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

P

panDomainAxes(double, PlotRenderingInfo, Point2D) - Method in class peakml.util.jfreechart.FastSpectrumPlot

panDomainAxes(double, PlotRenderingInfo, Point2D) - Method in class peakml.util.jfreechart.FastTimePlot

panRangeAxes(double, PlotRenderingInfo, Point2D) - Method in class peakml.util.jfreechart.FastSpectrumPlot

panRangeAxes(double, PlotRenderingInfo, Point2D) - Method in class peakml.util.jfreechart.FastTimePlot

PARAM_A - Static variable in class peakml.math.function.LinearFunction

The a-parameter from the array returned by LinearFunction.getParameters().

PARAM_B - Static variable in class peakml.math.function.LinearFunction

The b-parameter from the array returned by LinearFunction.getParameters().

PARAM_MEAN - Static variable in class peakml.math.function.LogNormalFunction

The index of the mean-parameter in the array returned by LogNormalFunction.getParameters()

PARAM_MEAN - Static variable in class peakml.math.function.NormalFunction

The index of the mean-parameter in the array returned by NormalFunction.getParameters()

PARAM_SCALE - Static variable in class peakml.math.function.LogNormalFunction

The index of the scale-parameter in the array returned by LogNormalFunction.getParameters()

PARAM_SCALE - Static variable in class peakml.math.function.NormalFunction

The index of the scale-parameter in the array returned by NormalFunction.getParameters()

PARAM_VARIANCE - Static variable in class peakml.math.function.LogNormalFunction

The index of the variance-parameter in the array returned by LogNormalFunction.getParameters()

PARAM_VARIANCE - Static variable in class peakml.math.function.NormalFunction

The index of the variance-parameter in the array returned by NormalFunction.getParameters()

parse(String) - Static method in class peakml.io.dac.DACParser

parse(String) - Static method in class peakml.io.ParseResult

Calls the correct parse function based on the filename extension.

parse(InputStream, boolean) - Static method in class peakml.io.peakml.PeakMLParser

Parse function for blindly loading data from a PeakML file.

parse(InputStream, ParserProgressListener, boolean) - Static method in class peakml.io.peakml.PeakMLParser

Parse function for blindly loading data from a PeakML file.

parse(InputStream, PeakMLProgressListener, boolean) - Static method in class peakml.io.peakml.PeakMLParser

Parse function for blindly loading data from a PeakML file.

parse(String) - Static method in class peakml.io.xrawfile.IXRawParser

parseBackgroundIons(InputStream, ParserProgressListener) - Static method in class peakml.io.peakml.PeakMLParser

Parse function for loading a PeakML file containing only backgroundion entries.

parseCMS(InputStream) - Static method in class peakml.io.mzml.MZMLParser

parseCMS(InputStream) - Static method in class peakml.io.mzxml.MzXmlParser

Parse function for loading the data stored in a mzXML or mzData file.

parseIPeakSet(InputStream, ParserProgressListener) - Static method in class peakml.io.peakml.PeakMLParser

Parse function for loading a PeakML file containing only peakset entries (containing other types of entries).

parseMassChromatograms(InputStream, ParserProgressListener) - Static method in class peakml.io.peakml.PeakMLParser

Parse function for loading a PeakML file containing only masschromatogram entries.

parseOBO(InputStream) - Method in class peakml.io.Vocabulary

Simple parser for OWL-files issued by the Open Biomedial Ontologies foundry.

ParseResult - Class in peakml.io

Central class for collecting the data and meta-data of a file containing mass spectrometry data.

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

Standard constructor, which initializes the members to null.

ParseResult(Header, Measurement) - Constructor for class peakml.io.ParseResult

Constructs a new ParseResult with the given header and measurement.

ParserProgressListener - Interface in peakml.io

Interface acting as a progress listener for the parser classes.

parseTxt(InputStream) - Static method in class peakml.io.chemistry.MoleculeIO

parseXml(InputStream) - Static method in class peakml.io.chemistry.MoleculeIO

PDF - Static variable in class peakml.graphics.JFreeChartTools

Write in the PDF format, which has the graphics in vector format.

Peak - Class in peakml

Base-class for a single peak, which can either be a single data-point (Centroid), or a collection of data-points making up the peak (Profile).

Peak() - Constructor for class peakml.Peak

PeakData<gPeak extends Peak> - Class in peakml

Implementation of a container for peak-data.

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

Creates a new PeakData instance associated to the given PeakData.PeakFactory and of the given size.

PeakData(PeakData.PeakFactory<gPeak>, int, int[], int[], int[], double[], double[], double[]) - Constructor for class peakml.PeakData

Creates a new PeakData instance associated to the given PeakData.PeakFactory and of the given size.

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

Highly optimized copy constructor, which makes a deep-copy of the data stored in the given PeakData instance.

PeakData.PeakFactory<gPeak extends Peak> - Interface in peakml

Interface describing a factory for the creation of instances of the generic gPeak type.

PeakDataIterator<gPeak extends Peak> - Class in peakml

An iterator for peak-data, allowing for sequential access to Peak data stored in a PeakData instance.

peakml - package peakml

peakml.chemistry - package peakml.chemistry

peakml.graphics - package peakml.graphics

peakml.io - package peakml.io

peakml.io.chemistry - package peakml.io.chemistry

peakml.io.dac - package peakml.io.dac

peakml.io.mzml - package peakml.io.mzml

peakml.io.mzxml - package peakml.io.mzxml

peakml.io.peakml - package peakml.io.peakml

peakml.io.xrawfile - package peakml.io.xrawfile

peakml.math - package peakml.math

peakml.math.filter - package peakml.math.filter

peakml.math.function - package peakml.math.function

peakml.math.wavelet - package peakml.math.wavelet

peakml.util - package peakml.util

peakml.util.jfreechart - package peakml.util.jfreechart

peakml.util.rjava - package peakml.util.rjava

peakml.util.swt - package peakml.util.swt

peakml.util.swt.dialog - package peakml.util.swt.dialog

peakml.util.swt.widget - package peakml.util.swt.widget

PeakMLParser - Class in peakml.io.peakml

Central class for parsing PeakML type files.

PeakMLProgressListener - Interface in peakml.io.peakml

PeakMLWriter - Class in peakml.io.peakml

Central class for writing PeakML type files.

peaksOfMeasurements(Vector<IPeak>, Vector<Integer>) - Static method in class peakml.IPeak

Returns the peaks with one of the given list of measurement id's

PEARSON_CORRELATION - Static variable in class peakml.math.Statistical

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

PEARSON_FISHER - Static variable in class peakml.math.Statistical

The fisher transformed correlation (normally distributed) in the result of the Statistical.pearsonsCorrelation(double[], double[]) method.

PEARSON_FISHER_STDDEV - Static variable in class peakml.math.Statistical

The fisher transformed standard error value in the result of the Statistical.pearsonsCorrelation(double[], double[]) method.

PEARSON_TTEST - Static variable in class peakml.math.Statistical

The student's t-test value in the result of the Statistical.pearsonsCorrelation(double[], double[]) method.

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

Calculates the Pearson's correlation between this and the given signal.

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

In statistics, the Pearson product-moment correlation coefficient (sometimes referred to as the MCV or PMCC, and typically denoted by r) is a common measure of the correlation (linear dependence) between two variables X and Y.

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

PeriodicTable - Class in peakml.chemistry

This class stores the periodic table of elements with precise masses.

PeriodicTable() - Constructor for class peakml.chemistry.PeriodicTable

PeriodicTable.Derivative - Class in peakml.chemistry

http://mass-spec.stanford.edu/assets/SUMS_common_ESI_ions.pdf http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator/

PeriodicTable.Derivative(int, int, int, String, String, double) - Constructor for class peakml.chemistry.PeriodicTable.Derivative

Constructs a new adduct instance with the given information.

PeriodicTable.Element - Class in peakml.chemistry

Central class describing all the properties of an element.

PeriodicTable.Element(int, String, String, double, double, int, PeriodicTable.Isotope...) - Constructor for class peakml.chemistry.PeriodicTable.Element

Constructs a new element with the given information.

PeriodicTable.Isotope - Class in peakml.chemistry

Central class describing all the properties of an isotope.

PeriodicTable.Isotope(int, double, double) - Constructor for class peakml.chemistry.PeriodicTable.Isotope

Constructs a new instance of an isotope with the given properties.

PeriodicTable.NaturalIsotope - Class in peakml.chemistry

PeriodicTable.NaturalIsotope(String, double) - Constructor for class peakml.chemistry.PeriodicTable.NaturalIsotope

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

Randomly permutes the values in the given vector.

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

Randomly permutes the values in the given matrix.

PHOSPHORUS - Static variable in class peakml.chemistry.PeriodicTable

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

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

PNG - Static variable in class peakml.graphics.JFreeChartTools

Write in the PNG format, which is pixel-based but readable anywhere.

Polarity - Enum in peakml.chemistry

The polarity setting of the instrument used when collecting the data.

PolynomialFunction - Class in peakml.math.function

Implementation of a polynomial function, which can be plugged with the order (n) to use.

PolynomialFunction(int) - Constructor for class peakml.math.function.PolynomialFunction

Constructs a new polynomial function of the given order.

PolynomialFunction(double...) - Constructor for class peakml.math.function.PolynomialFunction

Constructs a new polynomial function with the given parameters.

POTASSIUM - Static variable in class peakml.chemistry.PeriodicTable

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

PPM(double, double) - Static method in class peakml.chemistry.PeriodicTable

This method calculates the parts per million for the given mass.

PPMNr(double, double) - Static method in class peakml.chemistry.PeriodicTable

Calculates the ppm-value for the given deviation to the given mass.

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

The string that identifies the OLE-application in the windows registry.

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

The string that identifies the OLE-application in the windows registry.

ProgressDialog - Class in peakml.util.swt.dialog

Implementation of a progress-dialog.

ProgressDialog(Shell, String) - Constructor for class peakml.util.swt.dialog.ProgressDialog

Project - Class in peakml.util.rjava

Project() - Constructor for class peakml.util.rjava.Project

Project(String[], String[], String[]) - Constructor for class peakml.util.rjava.Project

Protein - Class in peakml.chemistry

Protein(String, String, Protein.Type) - Constructor for class peakml.chemistry.Protein

Protein.Type - Enum in peakml.chemistry

proton - Static variable in class peakml.chemistry.PeriodicTable

The precise mass of a proton