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

A

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

The natural abundance of the element.

ACETONITRILE - Static variable in class peakml.chemistry.PeriodicTable

The index of acetonitrile in the PeriodicTable.elements array.

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

addAnnotation(Annotation) - Method in class peakml.Annotatable

Adds the given annotation instance to the hashmap.

addAnnotation(String, String) - Method in class peakml.Annotatable

Creates a new annotation with the given label and value, where the valuetype is automatically set to STRING.

addAnnotation(String, int) - Method in class peakml.Annotatable

Creates a new annotation with the given label and value, where the valuetype is automatically set to INTEGER.

addAnnotation(String, double) - Method in class peakml.Annotatable

Creates a new annotation with the given label and value, where the valuetype is automatically set to DOUBLE.

addAnnotation(String, String, Annotation.ValueType) - Method in class peakml.Annotatable

Creates a new annotation with the given label, value, and valuetype.

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

addAnnotations(Collection<Annotation>) - Method in class peakml.Annotatable

Adds the list of annotations to the hashmap.

addApplicationInfo(ApplicationInfo) - Method in class peakml.io.Header

Adds the given application information to the header.

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

Adds the given set as a child to this set.

addCoFactors(Vector<String>) - Method in class peakml.chemistry.Protein

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

addData(FastSpectrumPlot.Data) - Method in class peakml.util.jfreechart.FastSpectrumPlot

addData(FastTimePlot.Data) - Method in class peakml.util.jfreechart.FastTimePlot

addData(String, double[]) - Method in class peakml.util.swt.widget.IntensityTrendGraph

addData(FastTimePlot.Data) - Method in class peakml.util.swt.widget.TimePlot

addFileInfo(FileInfo) - Method in class peakml.io.MeasurementInfo

Adds the file info instance to the list of file infos.

addFileInfos(Collection<FileInfo>) - Method in class peakml.io.MeasurementInfo

Adds the collection of file infos to the list of file infos.

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

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

addInhibitors(Vector<String>) - Method in class peakml.chemistry.Protein

addMassChromatogram(int, int[], double[], double[], double[], String) - Method in class peakml.util.rjava.Project

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

Adds the given measurement id to the list of id's.

addMeasurementInfo(MeasurementInfo) - Method in class peakml.io.Header

Adds the given measurement information to the header.

addMeasurementInfos(Collection<MeasurementInfo>) - Method in class peakml.io.Header

Adds the given measurement informations to the header.

addMSnSpectrum(Spectrum<gPeak>) - Method in class peakml.Spectrum

Adds the given MSn spectrum to the list.

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

addPeakSet(int[]) - Method in class peakml.util.rjava.Project

addProducts(Vector<String>) - Method in class peakml.chemistry.Protein

addSampleInfo(SampleInfo) - Method in class peakml.io.Header

Adds the given sample information instance to the header.

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

addScanInfo(ScanInfo) - Method in class peakml.io.MeasurementInfo

Adds the scan info instance to the list of scan infos.

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

addScanInfos(Collection<ScanInfo>) - Method in class peakml.io.MeasurementInfo

Adds the collection of scan infos to the list of scan infos.

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

Adds the given set information to the header.

addSetInfos(Collection<SetInfo>) - Method in class peakml.io.Header

Adds the given set informations to the header.

addSubstrates(Vector<String>) - Method in class peakml.chemistry.Protein

addTerm(Vocabulary.Term) - Method in class peakml.io.Vocabulary

Adds the given term to the hashmap, with the Vocabulary.Term.id field used as a key.

ADDUCT - Static variable in class peakml.chemistry.PeriodicTable

The derivative can only be an adduct

ADDUCT_DEDUCT - Static variable in class peakml.chemistry.PeriodicTable

The derivative can be both an adduct as well as a deduct

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

Indicates whether this is only an adduct (PeriodicTable.ADDUCT), deduct (PeriodicTable.DEDUCT), or both (PeriodicTable.ADDUCT_DEDUCT).

adducts_positive - Static variable in class peakml.chemistry.PeriodicTable

Static, at startup initialized array of all the positive adducts kept in this class.

addVocabulary(Vocabulary) - Method in class peakml.io.Header

Adds the given vocabulary to the list of vocabularies associated with the header.

alt_id - Variable in class peakml.io.Vocabulary.Term

Vector with all the alternative id's for this term.

ALUMINUM - Static variable in class peakml.chemistry.PeriodicTable

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

Annotatable - Class in peakml

Base-class for all classes that support annotations.

Annotatable() - Constructor for class peakml.Annotatable

Annotation - Class in peakml

Implementation of a label-value pair.

Annotation(String, String) - Constructor for class peakml.Annotation

Constructs a new annotation instance, with the given label and value.

Annotation(String, String, Annotation.ValueType) - Constructor for class peakml.Annotation

Constructs a new annotation instance, with the given label, value, and type.

Annotation(String, int) - Constructor for class peakml.Annotation

Constructs a new annotation instance, with the given label, value, and type.

Annotation(String, double) - Constructor for class peakml.Annotation

Constructs a new annotation instance, with the given label, value, and type.

Annotation.ValueType - Enum in peakml

This enum defines the different types of annotations that can occur.

ApplicationInfo - Class in peakml.io

Collects information on a single application applied to the data.

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

Standard constructor, which fills the class-members with the given values.

ARSENIC - Static variable in class peakml.chemistry.PeriodicTable

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

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

Integer representation of the mass (this is also used to indicate the isotope for example C13).