Uses of Interface
com.compomics.util.gui.interfaces.SpectrumAnnotation

Packages that use SpectrumAnnotation

Package	Description
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

Uses of SpectrumAnnotation in com.compomics.util.experiment.identification.spectrum_annotation

Methods in com.compomics.util.experiment.identification.spectrum_annotation that return types with arguments of type SpectrumAnnotation

Modifier and Type	Method	Description
static Vector<SpectrumAnnotation>	SpectrumAnnotator.getSpectrumAnnotation(IonMatch[] ionMatches)	Translates the list of ion matches into a vector of annotations which can be read by the SpectrumPanel.

Uses of SpectrumAnnotation in com.compomics.util.gui.spectrum

Classes in com.compomics.util.gui.spectrum that implement SpectrumAnnotation

Modifier and Type	Class	Description
class	DefaultSpectrumAnnotation	This class provides a default implementation of the SpectrumAnnotation interface.

Methods in com.compomics.util.gui.spectrum that return types with arguments of type SpectrumAnnotation

Modifier and Type	Method	Description
static Vector<SpectrumAnnotation>	SpectrumPanel.filterAnnotations(Vector<SpectrumAnnotation> annotations, HashMap<Ion.IonType,HashSet<Integer>> iontypes, ArrayList<NeutralLoss> neutralLosses, boolean singleChargeSelected, boolean doubleChargeSelected, boolean moreThanTwoChargesSelected)	Deprecated. used only in demo classes

Methods in com.compomics.util.gui.spectrum with parameters of type SpectrumAnnotation

Modifier and Type	Method	Description
protected void	GraphicsPanel.annotate(SpectrumAnnotation aSA, Graphics g, HashMap<String,Integer> aAlreadyAnnotated, boolean mirrored)	This method attempts to find the specified SpectrumAnnotation in the current peak list and if so, annotates it correspondingly on the screen.

Method parameters in com.compomics.util.gui.spectrum with type arguments of type SpectrumAnnotation

Modifier and Type	Method	Description
static Vector<SpectrumAnnotation>	SpectrumPanel.filterAnnotations(Vector<SpectrumAnnotation> annotations, HashMap<Ion.IonType,HashSet<Integer>> iontypes, ArrayList<NeutralLoss> neutralLosses, boolean singleChargeSelected, boolean doubleChargeSelected, boolean moreThanTwoChargesSelected)	Deprecated. used only in demo classes
void	GraphicsPanel.setAnnotations(List<SpectrumAnnotation> aAnnotations)	This method sets all the annotations on this instance.
void	GraphicsPanel.setAnnotations(List<SpectrumAnnotation> aAnnotations, boolean annotateHighestPeak)	This method sets all the annotations on this instance.
void	GraphicsPanel.setAnnotationsMirrored(List<SpectrumAnnotation> aAnnotations)	This method sets all the annotations for the mirrored spectra.
void	GraphicsPanel.setAnnotationsMirrored(List<SpectrumAnnotation> aAnnotations, boolean annotateHighestPeak)	This method sets all the annotations for the mirrored spectra.