermo OLE DLL.

getException() - Method in class peakml.io.xrawfile.IXRawfile.Label

Whether the peak was an exception (?).

getExFunctionInfo(int) - Method in class peakml.io.dac.DACExperimentInfo

getExFunctionInfos() - Method in class peakml.io.dac.DACExperimentInfo

getExperimentText() - Method in class peakml.io.dac.DACExperimentInfo

Returns the free-text experiment text.

getFactory() - Method in class peakml.PeakData

Returns the factory for the Peak type associated to this container.

getFaimsCV() - Method in class peakml.io.dac.DACExScanStats

getFastTimePlot() - Method in class peakml.util.swt.widget.TimePlot

getFileInfo(int) - Method in class peakml.io.MeasurementInfo

Returns the file info instance at the given index.

getFileInfos() - Method in class peakml.io.MeasurementInfo

Returns all the file info instances maintained in this class.

getFileName() - Method in class peakml.io.xrawfile.IXRawfile

Returns the fully qualified path name of an open raw file.

getFileNames() - Method in class peakml.util.rjava.Project

getFilterForScanNum(int) - Method in class peakml.io.xrawfile.IXRawfile

Returns the closest matching run time that corresponds to nScanNumber for the current controller.

getFilterForScanRT(double) - Method in class peakml.io.xrawfile.IXRawfile

Returns the closest matching run time that corresponds to nScanNumber for the current controller.

getFilters() - Method in class peakml.io.xrawfile.IXRawfile

Returns the list of unique scan filters for the raw file.

getFineLaserControl() - Method in class peakml.io.dac.DACExScanStats

getFirstSpectrumNumber() - Method in class peakml.io.xrawfile.IXRawfile

Gets the first scan or reading number for the current controller.

getFocus() - Method in class peakml.io.dac.DACExScanStats

getFormula() - Method in class peakml.chemistry.Molecule

Returns the molecular formula of the molecule.

getFragmented() - Method in class peakml.io.xrawfile.IXRawfile.Label

Whether the peak was fragmented.

getFrequency() - Method in class peakml.io.xrawfile.IXRawfile.ScanHeaderInfo

Returns the frequency for this scan.

getFunctionSetMass() - Method in class peakml.io.dac.DACFunctionInfo

getFunctionType() - Method in class peakml.io.dac.DACCalibrationInfo.StaticFunction

getFunctionType() - Method in class peakml.io.dac.DACFunctionInfo

getGasName() - Method in class peakml.io.dac.DACHeader

getGeneID() - Method in class peakml.chemistry.Protein

getGraph() - Method in class peakml.util.swt.widget.IntensityTrendGraph

getGraphImage(int, int) - Method in class peakml.util.swt.widget.IntensityTrendGraph

getGraphImage(int, int) - Method in class peakml.util.swt.widget.IPeakGraph

getGraphImage(int, int) - Method in class peakml.util.swt.widget.TimePlot

getGroupAnnotation(int, String) - Method in class peakml.util.rjava.Project

getGroupAnnotationLabels(int) - Method in class peakml.util.rjava.Project

getGuard() - Method in class peakml.io.dac.DACExScanStats

getHeader() - Method in class peakml.io.ParseResult

Returns the header instance.

getHeaderAnnotation(String) - Method in class peakml.util.rjava.Project

getHighMass() - Method in class peakml.io.dac.DACCalibrationInfo.DynamicParams

getHighMass() - Method in class peakml.io.dac.DACCalibrationInfo.FastParams

getHighMass() - Method in class peakml.io.dac.DACCalibrationInfo.StaticParams

getHighMass() - Method in class peakml.io.xrawfile.IXRawfile

Gets the highest mass or wavelength recorded for the current controller.

getHighMass() - Method in class peakml.io.xrawfile.IXRawfile.ScanHeaderInfo

Returns the highest detected mass of the scan.

getHighMassResolution() - Method in class peakml.io.dac.DACCalibrationInfo.DynamicParams

getHighMassResolution() - Method in class peakml.io.dac.DACCalibrationInfo.FastParams

getHighMassResolution() - Method in class peakml.io.dac.DACCalibrationInfo.StaticParams

getHiMass() - Method in class peakml.io.dac.DACScanStats

getHMResolution() - Method in class peakml.io.dac.DACExScanStats

getID() - Method in class peakml.chemistry.PeriodicTable.Element

Returns the index of the element in the table PeriodicTable.elements.

getID() - Method in class peakml.chemistry.Protein

getID() - Method in class peakml.io.MeasurementInfo

Returns the id of the measurement.

getID() - Method in class peakml.io.SampleInfo

Returns the id of the sample.

getID() - Method in class peakml.io.SetInfo

Returns the id of this set.

getIdentifier() - Method in class peakml.chemistry.PeriodicTable.Element

Returns the id (e.g.

getInChi() - Method in class peakml.chemistry.Molecule

Returns the InChi string describing the molecular structure of the molecule.

getIndex(int) - Method in class peakml.math.BinArray

getIndexLabel(int) - Method in class peakml.math.BinArray

getIndexMax(int) - Method in class peakml.math.BinArray

getIndexMin(int) - Method in class peakml.math.BinArray

getIndexOfMass(double) - Method in class peakml.PeakData

...

getIndexTableAscendingIntensity() - Method in class peakml.PeakData

getIndexTableAscendingMass() - Method in class peakml.PeakData

getIndicesInMassRange(double, double) - Method in class peakml.PeakData

getInhibitors() - Method in class peakml.chemistry.Protein

getInletID() - Method in class peakml.io.xrawfile.IXRawfile

Gets the inlet ID number for the current controller.

getInstChannelLabel(int) - Method in class peakml.io.xrawfile.IXRawfile

Returns the channel label, if available, at the specified index for the current controller.

getInstFlags() - Method in class peakml.io.xrawfile.IXRawfile

Returns the experiment flags, if available, for the current controller.

getInstHardwareVersion() - Method in class peakml.io.xrawfile.IXRawfile

Returns the current controller hardware or firmware revision information, if available.

GetInstMethod(int) - Method in class peakml.io.xrawfile.IXRawfile

Returns the channel label, if available, at the specified index for the current controller.

getInstModel() - Method in class peakml.io.xrawfile.IXRawfile

Returns the instrument model, if available, for the current controller.

getInstName() - Method in class peakml.io.xrawfile.IXRawfile

Returns the instrument name, if available, for the current controller.

getInstNumChannelLabels() - Method in class peakml.io.xrawfile.IXRawfile

Returns the number of channel labels specified for the current controller.

getInstrument() - Method in class peakml.io.dac.DACHeader

getInstrumentID() - Method in class peakml.io.xrawfile.IXRawfile

Gets the instrument ID number for the current controller.

getInstrumentType() - Method in class peakml.io.dac.DACHeader

getInstSerialNumber() - Method in class peakml.io.xrawfile.IXRawfile

Returns the serial number, if available, for the current controller.

getInstSoftwareVersion() - Method in class peakml.io.xrawfile.IXRawfile

Returns the current controller software revision information, if available.

getIntensities() - Method in class peakml.io.dac.DACSpectrum

getIntensities() - Method in class peakml.PeakData

Returns all the intensities stored in this container.

getIntensities(int) - Method in class peakml.util.rjava.Project

getIntensity() - Method in class peakml.BackgroundIon

getIntensity() - Method in class peakml.Centroid

getIntensity() - Method in class peakml.io.xrawfile.IXRawfile.Label

Returns the intensity.

getIntensity() - Method in class peakml.IPeak

Retrieves the measured intensity for this peak.

getIntensity() - Method in class peakml.IPeakSet

getIntensity() - Method in class peakml.MassChromatogram

getIntensity(int) - Method in class peakml.PeakData

Returns the intensity stored at the given index.

getIntensity() - Method in class peakml.Spectrum

getInterScanDelay() - Method in class peakml.io.dac.DACCalibrationInfo.DynamicParams

getInterScanDelay() - Method in class peakml.io.dac.DACCalibrationInfo.FastParams

getIonEnergy() - Method in class peakml.io.dac.DACCalibrationInfo.DynamicParams

getIonEnergy() - Method in class peakml.io.dac.DACCalibrationInfo.FastParams

getIonEnergy() - Method in class peakml.io.dac.DACCalibrationInfo.StaticParams

getIonEnergy() - Method in class peakml.io.dac.DACExScanStats

getIonisation(int, int) - Method in class peakml.util.rjava.Project

getIsolationMass() - Method in class peakml.io.xrawfile.IXRawfile.PrecursorInfo

Returns the user defined isolation mass used to trigger the data dependent scan.

getIsotope(int) - Method in class peakml.chemistry.PeriodicTable.Element

Returns the isotope instance at the given position (0 is the most abundant isotope).

getIsotopeMassDifference(int, int) - Static method in class peakml.chemistry.PeriodicTable

Returns the difference of the most common isotope of the given element to the given isotope.

getIsotopes() - Method in class peakml.chemistry.PeriodicTable.Element

Returns an array of all the isotopes for the element.

getJobCode() - Method in class peakml.io.dac.DACHeader

getLabel() - Method in class peakml.Annotation

Retrieves the label of this annotation.

getLabel() - Method in class peakml.io.FileInfo

Returns the optional label for the file.

getLabel() - Method in class peakml.io.MeasurementInfo

Returns the optional label for the measurement.

getLabel() - Method in class peakml.io.SampleInfo

Returns the label of the sample.

getLabelData(int) - Method in class peakml.io.xrawfile.IXRawfile

This method enables you to read the FT-PROFILE labels of a scan represented by the scanNumber.

getLabName() - Method in class peakml.io.dac.DACHeader

getLaserAimXPos() - Method in class peakml.io.dac.DACExScanStats

getLaserAimYPos() - Method in class peakml.io.dac.DACExScanStats

getLaserRepetitionRate() - Method in class peakml.io.dac.DACExScanStats

getLastSpectrumNumber() - Method in class peakml.io.xrawfile.IXRawfile

Gets the last scan or reading number for the current controller.

getLinearDetectorVoltage() - Method in class peakml.io.dac.DACExScanStats

getLinearSensitivity() - Method in class peakml.io.dac.DACExScanStats

getLMA() - Method in class peakml.math.function.LinearFunction

When a fit has been performed by calling LinearFunction.fit(double[], double[]) the returned object contains data on the fit.

getLMA() - Method in class peakml.math.function.LogNormalFunction

Returns the LMA-fit used for constructing this function.

getLMA() - Method in class peakml.math.function.NormalFunction

Returns the LMA-fit used for constructing this function.

getLMA() - Method in class peakml.math.function.PolynomialFunction

When a fit has been performed by calling PolynomialFunction.fit(int, double[], double[]) the returned object contains data on the fit.

getLMResolution() - Method in class peakml.io.dac.DACExScanStats

getLocalExtremes(int) - Method in class peakml.math.Signal

getLocalMaxima(int) - Method in class peakml.math.Signal

getLocalMinima(int) - Method in class peakml.math.Signal

getLocation() - Method in class peakml.io.FileInfo

Returns the complete path to the file.

getLockMassCorrection() - Method in class peakml.io.dac.DACExScanStats

getLogAxis() - Method in class peakml.util.jfreechart.FastErrorBarPlot

getLogAxis() - Method in class peakml.util.swt.widget.IntensityTrendGraph

getLogScale() - Method in class peakml.util.jfreechart.LognAxis

getLoMass() - Method in class peakml.io.dac.DACScanStats

getLowMass() - Method in class peakml.io.dac.DACCalibrationInfo.DynamicParams

getLowMass() - Method in class peakml.io.dac.DACCalibrationInfo.FastParams

getLowMass() - Method in class peakml.io.dac.DACCalibrationInfo.StaticParams

getLowMass() - Method in class peakml.io.xrawfile.IXRawfile

Gets the lowest mass or wavelength recorded for the current controller.

getLowMass() - Method in class peakml.io.xrawfile.IXRawfile.ScanHeaderInfo

Returns the lowest detected mass of the scan.

getLowMassResolution() - Method in class peakml.io.dac.DACCalibrationInfo.DynamicParams

getLowMassResolution() - Method in class peakml.io.dac.DACCalibrationInfo.FastParams

getLowMassResolution() - Method in class peakml.io.dac.DACCalibrationInfo.StaticParams

getMass() - Method in class peakml.BackgroundIon

getMass() - Method in class peakml.Centroid

getMass(Mass) - Method in class peakml.chemistry.MolecularFormula

Calculates the mass for this molecular formula.

getMass(Mass) - Method in class peakml.chemistry.MolecularFormula.SubFormula

getMass(int, Mass) - Method in class peakml.chemistry.MolecularFormula.SubFormula

getMass(Mass) - Method in class peakml.chemistry.Molecule

Returns the mass of the molecule.

getMass() - Method in class peakml.chemistry.PeriodicTable.Derivative

Returns the mass difference of the adduct.

getMass(double, int) - Method in class peakml.chemistry.PeriodicTable.Derivative

Calculates the mass of the peak of the given basepeak mass and the adduct.

getMass(Mass) - Method in class peakml.chemistry.PeriodicTable.Element

Returns the mass of the element.

getMass() - Method in class peakml.io.xrawfile.IXRawfile.Label

Returns the mass.

getMass() - Method in class peakml.io.xrawfile.IXRawfile.Noise

Returns the mass of this noise packet.

getMass() - Method in class peakml.IPeak

Retrieves the mass of this peak.

getMass() - Method in class peakml.IPeakSet

getMass() - Method in class peakml.MassChromatogram

getMass(Vector<Type>) - Method in interface peakml.MassChromatogram.MassCalculator

This method calculates the mass for the given peaks.

getMass(int) - Method in class peakml.PeakData

Returns the mass stored at the given index.

getMass() - Method in class peakml.Spectrum

getMassChromatograms() - Method in class peakml.util.rjava.Project

getMasses() - Method in class peakml.io.dac.DACSpectrum

getMasses() - Method in class peakml.PeakData

Returns all the masses stored in this container.

getMasses(int) - Method in class peakml.util.rjava.Project

getMassListFromScanNum(int, boolean) - Method in class peakml.io.xrawfile.IXRawfile

Returns the mass list array.

getMassResolution() - Method in class peakml.io.xrawfile.IXRawfile

Gets the mass resolution value recorded for the current controller.

getMassStdDev() - Method in class peakml.IPeakSet

Calculates the standard deviation on the mass.

getMassVariance() - Method in class peakml.chemistry.MolecularFormula

Calculates the mass-variance of the molecule.

getMassVariance() - Method in class peakml.chemistry.MolecularFormula.SubFormula

getMassVariance() - Method in class peakml.chemistry.PeriodicTable.Element

Returns the mass variance for the element.

getMatrix() - Method in class peakml.math.DataFrame.Double

Returns a matrix with all the data in the dataframe.

getMax() - Method in class peakml.math.BinArray

getMaxIntensity() - Method in class peakml.io.xrawfile.IXRawfile

Gets the highest base peak of all the scans for the current controller.

getMaxIntensity() - Method in class peakml.IPeakSet

Returns the maximum intensity of all the peaks stored in this peakset.

getMaxIntensity() - Method in class peakml.MassChromatogram

Returns the maximum intensity of all the peaks associated with this mass chromatogram.

getMaxMass() - Method in class peakml.BackgroundIon

Returns the highest mass of the peaks in this background ion.

getMaxMass() - Method in class peakml.IPeakSet

Returns the maximum mass of all the peaks stored in this peakset.

getMaxMass() - Method in class peakml.MassChromatogram

Returns the maximum mass of all the peaks associated with this mass chromatogram.

getMaxRetentionTime() - Method in class peakml.BackgroundIon

Returns the retention time where this background ion ends.

getMaxRetentionTime() - Method in class peakml.io.MeasurementInfo

getMaxRetentionTime() - Method in class peakml.IPeakSet

Returns the maximum retention time of all the peaks stored in this peakset.

getMaxRetentionTime() - Method in class peakml.MassChromatogram

Returns the retention time where the mass chromatogram ends (e.g.

getMaxScanID() - Method in class peakml.BackgroundIon

Returns the scan-id where this background ion ends.

getMaxScanID() - Method in class peakml.IPeakSet

Returns the maximum scan-id of all the peaks stored in this peakset.

getMaxScanID() - Method in class peakml.MassChromatogram

Returns the maximum scan of all the peaks associated with this mass chromatogram.

getMaxValue() - Method in class peakml.math.BinArray

getMaxX() - Method in class peakml.math.Signal

Returns the maximum x-value.

getMaxY() - Method in class peakml.math.Signal

Returns the maximum y-value.

getMaxY() - Method in class peakml.util.jfreechart.FastErrorBarPlot.Data

getMean() - Method in class peakml.math.function.LogNormalFunction

getMeanIntensity() - Method in class peakml.BackgroundIon

Returns the mean intensity of the peaks in this background ion.

getMeanIntensity() - Method in class peakml.IPeakSet

Returns the mean intensity of all the peaks stored in this peakset.

getMeanMass() - Method in class peakml.BackgroundIon

Returns the mean mass of the peaks in this background ion.

getMeanMass() - Method in class peakml.IPeakSet

Returns the mean mass of all the peaks stored in this peakset.

getMeanRetentionTime() - Method in class peakml.IPeakSet

Returns the mean retention time of all the peaks stored in this peakset.

getMeanScanID() - Method in class peakml.IPeakSet

Returns the mean scan-id of all the peaks stored in this peakset.

getMeanY() - Method in class peakml.math.Signal

Returns the mean y-value.

getMeanY() - Method in class peakml.util.jfreechart.FastErrorBarPlot.Data

getMeasurement() - Method in class peakml.io.ParseResult

Returns the measurement instance.

getMeasurementID() - Method in class peakml.BackgroundIon

getMeasurementID() - Method in class peakml.Centroid

getMeasurementID(int) - Method in class peakml.io.SetInfo

Returns the measurement id at the given index in this set information.

getMeasurementID() - Method in class peakml.IPeak

Returns an optional measurement-id for this peak.

getMeasurementID() - Method in class peakml.IPeakSet

getMeasurementID() - Method in class peakml.MassChromatogram

getMeasurementID(int) - Method in class peakml.PeakData

Returns the measurement-id stored at the given index.

getMeasurementID() - Method in class peakml.Spectrum

getMeasurementID(int) - Method in class peakml.util.rjava.Project

getMeasurementIDs() - Method in class peakml.io.SetInfo

Returns a list of all the measurement id's associated with this set (excluding all the child sets).

getMeasurementIDs() - Method in class peakml.PeakData

Returns all the measurement-id's stored in this container.

getMeasurementInfo(int) - Method in class peakml.io.Header

Returns the measurement information with the given id.

getMeasurementInfos() - Method in class peakml.io.Header

Returns the list of measurement informations associated with the header.

getMeasurementInfos(SetInfo) - Method in class peakml.io.Header

Returns the list of measurement informations associated to the given set.

getMeasurementNames() - Method in class peakml.util.rjava.Project

getMeasurementRetentionTimes(int) - Method in class peakml.util.rjava.Project

getMeasurementRetentionTimes(String) - Method in class peakml.util.rjava.Project

getMedian() - Method in class peakml.math.function.LogNormalFunction

getMedianIntensity() - Method in class peakml.BackgroundIon

Returns the median intensity of the peaks in this background ion.

getMedianIntensity() - Method in class peakml.IPeakSet

Returns the median intensity of all the peaks stored in this peakset.

getMedianMass() - Method in class peakml.BackgroundIon

Returns the median mass of the peaks in this background ion.

getMedianMass() - Method in class peakml.IPeakSet

Returns the median mass of all the peaks stored in this peakset.

getMer() - Method in class peakml.chemistry.PeriodicTable.Derivative

Returns the number of *-mer's needed for the basepeak.

getMerged() - Method in class peakml.io.xrawfile.IXRawfile.Label

Whether the peak was merged.

getMin() - Method in class peakml.math.BinArray

getMinIntensity() - Method in class peakml.IPeakSet

Returns the minimum intensity of all the peaks stored in this peakset.

getMinIntensity() - Method in class peakml.MassChromatogram

Returns the minimum intensity of all the peaks associated with this mass chromatogram.

getMinMass() - Method in class peakml.BackgroundIon

Returns the lowest mass of the peaks in this background ion.

getMinMass() - Method in class peakml.IPeakSet

Returns the minimum mass of all the peaks stored in this peakset.

getMinMass() - Method in class peakml.MassChromatogram

Returns the minimum mass of all the peaks associated with this mass chromatogram.

getMinRetentionTime() - Method in class peakml.BackgroundIon

Returns the retention time where this background ion starts.

getMinRetentionTime() - Method in class peakml.io.MeasurementInfo

getMinRetentionTime() - Method in class peakml.IPeakSet

Returns the minimum retention time of all the peaks stored in this peakset.

getMinRetentionTime() - Method in class peakml.MassChromatogram

Returns the retention time where the mass chromatogram begins (e.g.

getMinScanID() - Method in class peakml.BackgroundIon

Returns the scan-id where this background ion starts.

getMinScanID() - Method in class peakml.IPeakSet

Returns the minimum scan-id of all the peaks stored in this peakset.

getMinScanID() - Method in class peakml.MassChromatogram

Returns the minimum scan of all the peaks associated with this mass chromatogram.

getMinX() - Method in class peakml.math.Signal

Returns the minimum x-value.

getMinY() - Method in class peakml.math.Signal

Returns the minimum y-value.

getMinY() - Method in class peakml.util.jfreechart.FastErrorBarPlot.Data

getMode() - Method in class peakml.math.function.LogNormalFunction

This function retrieves the mode of this function.

getModified() - Method in class peakml.io.xrawfile.IXRawfile.Label

Whether the peak was modified.

getMolecularMass() - Method in class peakml.io.dac.DACScanStats

getMolecularWeight() - Method in class peakml.chemistry.PeriodicTable.Element

Returns the molecular weight of the isotope (the mixture of all isotopes as they occur naturally).

getMonoIsotopicMass() - Method in class peakml.io.xrawfile.IXRawfile.PrecursorInfo

Returns the monoisotopic mass as determined by the instrument firmware.

getMonoIsotopicWeight() - Method in class peakml.chemistry.PeriodicTable.Element

Returns the mono-isotopic weight of the most abundant isotope.

getMonoIsotopicWeight(int) - Method in class peakml.chemistry.PeriodicTable.Element

Returns the mono isotopic weight of the isotope at the given index.

getMRMDaughters() - Method in class peakml.io.dac.DACFunctionInfo

getMRMParents() - Method in class peakml.io.dac.DACFunctionInfo

getMS1DynamicParams() - Method in class peakml.io.dac.DACCalibrationInfo

getMS1FastParams() - Method in class peakml.io.dac.DACCalibrationInfo

getMS1StaticFunction() - Method in class peakml.io.dac.DACCalibrationInfo

getMS1StaticParams() - Method in class peakml.io.dac.DACCalibrationInfo

getMS2DynamicParams() - Method in class peakml.io.dac.DACCalibrationInfo

getMS2FastParams() - Method in class peakml.io.dac.DACCalibrationInfo

getMS2StaticFunction() - Method in class peakml.io.dac.DACCalibrationInfo

getMS2StaticParams() - Method in class peakml.io.dac.DACCalibrationInfo

getMSnSpectrum(int) - Method in class peakml.Spectrum

Returns the MSn spectrum at the given index.

getMultiplier1() - Method in class peakml.io.dac.DACExScanStats

getMultiplier2() - Method in class peakml.io.dac.DACExScanStats

getMuxStream() - Method in class peakml.io.dac.DACHeader

getName() - Method in class peakml.Centroid.Factory

PeakData.PeakFactory.getName()

getName() - Method in class peakml.chemistry.MolecularFormula.SubFormula

getName() - Method in class peakml.chemistry.Molecule

Returns the name of the molecule.

getName() - Method in class peakml.chemistry.PeriodicTable.Derivative

Returns the name of the adduct.

getName() - Method in class peakml.chemistry.PeriodicTable.Element

Returns the full name of the element.

getName() - Method in class peakml.chemistry.Protein

getName() - Method in class peakml.io.ApplicationInfo

Returns the name of the application.

getName() - Method in class peakml.io.FileInfo

Returns the filename excluding the complete path, which can be retrieved with FileInfo.getLocation().

getName() - Method in interface peakml.PeakData.PeakFactory

Returns the name of the type associated to the factory.

getNeedle() - Method in class peakml.io.dac.DACExScanStats

getNoise() - Method in class peakml.io.xrawfile.IXRawfile.Label

Returns the noise-level.

getNoise() - Method in class peakml.io.xrawfile.IXRawfile.Noise

Returns the noise level of this mass.

getNoiseData(int) - Method in class peakml.io.xrawfile.IXRawfile

getNrApplicationInfos() - Method in class peakml.io.Header

Returns the number of application information instances stored in the header.

getNrAtoms() - Method in class peakml.chemistry.MolecularFormula

Counts the total amount of atoms in the molecule, without taking an atom type into account.

getNrAtoms(int) - Method in class peakml.chemistry.MolecularFormula

getNrAtoms(int, int) - Method in class peakml.chemistry.MolecularFormula

getNrAtoms() - Method in class peakml.chemistry.MolecularFormula.SubFormula

getNrChildren() - Method in class peakml.io.SetInfo

Returns the number of children in this set.

getNrColors() - Method in class peakml.graphics.Colormap

Returns the number of colors stored in this color model.

getNrColumns() - Method in class peakml.math.DataFrame

Returns the number of columns in the matrix.

getNrFileInfos() - Method in class peakml.io.MeasurementInfo

Returns the number of file info instances maintained within this class.

getNrIsotopes() - Method in class peakml.chemistry.PeriodicTable.Element

Returns the number of isotopes for this element.

getNrMassChromatograms() - Method in class peakml.util.rjava.Project

getNrMeasurementIDs() - Method in class peakml.io.SetInfo

Returns the number of measurement id's associated to this set.

getNrMeasurementInfos() - Method in class peakml.io.Header

Returns the number of measurement informations associated with the header.

getNrMSnSpecra() - Method in class peakml.Spectrum

Returns the number of MSn spectra associated with this spectrum.

getNrPeaks() - Method in class peakml.io.Header

Returns the number of peaks associated with this header.

getNrPeaks() - Method in class peakml.MassChromatogram

Returns the number of peaks associated with this mass chromatogram.

getNrPeaks() - Method in class peakml.Spectrum

Returns the number of peaks associated to this spectrum.

getNrPeaksets() - Method in class peakml.util.rjava.Project

getNrRows() - Method in class peakml.math.DataFrame

Returns the number of rows in the matrix.

getNrSampleInfos() - Method in class peakml.io.Header

Returns the number of sample information instances associated with the header.

getNrScanInfos() - Method in class peakml.io.MeasurementInfo

Returns the number of scan info instances maintained within this class.

getNrScans() - Method in class peakml.ChromatographyMS

Returns the number of scans stored in this class.

getNrScans(int) - Method in class peakml.util.rjava.Project

getNrSetInfos() - Method in class peakml.io.Header

Returns the number of set informations stored in the header.

getNrVocabularies() - Method in class peakml.io.Header

Returns the number of vocabularies associated with the header.

getNumberChannels() - Method in class peakml.io.xrawfile.IXRawfile.ScanHeaderInfo

Returns the number of channels for this scan.

getNumberOfControllers() - Method in class peakml.io.xrawfile.IXRawfile

Returns the number of registered device controllers in the raw file.

getNumberOfControllersOfType(int) - Method in class peakml.io.xrawfile.IXRawfile

Returns the number of registered device controllers of a particular type in the raw file.

getNumberOfFunctions(String) - Static method in class peakml.io.dac.DACFunctionInfo

getNumberPackets() - Method in class peakml.io.xrawfile.IXRawfile.ScanHeaderInfo

Returns the number of packets collected for this scan.

getNumCalFunctions() - Method in class peakml.io.dac.DACCalibrationInfo

getNumErrorLog() - Method in class peakml.io.xrawfile.IXRawfile

Gets the number of error log entries recorded for the current controller.

getNumFunctions() - Method in class peakml.io.dac.DACExperimentInfo

Returns the number of functions (or data-streams) associated to the given file.

getNumInstMethods() - Method in class peakml.io.xrawfile.IXRawfile

Returns the number of instrument methods contained in the raw file.

getNumPeaks() - Method in class peakml.io.dac.DACSpectrum

getNumProcesses() - Method in class peakml.io.dac.DACProcessInfo

getNumScans() - Method in class peakml.io.dac.DACFunctionInfo

getNumSegments() - Method in class peakml.io.dac.DACFunctionInfo

getNumShotsPerformed() - Method in class peakml.io.dac.DACExScanStats

getNumShotsSummed() - Method in class peakml.io.dac.DACExScanStats

getNumSpectra() - Method in class peakml.io.xrawfile.IXRawfile

Gets the number of spectra acquired by the current controller.

getNumStatusLog() - Method in class peakml.io.xrawfile.IXRawfile

Gets the number of status log entries recorded for the current controller.

getNumTrailerExtra() - Method in class peakml.io.xrawfile.IXRawfile

Gets the trailer extra entries recorded for the current controller.

getNumTuneData() - Method in class peakml.io.xrawfile.IXRawfile

Gets the number of tune data entries recorded for the current controller.

getOntologyRef() - Method in class peakml.Annotation

Returns the ontology-ref (eg GO:0051458) for the annotation.

getOrder() - Method in class peakml.math.function.PolynomialFunction

Returns the order of the polynomial function.

getOrientation() - Method in class peakml.util.jfreechart.FastSpectrumPlot

getOrientation() - Method in class peakml.util.jfreechart.FastTimePlot

getOverload() - Method in class peakml.io.dac.DACScanStats

getOwner() - Method in class peakml.io.Header

Returns the owner of the file.

getParameters() - Method in class peakml.io.ApplicationInfo

Returns the parameters used for the application.

getParameters() - Method in class peakml.math.function.LinearFunction

Returns the array with the a (first element) and b (second element) parameters stored in the instance of this class.

getParameters() - Method in class peakml.math.function.LogNormalFunction

getParameters() - Method in class peakml.math.function.NormalFunction

getParameters() - Method in class peakml.math.function.PolynomialFunction

Returns the array with the parameters of this function.

getPartialDerivate(double, double[], int) - Method in class peakml.math.function.LinearFunction

getPartialDerivate(double, double[], int) - Method in class peakml.math.function.LogNormalFunction

getPartialDerivate(double, double[], int) - Method in class peakml.math.function.NormalFunction

getPartialDerivate(double, double[], int) - Method in class peakml.math.function.PolynomialFunction

getPatternID() - Method in class peakml.BackgroundIon

getPatternID() - Method in class peakml.Centroid

getPatternID() - Method in class peakml.IPeak

Returns an optional id for the peak.

getPatternID() - Method in class peakml.IPeakSet

getPatternID() - Method in class peakml.MassChromatogram

getPatternID(int) - Method in class peakml.PeakData

Returns the pattern-id stored at the given index.

getPatternID() - Method in class peakml.Spectrum

getPatternIDs() - Method in class peakml.PeakData

Returns all the pattern-id's stored in this container.

getPeak(int) - Method in class peakml.MassChromatogram

Retrieves the peak at position pos.

getPeak(int) - Method in class peakml.PeakData

Returns a Peak instance using the data stored at the given index in this container.

getPeakClass() - Method in class peakml.Centroid.Factory

PeakData.PeakFactory.getPeakClass()

getPeakClass() - Method in interface peakml.PeakData.PeakFactory

Returns the Class instance of the generic type associated to the factory.

getPeakData() - Method in class peakml.BackgroundIon

getPeakData() - Method in class peakml.MassChromatogram

Returns the PeakData instance associated to this MassChromatogram, containing all the peak-information.

getPeakData() - Method in class peakml.Spectrum

Returns the PeakData container associated to this spectrum.

getPeakRetentionTime() - Method in class peakml.MassChromatogram

Returns the retention time where the mass chromatogram is most intense.

getPeaks() - Method in class peakml.IPeakSet

Returns the list of peaks stored in this peakset.

getPeaks() - Method in class peakml.MassChromatogram

Returns the vector filled with all the peaks associated to this mass chromatogram.

getPeaks() - Method in class peakml.PeakData

Returns a vector with Peak instances covering all the data stored in this container.

getPeaks() - Method in class peakml.Spectrum

Returns a vector with all the peaks.

getPeakScanID() - Method in class peakml.MassChromatogram

Returns the scan where the mass chromatogram is most intense.

getPeaksInMassRange(double, double) - Method in class peakml.IPeakSet

Returns all the peaks in this peakset with a mass in the range minmass ..

getPeaksInRetentionTimeRange(double, double) - Method in class peakml.IPeakSet

Returns all the peaks in the given retention time range.

getPeaksInScan() - Method in class peakml.io.dac.DACScanStats

getPeaksInScanRange(int, int) - Method in class peakml.IPeakSet

Returns all the peaks in the given scan-range.

getPeaksOfMass(double, double) - Method in class peakml.IPeakSet

Returns all the peaks in this peakset with a mass in the range mass-delta ..

getPeakX() - Method in class peakml.math.Signal

Returns the x-value where the signal reaches its maximum y-value.

getPepFileName() - Method in class peakml.io.dac.DACHeader

getPlateDesc() - Method in class peakml.io.dac.DACHeader

getPlotType() - Method in class peakml.util.jfreechart.FastErrorBarPlot

getPlotType() - Method in class peakml.util.jfreechart.FastSpectrumPlot

getPlotType() - Method in class peakml.util.jfreechart.FastTimePlot

getPolarity() - Method in class peakml.io.dac.DACExperimentInfo.ExFunctionInfo

getPolarity() - Method in class peakml.io.ScanInfo

Returns the polarity of the scan.

getPolarity() - Method in class peakml.Spectrum

Returns the polarity of the data in the spectrum.

getPrecursorInfoFromScanNum(int) - Method in class peakml.io.xrawfile.IXRawfile

This function is used to retrieve information about the parent scans of a data dependent MSn scan.

getProbeTemperature() - Method in class peakml.io.dac.DACExScanStats

getProcess() - Method in class peakml.io.dac.DACHeader

getProcessDescs() - Method in class peakml.io.dac.DACProcessInfo

getProducts() - Method in class peakml.chemistry.Protein

getPSDFactor1() - Method in class peakml.io.dac.DACExScanStats

getPSDMajorStep() - Method in class peakml.io.dac.DACExScanStats

getPSDMinorStep() - Method in class peakml.io.dac.DACExScanStats

getPSDSegmentType() - Method in class peakml.io.dac.DACExScanStats

getQuality() - Method in class peakml.math.function.LogNormalFunction

Returns the quality of the fit when an LMA-fit was done.

getReference() - Method in class peakml.io.xrawfile.IXRawfile.Label

Whether the peak has a reference (?).

getReferenceFile() - Method in class peakml.io.dac.DACCalibrationInfo.DynamicParams

getReferenceFile() - Method in class peakml.io.dac.DACCalibrationInfo.FastParams

getReferenceFile() - Method in class peakml.io.dac.DACCalibrationInfo.StaticParams

getReferenceScan() - Method in class peakml.io.dac.DACExScanStats

getReflectron() - Method in class peakml.io.dac.DACExScanStats

getReflectronDetectorVoltage() - Method in class peakml.io.dac.DACExScanStats

getReflectronFieldLength() - Method in class peakml.io.dac.DACExScanStats

getReflectronFieldLengthAlt() - Method in class peakml.io.dac.DACExScanStats

getReflectronLength() - Method in class peakml.io.dac.DACExScanStats

getReflectronLengthAlt() - Method in class peakml.io.dac.DACExScanStats

getReflectronLensVoltage() - Method in class peakml.io.dac.DACExScanStats

getReflectronSensitivity() - Method in class peakml.io.dac.DACExScanStats

getReflectronVoltage() - Method in class peakml.io.dac.DACExScanStats

getResolution() - Method in class peakml.io.xrawfile.IXRawfile.Label

Returns the resolution.

getResolved() - Method in class peakml.io.dac.DACHeader

getRetentionTime() - Method in class peakml.BackgroundIon

getRetentionTime() - Method in class peakml.Centroid

getRetentionTime() - Method in class peakml.chemistry.Molecule

Returns the optional expected retention time for this molecule.

getRetentionTime() - Method in class peakml.io.ScanInfo

Returns the retention time of the scan in seconds.

getRetentionTime() - Method in class peakml.IPeak

Retrieves the retention time for this peak.

getRetentionTime() - Method in class peakml.IPeakSet

getRetentionTime() - Method in class peakml.MassChromatogram

getRetentionTime(int) - Method in class peakml.PeakData

Returns the retention-time stored at the given index.

getRetentionTime() - Method in class peakml.Spectrum

getRetentionTimes() - Method in class peakml.PeakData

Returns all the retention-times stored in this container.

getRetentionTimes(int) - Method in class peakml.util.rjava.Project

getRetnTime() - Method in class peakml.io.dac.DACScanStats

getReturnCode() - Method in exception peakml.io.xrawfile.IXRawfileException

getRFVoltage() - Method in class peakml.io.dac.DACExScanStats

getRow(String) - Method in class peakml.math.DataFrame.Double

Returns the complete row with the given name.

getRow(int) - Method in class peakml.math.DataFrame.Double

Returns the complete row at the given index.

getRowIndexOf(String) - Method in class peakml.math.DataFrame

Returns the index of the row with the given name.

getRowName(int) - Method in class peakml.math.DataFrame

Returns the name of the row at the given index.

getRowNames() - Method in class peakml.math.DataFrame

Returns a list with all the row-names.

getSampleDesc() - Method in class peakml.io.dac.DACHeader

getSampleID() - Method in class peakml.io.dac.DACHeader

getSampleID() - Method in class peakml.io.MeasurementInfo

Returns the id of the sample associated to the measurement.

getSampleInfo(String) - Method in class peakml.io.Header

Returns the sample information with the given id.

getSampleInfos() - Method in class peakml.io.Header

Returns a list of all the sample information instances associated with the header.

getSamplePlateVoltage() - Method in class peakml.io.dac.DACExScanStats

getSamplingConeVoltage() - Method in class peakml.io.dac.DACExScanStats

getSaturated() - Method in class peakml.io.xrawfile.IXRawfile.Label

Whether the peak was saturated.

getScale() - Method in class peakml.math.wavelet.ContinuousWaveletTransform

getScale() - Method in class peakml.math.wavelet.MarrWavelet

getScale() - Method in class peakml.math.wavelet.TemplateWavelet

getScale() - Method in class peakml.math.wavelet.Wavelet

getScan(int) - Method in class peakml.ChromatographyMS

Returns the scan at the given index.

getScanAnnotation(int, int, String) - Method in class peakml.util.rjava.Project

getScanHeaderInfoForScanNum(int) - Method in class peakml.io.xrawfile.IXRawfile

For a given scan number, this function returns information from the scan header for the current controller.

getScanID() - Method in class peakml.BackgroundIon

getScanID() - Method in class peakml.Centroid

getScanID() - Method in class peakml.IPeak

Retrieves the scan-id for this peak.

getScanID() - Method in class peakml.IPeakSet

getScanID() - Method in class peakml.MassChromatogram

getScanID(int) - Method in class peakml.PeakData

Returns the scan-id stored at the given index.

getScanID() - Method in class peakml.Spectrum

getScanIDs() - Method in class peakml.PeakData

Returns all the scan-id's stored in this container.

getScanIDs(int) - Method in class peakml.util.rjava.Project

getScanInfo(int) - Method in class peakml.io.MeasurementInfo

Returns the scan info instance at the given index.

getScanInfos() - Method in class peakml.io.MeasurementInfo

Returns all the scan info instances maintained in this class.

getScanNumber() - Method in class peakml.io.xrawfile.IXRawfile.PrecursorInfo

Returns the scannumber of the parent scan.

getScanNumber() - Method in class peakml.io.xrawfile.IXRawfile.ScanHeaderInfo

Returns the scannumber of this scan.

getScans() - Method in class peakml.ChromatographyMS

Returns a reference to the vector with scans stored in this class.

getScanTime() - Method in class peakml.io.dac.DACCalibrationInfo.DynamicParams

getScanTime() - Method in class peakml.io.dac.DACCalibrationInfo.FastParams

getSegment() - Method in class peakml.io.dac.DACScanStats

getSegmentNumber() - Method in class peakml.io.dac.DACExScanStats

getSetInfo(String) - Method in class peakml.io.Header

Returns the set information with the given id.

getSetInfoForMeasurementID(int) - Method in class peakml.io.Header

Returns the set information which contains the given measurement id.

getSetInfos() - Method in class peakml.io.Header

Returns all the set informations stored in the header.

getSetMass() - Method in class peakml.io.dac.DACExScanStats

getSetNames() - Method in class peakml.util.rjava.Project

getShowAll() - Method in class peakml.util.jfreechart.FastErrorBarPlot

getShowAll() - Method in class peakml.util.swt.widget.IntensityTrendGraph

getSignal() - Method in class peakml.BackgroundIon

getSignal() - Method in class peakml.Centroid

getSignal() - Method in class peakml.IPeak

Calculates the signal for this IPeak object.

getSignal() - Method in class peakml.IPeakSet

getSignal() - Method in class peakml.MassChromatogram

getSignal() - Method in class peakml.Spectrum

getSIRChannels() - Method in class peakml.io.dac.DACFunctionInfo

getSize() - Method in class peakml.math.Signal

Returns the number of data-points in this signal.

getSkewness() - Method in class peakml.math.function.LogNormalFunction

getSkimmer() - Method in class peakml.io.dac.DACExScanStats

getSkimmerLens() - Method in class peakml.io.dac.DACExScanStats

getSmiles() - Method in class peakml.chemistry.Molecule

Returns the smiles string describing the molecular structure of the molecule.

getSolventDelay() - Method in class peakml.io.dac.DACHeader

getSourceAperture() - Method in class peakml.io.dac.DACExScanStats

getSourceCode() - Method in class peakml.io.dac.DACExScanStats

getSourceRegion1() - Method in class peakml.io.dac.DACExScanStats

getSourceRegion2() - Method in class peakml.io.dac.DACExScanStats

getSourceTemperature() - Method in class peakml.io.dac.DACExScanStats

getSpan() - Method in class peakml.io.dac.DACCalibrationInfo.StaticParams

getStandardDeviation() - Method in class peakml.math.function.LogNormalFunction

getStartRT() - Method in class peakml.io.dac.DACFunctionInfo

getStartTime() - Method in class peakml.ChromatographyMS

getStartTime() - Method in class peakml.io.xrawfile.IXRawfile

Gets the start time of the first scan or reading for the current controller.

getStartTime() - Method in class peakml.io.xrawfile.IXRawfile.ScanHeaderInfo

Returns the start time of the scan in minutes.

getStartX() - Method in class peakml.math.function.LogNormalFunction

Returns the starting position of the log-normal distribution.

getStatusLogForScanNum(int) - Method in class peakml.io.xrawfile.IXRawfile

Returns the recorded status log entry labels and values for the current controller.

getStatusLogLabelsForScanNum(int) - Method in class peakml.io.xrawfile.IXRawfile

Returns the recorded status log entry labels for the current controller.

getStatusLogValueForScanNum(int, String) - Method in class peakml.io.xrawfile.IXRawfile

Returns the recorded status log parameter value for the specified status log parameter label for the current controller.

getSteering() - Method in class peakml.io.dac.DACExScanStats

getSubFormulas() - Method in class peakml.chemistry.MolecularFormula

getSubmitter() - Method in class peakml.io.dac.DACHeader

getSubstrates() - Method in class peakml.chemistry.Protein

getSynonyms() - Method in class peakml.chemistry.Molecule

Returns the list of synonyms associated to this molecule.

getTaskCode() - Method in class peakml.io.dac.DACHeader

getTempCoefficient() - Method in class peakml.io.dac.DACExScanStats

getTempCorrection() - Method in class peakml.io.dac.DACExScanStats

getTerm(String) - Method in class peakml.io.Vocabulary

Returns the term with the given id.

getTFMWell() - Method in class peakml.io.dac.DACExScanStats

getTIC() - Method in class peakml.io.dac.DACScanStats

getTIC() - Method in class peakml.io.xrawfile.IXRawfile.ScanHeaderInfo

Returns the total detected intensity of the scan.

getTIC_A() - Method in class peakml.io.dac.DACExScanStats

getTIC_B() - Method in class peakml.io.dac.DACExScanStats

getTOF() - Method in class peakml.io.dac.DACExScanStats

getTOFAperture() - Method in class peakml.io.dac.DACExScanStats

getTotalIntensity() - Method in class peakml.MassChromatogram

Returns the total intensity of the mass chromatogram.

getTrailerExtraForScanNum(int) - Method in class peakml.io.xrawfile.IXRawfile

Returns the recorded trailer extra entry labels and values for the current controller.

getTransportDC() - Method in class peakml.io.dac.DACExScanStats

getTransportRF() - Method in class peakml.io.dac.DACExScanStats

getTuneData(int) - Method in class peakml.io.xrawfile.IXRawfile

Returns the recorded tune parameter labels and values for the current controller.

getType() - Method in class peakml.graphics.Colormap

Returns the type of color model stored in the instance.

getType() - Method in class peakml.io.SetInfo

Returns the type of this set.

getType() - Method in class peakml.Spectrum

Returns the type of the spectrum.

getUniformTime() - Method in class peakml.io.xrawfile.IXRawfile.ScanHeaderInfo

Returns the uniform time for this scan.

getUseLockMassCorrection() - Method in class peakml.io.dac.DACExScanStats

getUserName() - Method in class peakml.io.dac.DACHeader

getUseTempCorrection() - Method in class peakml.io.dac.DACExScanStats

getValency() - Method in class peakml.chemistry.PeriodicTable.Element

Returns the valency of the element.

getValue() - Method in class peakml.Annotation

Returns the value of this annotation as a string.

getValueAsDouble() - Method in class peakml.Annotation

Returns the value of the annotation as a double.

getValueAsInteger() - Method in class peakml.Annotation

Returns the value of the annotation as an integer.

getValueAsString() - Method in class peakml.Annotation

See Annotation.getValue().

getValueType() - Method in class peakml.Annotation

Returns the type of the annotation.

getVariation() - Method in class peakml.math.function.LogNormalFunction

getVersion() - Method in class peakml.io.ApplicationInfo

Returns the version of the application.

getVersionMajor() - Method in class peakml.io.dac.DACHeader

getVersionMinor() - Method in class peakml.io.dac.DACHeader

getVersionNumber() - Method in class peakml.io.xrawfile.IXRawfile

Returns the file format version number.

getVisible() - Method in class peakml.io.MeasurementInfo

For more information see MeasurementInfo.setVisible(boolean).

getVisible() - Method in class peakml.io.SetInfo

For more information see SetInfo.setVisible(boolean).

getVocabularies() - Method in class peakml.io.Header

Returns a list of all vocabularies associated with the header.

getVocabulary(String) - Method in class peakml.io.Header

Returns the vocabulary of the given namespace.

getVocabulary(String) - Static method in class peakml.io.Vocabulary

getX() - Method in class peakml.math.Signal

Returns the internal array with all the x-values.

getXVals() - Method in class peakml.math.function.LinearFunction

When a fit has been performed by calling LinearFunction.fit(double[], double[]) the returned array contains the x-values used for the fit.

getXY() - Method in class peakml.math.Signal

Returns a matrix with the x- and y-values.

getY(double) - Method in class peakml.math.function.CubicSplineFunction

getY(double) - Method in interface peakml.math.function.Function

Calculates the y-value for the given x-value with the function defined here.

getY(double) - Method in class peakml.math.function.LinearFunction

Returns the y-value for the given x-value with the parameters stored in the instance of the class.

getY(double, double[]) - Method in class peakml.math.function.LinearFunction

Returns the y-value for the given x-value with the given parameters

getY(double) - Method in class peakml.math.function.LogNormalFunction

Returns the y-value for the given x-value with the parameters stored in the instance of the class.

getY(double, double[]) - Method in class peakml.math.function.LogNormalFunction

getY(double) - Method in class peakml.math.function.NormalFunction

Returns the y-value for the given x-value with the parameters stored in the instance of the class.

getY(double, double[]) - Method in class peakml.math.function.NormalFunction

getY(double) - Method in class peakml.math.function.PolynomialFunction

Returns the y-value for the given x-value with the parameters stored in the instance of the class.

getY(double, double[]) - Method in class peakml.math.function.PolynomialFunction

Returns the y-value for the given x-value with the given parameters

getY() - Method in class peakml.math.Signal

Returns the internal array with all the y-values.

getY(double) - Method in class peakml.math.Signal

Returns the y-value at the given x-value.

getYVals() - Method in class peakml.math.function.LinearFunction

When a fit has been performed by calling LinearFunction.fit(double[], double[]) the returned array contains the y-values used for the fit.

GRAYSCALE - Static variable in class peakml.graphics.Colormap

A greyscale color model.

GZIP - Static variable in class peakml.util.Base64

Specify that data should be gzip-compressed.