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

C

CALCIUM - Static variable in class peakml.chemistry.PeriodicTable

The index of the calcium element in the PeriodicTable.elements array.

CARBON - Static variable in class peakml.chemistry.PeriodicTable

The index of the carbon element in the PeriodicTable.elements array.

Centroid - Class in peakml

Implementation of a centroid or data-point in a mass spectrometry spectrum or profile.

Centroid(PeakData<Centroid>, int) - Constructor for class peakml.Centroid

Constructs a new Centroid instance linked to the given PeakData instance.

Centroid.Factory - Class in peakml

Factory for creating a Centroid instance.

Centroid.Factory() - Constructor for class peakml.Centroid.Factory

CESIUM - Static variable in class peakml.chemistry.PeriodicTable

The index of the cesium element in the PeriodicTable.elements array.

charge - Variable in class peakml.chemistry.PeriodicTable.Derivative

The charge needed for the basepeak of the adduct.

CHLORINE - Static variable in class peakml.chemistry.PeriodicTable

The index of the chlorine element in the PeriodicTable.elements array.

ChromatographyMS<gPeak extends Peak> - Class in peakml

This class combines the information from a setup combining a chromatograph (LC or GC) with a mass spectrometer.

ChromatographyMS() - Constructor for class peakml.ChromatographyMS

ChromatographyMS(Vector<Spectrum<gPeak>>) - Constructor for class peakml.ChromatographyMS

CHROMIUM - Static variable in class peakml.chemistry.PeriodicTable

The index of the chromium element in the PeriodicTable.elements array.

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

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

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

clear() - Method in class peakml.util.swt.widget.DerivativeGraph

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

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

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

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

Closes a raw file and frees the associated memory.

close() - Method in class peakml.util.Base64.OutputStream

Flushes and closes (I think, in the superclass) the stream.

COBALT - Static variable in class peakml.chemistry.PeriodicTable

The index of the cobalt element in the PeriodicTable.elements array.

coda() - Method in class peakml.MassChromatogram

Simplistic implementation of the CoDA algorithm working on individual mass chromatograms.

codaDW() - Method in class peakml.MassChromatogram

Implementation of a CoDA-like approach for evalution of an individual mass chromatogram based on the Durbin-Watson statistic.

codaSW() - Method in class peakml.MassChromatogram

Implementation of a CoDA-like approach for evaluation of an individual mass chromatogram based on the Shapiro-Wilk test.

Colormap - Class in peakml.graphics

Defines different color models for visualization purposes (like heatmaps and graphs).

Colormap(int) - Constructor for class peakml.graphics.Colormap

Constructor for creating the specified color model.

COLUMN - Static variable in class peakml.math.Statistical

Indicates that the column should be processed

compare(IPeak, IPeak) - Method in class peakml.IPeak.AnnotationAscending

Compare function, which converts the data in the IPeak instances to comparable data and sorts accordingly.

compare(IPeak, IPeak) - Method in class peakml.IPeak.AnnotationDescending

Compare function, which converts the data in the IPeak instances to comparable data and sorts accordingly.

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

Compares the given signal to this signal.

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

Returns true when the given id is associated to this set (including all the child sets).

ContinuousWaveletTransform - Class in peakml.math.wavelet

ContinuousWaveletTransform(Wavelet) - Constructor for class peakml.math.wavelet.ContinuousWaveletTransform

CONTROLLER_AD_CARD - Static variable in class peakml.io.xrawfile.IXRawfile

This code indicates that the controller was a analog-to-digital converter.

CONTROLLER_ANALOG - Static variable in class peakml.io.xrawfile.IXRawfile

This code final indicates that the controller was an analog device.

CONTROLLER_MS - Static variable in class peakml.io.xrawfile.IXRawfile

This code indicates that the controller was a mass spectrometer.

CONTROLLER_NO_DEVICE - Static variable in class peakml.io.xrawfile.IXRawfile

This code indicates that there was no controller available.

CONTROLLER_PDA - Static variable in class peakml.io.xrawfile.IXRawfile

This code indicates that the controller was a photo-diode-array device (whole range UV detector).

CONTROLLER_UV - Static variable in class peakml.io.xrawfile.IXRawfile

This code indicates that the controller was a UV detector.

convertToString() - Static method in class peakml.Version

This method converts the static version to a string.

COPPER - Static variable in class peakml.chemistry.PeriodicTable

The index of the copper element in the PeriodicTable.elements array.

copyfile(InputStream, OutputStream) - Static method in class peakml.util.IO

create(PeakData<Centroid>, int) - Method in class peakml.Centroid.Factory

PeakData.PeakFactory.create(PeakData, int)

create(PeakData<gPeak>, int) - Method in interface peakml.PeakData.PeakFactory

Creates a new instance of the gPeak type and initiates it with the given PeakData instance and index indicating the location of the data associated to the new instance.

createGraph(String, String, String) - Method in class peakml.math.Signal

createGraphImage(String, String, String, int, int) - Method in class peakml.math.Signal

createImage(int, int, int) - Static method in class peakml.graphics.Colormap

createMenu(Menu, String) - Static method in class peakml.util.swt.SWTTools

Creates a menu-option in the given menu with the given name.

createMenuItem(Listener, Menu, String, Image, int, int) - Static method in class peakml.util.swt.SWTTools

Creates an item in the given menu-option.

CubicSplineFunction - Class in peakml.math.function

This class calculates the natural cubic spline for a given set of input values.

CubicSplineFunction(double[], double[]) - Constructor for class peakml.math.function.CubicSplineFunction

Constructs (i.e.