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

M

MAGNESIUM - Static variable in class peakml.chemistry.PeriodicTable

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

main(String[]) - Static method in class peakml.chemistry.MolecularFormula

main(String[]) - Static method in class peakml.graphics.Colormap

main(String[]) - Static method in class peakml.math.wavelet.MarrWavelet

maintenance - Static variable in class peakml.Version

The maintenance part of the version, which is changed for bug-fixes

major - Static variable in class peakml.Version

The major part of the version, which is changed for major interface changes

MANGANESE - Static variable in class peakml.chemistry.PeriodicTable

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

MarrWavelet - Class in peakml.math.wavelet

MarrWavelet(double, double) - Constructor for class peakml.math.wavelet.MarrWavelet

scale - peak width spacing - 0.001

Mass - Enum in peakml.chemistry

In chemistry two methods for calculating the mass of a molecule are used.

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

The additional mass of the adduct.

mass - Variable in class peakml.chemistry.PeriodicTable.NaturalIsotope

MassChromatogram<gPeak extends Peak> - Class in peakml

Implementation of a mass chromatogram, usable for LC-MS, GC-MS, or any 2 dimensional mass spectrometry method.

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

Constructs a new mass chromatogram instance out of the given set of peaks (either Centroid or Profile).

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

Constructs a new mass chromatogram instance out of the given set of peaks (either Centroid or Profile).

MassChromatogram.MassCalculator<Type extends Peak> - Interface in peakml

In order to accommodate for a different calculation of the mass for a mass chromatogram, implement this interface.

massvariance - Variable in class peakml.chemistry.PeriodicTable.Element

The mass variance of the element.

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

A ready to-go implementation of the match-function, which works on IPeak.

match(Vector<IPeakSet<IPeak>>, double, IPeak.MatchCompare) - Static method in class peakml.IPeak

General function for matching peaks together.

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

Calculates the maximum value from the values in the given array.

maxima - Variable in class peakml.math.Signal.Extremes

MAXIMUM - Static variable in class peakml.math.Statistical

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

MEAN - Static variable in class peakml.math.Statistical

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

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

Calculates the mean of the values in the given array.

measurement - Variable in class peakml.io.ParseResult

The data associated to the measurement.

Measurement - Interface in peakml

Binding type for all classes that contain data from a measurement.

MeasurementInfo - Class in peakml.io

Central point for collecting all information about a measurement.

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

Constructs a new measurement information with the given id of the measurement and the given id of the sample.

MeasurementInfo(int, MeasurementInfo) - Constructor for class peakml.io.MeasurementInfo

Copy-constructor which copies the contents of the given measurement information into this instance.

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

Calculates the median of the values in the given array.

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

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

METHANOL - Static variable in class peakml.chemistry.PeriodicTable

The index of methanol in the PeriodicTable.elements array.

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

Calculates the minimum value from the values in the given array.

minima - Variable in class peakml.math.Signal.Extremes

MINIMUM - Static variable in class peakml.math.Statistical

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

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

minor - Static variable in class peakml.Version

The minor part of the version, which is changed when interfaces have been added

MLE(double[]) - Static method in class peakml.math.function.LinearFunction

Performs an estimation of the best starting parameters for the fitting procedure.

MLE(double[]) - Static method in class peakml.math.function.LogNormalFunction

Implementation of the maximum likelihood estimation for log-normal distributions, which can be used as an initial best guess for the parameters for the LMA fit algorithm.

MLE(double[]) - Static method in class peakml.math.function.NormalFunction

Implementation of the maximum likelihood estimation for normal distributions, which can be used as an initial best guess for the parameters for the LMA fit algorithm.

MLE(int, double[]) - Static method in class peakml.math.function.PolynomialFunction

Performs an estimation of the best starting parameters for the fitting procedure.

MolecularFormula - Class in peakml.chemistry

Implementation of a container keeping track of the atom counts for a molecular formula.

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

Constructs an empty formula.

MolecularFormula(String) - Constructor for class peakml.chemistry.MolecularFormula

Constructs a new class with the given formula by calling MolecularFormula.Init(String,String).

MolecularFormula(String, String) - Constructor for class peakml.chemistry.MolecularFormula

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

Copy-constructor, which copies the complete contents of the given instance.

MolecularFormula.SubFormula - Class in peakml.chemistry

MolecularFormula.SubFormula(String, int, int, int[]) - Constructor for class peakml.chemistry.MolecularFormula.SubFormula

MolecularFormula.SubFormula(MolecularFormula.SubFormula) - Constructor for class peakml.chemistry.MolecularFormula.SubFormula

molecularweight - Variable in class peakml.chemistry.PeriodicTable.Element

The molecular weight of the element.

Molecule - Class in peakml.chemistry

Implementation of a class tracking all the properties of a molecule.

Molecule(String, String, String) - Constructor for class peakml.chemistry.Molecule

Constructs a new Molecule instance with the given id, name and molecular formula.

Molecule(String, String, MolecularFormula) - Constructor for class peakml.chemistry.Molecule

Constructs a new Molecule instance with the given id, name and molecular formula.

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

Constructs a new Molecule instance with the given id, name and mass.

MoleculeDB - Class in peakml.chemistry

MoleculeDB(String, HashMap<String, Molecule>) - Constructor for class peakml.chemistry.MoleculeDB

MoleculeIO - Class in peakml.io.chemistry

MoleculeIO() - Constructor for class peakml.io.chemistry.MoleculeIO

MOLYBDENUM - Static variable in class peakml.chemistry.PeriodicTable

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

monoisotopicweight - Variable in class peakml.chemistry.PeriodicTable.Isotope

The precise mass of the isotope.

MZMLParser - Class in peakml.io.mzml

MZMLParser() - Constructor for class peakml.io.mzml.MZMLParser

MZMLWriter - Class in peakml.io.mzml

MZMLWriter() - Constructor for class peakml.io.mzml.MZMLWriter

MzXmlParser - Class in peakml.io.mzxml

Implementation of a parser for the mzXML file format, with additional, hidden support for the mzData file format.

MzXmlParser() - Constructor for class peakml.io.mzxml.MzXmlParser

MzXmlWriter - Class in peakml.io.mzxml

MzXmlWriter() - Constructor for class peakml.io.mzxml.MzXmlWriter