Uses of Class
peakml.IPeak

Packages that use IPeak

peakml
peakml.io.peakml
peakml.util.swt.widget

Uses of IPeak in peakml

Classes in peakml with type parameters of type IPeak

class

IPeakSet<Type extends IPeak> Implementation of a class maintaining a set of peaks.

Subclasses of IPeak in peakml

class	BackgroundIon<gPeak extends Peak> Implementation of a background ion, useable for all types of mass spectrometry (e.g.
class	Centroid Implementation of a centroid or data-point in a mass spectrometry spectrum or profile.
class	IPeakSet<Type extends IPeak> Implementation of a class maintaining a set of peaks.
class	MassChromatogram<gPeak extends Peak> Implementation of a mass chromatogram, usable for LC-MS, GC-MS, or any 2 dimensional mass spectrometry method.
class	Peak 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).
class	Spectrum<gPeak extends Peak> Type-binding for a spectrum (a single measurement on a mass spectrometer).

Methods in peakml that return IPeak

static IPeak	IPeak.getBestPeakOnMass(java.util.Vector<IPeak> peaks, double mass) Locates the closest matching peak on the given mass from the list of peaks.
static IPeak	IPeak.getBestPeakOnRT(java.util.Vector<IPeak> peaks, double rt) Locates the closest matching peak on the given retention time from the list of peaks.

Methods in peakml that return types with arguments of type IPeak

static java.util.Vector<IPeak>	IPeak.findRelatedPeaks(java.util.Vector<IPeak> peaks, double minrt, double rtwindow, IPeak.RelationCompare<IPeak> compare) This method attempts to find all the peaks that are related to each other.
static java.util.Vector<IPeakSet<IPeak>>	IPeak.match(java.util.Vector<IPeakSet<IPeak>> samples, double ppm) A ready to-go implementation of the match-function, which works on IPeak.
static java.util.Vector<IPeakSet<IPeak>>	IPeak.match(java.util.Vector<IPeakSet<IPeak>> samples, double ppm, IPeak.MatchCompare compare) General function for matching peaks together.
static java.util.Vector<IPeak>	IPeak.peaksOfMeasurements(java.util.Vector<IPeak> peaks, java.util.Vector<java.lang.Integer> measurementids) Returns the peaks with one of the given list of measurement id's
static java.util.Vector<IPeak>	IPeak.unpack(IPeak peak) Recursive function, which unpacks all the of the IPeakSet lists and returns a vector with all the non-list instances contained in the given peak.

Methods in peakml with parameters of type IPeak

int	IPeak.AnnotationAscending.compare(IPeak arg0, IPeak arg1) Compare function, which converts the data in the IPeak instances to comparable data and sorts accordingly.
int	IPeak.AnnotationDescending.compare(IPeak arg0, IPeak arg1) Compare function, which converts the data in the IPeak instances to comparable data and sorts accordingly.
static java.util.Vector<IPeak>	IPeak.unpack(IPeak peak) Recursive function, which unpacks all the of the IPeakSet lists and returns a vector with all the non-list instances contained in the given peak.

Method parameters in peakml with type arguments of type IPeak

static java.util.Vector<IPeak>	IPeak.findRelatedPeaks(java.util.Vector<IPeak> peaks, double minrt, double rtwindow, IPeak.RelationCompare<IPeak> compare) This method attempts to find all the peaks that are related to each other.
static java.util.Vector<IPeak>	IPeak.findRelatedPeaks(java.util.Vector<IPeak> peaks, double minrt, double rtwindow, IPeak.RelationCompare<IPeak> compare) This method attempts to find all the peaks that are related to each other.
static IPeak	IPeak.getBestPeakOnMass(java.util.Vector<IPeak> peaks, double mass) Locates the closest matching peak on the given mass from the list of peaks.
static IPeak	IPeak.getBestPeakOnRT(java.util.Vector<IPeak> peaks, double rt) Locates the closest matching peak on the given retention time from the list of peaks.
static java.util.Vector<IPeakSet<IPeak>>	IPeak.match(java.util.Vector<IPeakSet<IPeak>> samples, double ppm) A ready to-go implementation of the match-function, which works on IPeak.
static java.util.Vector<IPeakSet<IPeak>>	IPeak.match(java.util.Vector<IPeakSet<IPeak>> samples, double ppm, IPeak.MatchCompare compare) General function for matching peaks together.
static java.util.Vector<IPeak>	IPeak.peaksOfMeasurements(java.util.Vector<IPeak> peaks, java.util.Vector<java.lang.Integer> measurementids) Returns the peaks with one of the given list of measurement id's

Constructors in peakml with parameters of type IPeak

IPeakSet(Type[] set)
Constructs a new peakset with the given set of peaks.

Uses of IPeak in peakml.io.peakml

Methods in peakml.io.peakml with parameters of type IPeak

void	PeakMLProgressListener.onIPeak(IPeak peak)

Method parameters in peakml.io.peakml with type arguments of type IPeak

static void	PeakMLWriter.write(Header header, java.util.Vector<? extends IPeak> peaks, WriterProgressListener listener, java.io.OutputStream out, java.lang.String stylesheet) Generic method for writing a set of IPeak elements (the real class unknown).
static void	PeakMLWriter.writeIPeakSets(Header header, java.util.Vector<IPeakSet<IPeak>> peaksets, WriterProgressListener listener, java.io.OutputStream out, java.lang.String stylesheet) Method for writing a set of IPeakSet peaks to a PeakML file.

Uses of IPeak in peakml.util.swt.widget

Methods in peakml.util.swt.widget with parameters of type IPeak

void	IPeakGraph.setPeak(IPeak peak, Header header, java.util.HashMap<java.lang.String,java.lang.Integer> colors)
void	DerivativeGraph.setPeak(IPeak peak, java.util.Vector<IPeak> peaks, Header header)

Method parameters in peakml.util.swt.widget with type arguments of type IPeak

void	DerivativeGraph.setPeak(IPeak peak, java.util.Vector<IPeak> peaks, Header header)