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

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SampleInfo - Class in peakml.io

Central point for storing all information about a sample.

SampleInfo(String) - Constructor for class peakml.io.SampleInfo

Standard constructor, which sets the obligatory id-value for the sample.

SampleInfo(String, String) - Constructor for class peakml.io.SampleInfo

Standard constructor, which sets the obligatory id-value for the sample and the name.

savitzkyGolay() - Method in class peakml.MassChromatogram

savitzkyGolay(SavitzkyGolayFilter.Points) - Method in class peakml.MassChromatogram

SavitzkyGolayFilter - Class in peakml.math.filter

Implementation of the Savitzky-Golay filter taken from Numerical Recipes in C (chapter 14.8, page 650).

SavitzkyGolayFilter(SavitzkyGolayFilter.Points) - Constructor for class peakml.math.filter.SavitzkyGolayFilter

Standard constructor, which accepts the number of data points to use in for the smoothing filter.

SavitzkyGolayFilter.Points - Enum in peakml.math.filter

Fixed definition of the number of data points to use for smoothing.

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

Applies a Savitzky-Golay smoother to the signal and returns the resulting new signal.

savitzkyGolaySmooth(SavitzkyGolayFilter.Points) - Method in class peakml.math.Signal

Applies a Savitzky-Golay smoother to the signal and returns the resulting new signal.

scale(double[][], int) - Static method in class peakml.math.Statistical

Calculates the standard score for either each row or each column.

ScanInfo - Class in peakml.io

Central point for collecting all information about a scan.

ScanInfo(double, Polarity) - Constructor for class peakml.io.ScanInfo

Constructs a new ScanInfo instance with the given retention-time and polarity.

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

Returns the closest matching scan number that corresponds to dRT for the current controller.

SELENIUM - Static variable in class peakml.chemistry.PeriodicTable

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

SET - Static variable in class peakml.io.SetInfo

Type indicating that this set is used to combine other sets

set(double, double) - Method in class peakml.math.BinArray

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

Sets the given value at the given row and column.

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

Sets the given value at the given row and column.

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

Sets the given value at the given row and column.

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

Sets the given value at the given row and column.

set(int, gPeak) - Method in class peakml.PeakData

set(int, int, double, double, double) - Method in class peakml.PeakData

Set all the properties of a peak at the given index at one go.

setAxisLabels(String, String) - Method in class peakml.util.jfreechart.FastTimePlot

setCharge(int) - Method in class peakml.chemistry.MolecularFormula.SubFormula

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

Sets the name of the column at the given index.

setColNames(Vector<String>) - Method in class peakml.math.DataFrame

Sets all the column-names in one step.

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

Sets all the column-names in one step.

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

Sets the current controller in the raw file.

setDatabaseID(String) - Method in class peakml.chemistry.Molecule

setDate(String) - Method in class peakml.io.ApplicationInfo

Sets the date of running the application.

setDate(Date) - Method in class peakml.io.Header

Sets the new date of the file to the given value.

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

Sets the new date of the file to the given value.

setDefaultN(int) - Method in class peakml.chemistry.MolecularFormula.SubFormula

setDescription(String) - Method in class peakml.chemistry.Molecule

Optional description for the molecule.

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

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

setGeneID(String) - Method in class peakml.chemistry.Protein

setID(String) - Method in class peakml.io.SampleInfo

Sets the id of the sample.

setInChi(String) - Method in class peakml.chemistry.Molecule

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

SetInfo - Class in peakml.io

Central point for collecting all information about a set.

SetInfo(String, int, int...) - Constructor for class peakml.io.SetInfo

Constructs a new set with the given id, type and measurement id's.

SetInfo(SetInfo) - Constructor for class peakml.io.SetInfo

Copy constructor, which makes a deep copy of the given SetInfo instance.

setIntensity(double) - Method in class peakml.BackgroundIon

setIntensity(double) - Method in class peakml.Centroid

setIntensity(double) - Method in class peakml.IPeak

Sets the intensity of this peak, for more information on mass see IPeak.getIntensity().

setIntensity(double) - Method in class peakml.IPeakSet

setIntensity(double) - Method in class peakml.MassChromatogram

setIntensity(int, double) - Method in class peakml.PeakData

Sets the given intensity at the given index.

setIntensity(double) - Method in class peakml.Spectrum

setLabel(String) - Method in class peakml.io.FileInfo

Sets the optional label for the file.

setLabel(String) - Method in class peakml.io.MeasurementInfo

Sets the optional label for the measurement.

setLabel(String) - Method in class peakml.io.SampleInfo

Sets the label of the sample.

setLocation(String) - Method in class peakml.io.FileInfo

Sets the complete path to the file.

setLogAxis(boolean) - Method in class peakml.util.jfreechart.FastErrorBarPlot

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

setLogScale(int) - Method in class peakml.util.jfreechart.LognAxis

setMass(double) - Method in class peakml.BackgroundIon

setMass(double) - Method in class peakml.Centroid

setMass(double) - Method in class peakml.IPeak

Sets the mass of this peak, for more information on mass see IPeak.getMass().

setMass(double) - Method in class peakml.IPeakSet

setMass(double) - Method in class peakml.MassChromatogram

setMass(int, double) - Method in class peakml.PeakData

Sets the given mass at the given index.

setMass(double) - Method in class peakml.Spectrum

setMeasurementID(int) - Method in class peakml.BackgroundIon

setMeasurementID(int) - Method in class peakml.Centroid

setMeasurementID(int) - Method in class peakml.IPeak

Sets the profile-id of this peak, for more information on mass see IPeak.getMeasurementID().

setMeasurementID(int) - Method in class peakml.IPeakSet

setMeasurementID(int) - Method in class peakml.MassChromatogram

setMeasurementID(int, int) - Method in class peakml.PeakData

Sets the given measurement-id at the given index.

setMeasurementID(int) - Method in class peakml.Spectrum

setName(String) - Method in class peakml.chemistry.MolecularFormula.SubFormula

setName(String) - Method in class peakml.chemistry.Molecule

setName(String) - Method in class peakml.io.ApplicationInfo

Sets the name of the application.

setName(String) - Method in class peakml.io.FileInfo

Sets the filename excluding the complete path of the file.

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

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

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

Sets the number of peaks associated with this header.

setOntologyRef(String) - Method in class peakml.Annotation

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

setOrientation(PlotOrientation) - Method in class peakml.util.jfreechart.FastTimePlot

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

Sets the new owner of the file.

setParameters(String) - Method in class peakml.io.ApplicationInfo

Sets the parameters used for the application.

setPatternID(int) - Method in class peakml.BackgroundIon

setPatternID(int) - Method in class peakml.Centroid

setPatternID(int) - Method in class peakml.IPeak

Sets the pattern-id of this peak, for more information on mass see IPeak.getPatternID().

setPatternID(int) - Method in class peakml.IPeakSet

setPatternID(int) - Method in class peakml.MassChromatogram

setPatternID(int, int) - Method in class peakml.PeakData

Sets the given pattern-id at the given index.

setPatternID(int) - Method in class peakml.Spectrum

setPeak(IPeak, Vector<IPeak>, Header) - Method in class peakml.util.swt.widget.DerivativeGraph

setPeak(IPeak, Header, HashMap<String, Integer>) - Method in class peakml.util.swt.widget.IPeakGraph

setProgress(double) - Method in class peakml.util.swt.dialog.ProgressDialog

setRetentionTime(double) - Method in class peakml.BackgroundIon

setRetentionTime(double) - Method in class peakml.Centroid

setRetentionTime(double) - Method in class peakml.chemistry.Molecule

Sets the optional expected retention time for this molecule.

setRetentionTime(double) - Method in class peakml.IPeak

Sets the retention time for this peak, for more information on retention time see IPeak.setRetentionTime(double).

setRetentionTime(double) - Method in class peakml.IPeakSet

setRetentionTime(double) - Method in class peakml.MassChromatogram

setRetentionTime(int, double) - Method in class peakml.PeakData

Sets the given retention-time at the given index.

setRetentionTime(double) - Method in class peakml.Spectrum

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

Sets the name of the row at the given index.

setRowNames(Vector<String>) - Method in class peakml.math.DataFrame

Sets all the row-names in one step.

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

Sets all the row-names in one step.

setScanID(int) - Method in class peakml.BackgroundIon

setScanID(int) - Method in class peakml.Centroid

setScanID(int) - Method in class peakml.IPeak

Sets the scan-id for this peak, for more information on scan-id see IPeak.getScanID().

setScanID(int) - Method in class peakml.IPeakSet

setScanID(int) - Method in class peakml.MassChromatogram

setScanID(int, int) - Method in class peakml.PeakData

Sets the given scan-id at the given index.

setScanID(int) - Method in class peakml.Spectrum

setShowAll(boolean) - Method in class peakml.util.jfreechart.FastErrorBarPlot

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

setSmiles(String) - Method in class peakml.chemistry.Molecule

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

setSynonyms(String[]) - Method in class peakml.chemistry.Molecule

Adds the list of synonyms to the internal synonyms list.

setSynonyms(Collection<String>) - Method in class peakml.chemistry.Molecule

Adds the list of synonyms to the internal synonyms list.

setTask(Runnable) - Method in class peakml.util.swt.dialog.ProgressDialog

setValue(String) - Method in class peakml.Annotation

Sets the given value.

setValue(int) - Method in class peakml.Annotation

Sets the given value.

setValue(double) - Method in class peakml.Annotation

Sets the given value.

setVersion(String) - Method in class peakml.io.ApplicationInfo

Sets the version of the application.

setVisible(boolean) - Method in class peakml.io.MeasurementInfo

Convenience function for user interface applications to keep track off whether to show this measurement or not.

setVisible(boolean) - Method in class peakml.io.SetInfo

Convenience function for user interface applications to keep track off whether to show this set or not.

sha1() - Method in class peakml.IPeak

Calculates the SHA-1 hash for this IPeak instance.

SHAPIRO_WILK_PVALUE - Static variable in class peakml.math.Statistical

The p-value in the result of the Statistical.shapiroWilk(double[]) method.

SHAPIRO_WILK_WSTAT - Static variable in class peakml.math.Statistical

The w-statistic in the result of the Statistical.shapiroWilk(double[]) method.

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

The Shapiro-Wilk test tests the null hypothesis that a sample x1, ..., xn came from a normally distributed population.

Signal - Class in peakml.math

Implementation of a approaches for interpreting and analysing signals.

Signal() - Constructor for class peakml.math.Signal

This constructor creates an empty signal (no elements).

Signal(int) - Constructor for class peakml.math.Signal

This constructor creates a signal of the given size.

Signal(double[]) - Constructor for class peakml.math.Signal

This constructor creates a signal out of the given y-values.

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

This constructor creates a signal out of the given x- and y-values.

Signal(Signal) - Constructor for class peakml.math.Signal

Copy-constructor, which copies the contents of the given signal to this signal.

Signal.Extremes - Class in peakml.math

Signal.Extremes() - Constructor for class peakml.math.Signal.Extremes

SILICON - Static variable in class peakml.chemistry.PeriodicTable

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

size() - Method in class peakml.IPeakSet

Returns the number of peaks in this peakset.

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

size() - Method in class peakml.PeakData

Returns the size of the container.

smooth(Filter) - Method in class peakml.math.Signal

Applies the given filter to the y-values and returns the resulting new signal.

sort_intensity_ascending - Static variable in class peakml.IPeak

Comparator sorting a set of IPeak on ascending intensity.

sort_intensity_descending - Static variable in class peakml.IPeak

Comparator sorting a set of IPeak on descending intensity.

sort_mass_ascending - Static variable in class peakml.IPeak

Comparator sorting a set of IPeak on ascending mass.

sort_mass_descending - Static variable in class peakml.IPeak

Comparator sorting a set of IPeak on descending mass.

sort_patternid_ascending - Static variable in class peakml.IPeak

Comparator sorting a set of IPeak on ascending pattern-id.

sort_patternid_descending - Static variable in class peakml.IPeak

Comparator sorting a set of IPeak on descending pattern-id.

sort_profileid_ascending - Static variable in class peakml.IPeak

Comparator sorting a set of IPeak on ascending profile-id.

sort_profileid_descending - Static variable in class peakml.IPeak

Comparator sorting a set of IPeak on descending profile-id.

sort_retentiontime_ascending - Static variable in class peakml.IPeak

Comparator sorting a set of IPeak on ascending retention time.

sort_retentiontime_descending - Static variable in class peakml.IPeak

Comparator sorting a set of IPeak on descending retention time.

sort_scanid_ascending - Static variable in class peakml.IPeak

Comparator sorting a set of IPeak on ascending scan-id.

sort_scanid_descending - Static variable in class peakml.IPeak

Comparator sorting a set of IPeak on descending scan-id.

SPEARMAN_CORRELATION - Static variable in class peakml.math.Statistical

The correlation value in the result of the Statistical.spearmanCorrelation(double[], double[]) method.

SPEARMAN_TWOSIDED_SIGNIFICANCE - Static variable in class peakml.math.Statistical

The significant level in the result of the Statistical.spearmanCorrelation(double[], double[]) method.

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

Calculates the Spearman correlation between this and the given signal.

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

Calculates the Spearman rank correlation and the two-sided significance levels of its deviation from zero between the two given arrays.

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

Spectrum<gPeak extends Peak> - Class in peakml

Type-binding for a spectrum (a single measurement on a mass spectrometer).

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

Calls the constructor Spectrum.Spectrum(PeakData, Type, Polarity, double) and assumes for type Spectrum.Type.MS1, for polarity Polarity.NEUTRAL and for precursormass -1.

Spectrum(PeakData<gPeak>, Polarity) - Constructor for class peakml.Spectrum

Calls the constructor Spectrum.Spectrum(PeakData, Type, Polarity, double) and assumes for type Spectrum.Type.MS1 and for precursormass -1.

Spectrum(PeakData<gPeak>, Spectrum.Type, Polarity) - Constructor for class peakml.Spectrum

Calls the constructor Spectrum.Spectrum(PeakData, Type, Polarity, double) and assumes for precursor mass -1.

Spectrum(PeakData<gPeak>, Spectrum.Type, Polarity, double) - Constructor for class peakml.Spectrum

Standard constructor for the spectrum.

Spectrum.DataFormat - Enum in peakml

The format (centroid or profile) of the data

Spectrum.Type - Enum in peakml

The type of data stored in the spectrum.

standard_masscalculator - Static variable in class peakml.MassChromatogram

Standard implementation of the mass calculator, which reduces memory requirements.

Statistical - Class in peakml.math

The class Statistical contains methods for performing basis statistical operations, such as mean, median, standard deviation.

Statistical() - Constructor for class peakml.math.Statistical

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

Calculates some basic statistics on the given array of data.

STDDEV - Static variable in class peakml.math.Statistical

The standard deviation value in the result of the Statistical.stats(double[]) method.

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

The standard deviation of a sample is one measure of statistical dispersion, calculated by taking the square root of the deviation.

subtract(double, double) - Method in class peakml.math.BinArray

SULFUR - Static variable in class peakml.chemistry.PeriodicTable

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

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

Calculates the sum of the values in the given array.

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

Suspends encoding of the stream.

SWTTools - Class in peakml.util.swt

Provides utility functions for SWT-applications.

SWTTools() - Constructor for class peakml.util.swt.SWTTools