Uses of Class
com.compomics.util.experiment.biology.ions.Ion

Packages that use Ion

Package	Description
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
com.compomics.util.experiment.biology.ions.impl	Ion implementations.
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
com.compomics.util.experiment.identification.peptide_fragmentation	Peptide fragment intensities.
com.compomics.util.experiment.identification.peptide_fragmentation.models	Predictors for peptide fragment intensities.
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators	This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

Uses of Ion in com.compomics.util.experiment.biology.ions

Methods in com.compomics.util.experiment.biology.ions that return Ion

Modifier and Type	Method	Description
static Ion	Ion.getGenericIon(Ion.IonType ionType, int subType)	Convenience method returning a generic ion based on the given ion type without neutral losses.
static Ion	Ion.getGenericIon(Ion.IonType ionType, int subType, NeutralLoss[] neutralLosses)	Convenience method returning a generic ion based on the given ion type.

Methods in com.compomics.util.experiment.biology.ions that return types with arguments of type Ion

Modifier and Type	Method	Description
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>	IonFactory.getFragmentIons(Peptide peptide, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	This method returns the theoretic ions expected from a peptide.
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>	IonFactory.getFragmentIons(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	This method returns all the theoretic ions expected from a peptide.
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>	IonFactory.getFragmentIons(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	This method returns the theoretic ions expected from a tag.

Methods in com.compomics.util.experiment.biology.ions with parameters of type Ion

Modifier and Type	Method	Description
abstract boolean	Ion.isSameAs(Ion anotherIon)	Returns a boolean indicating whether the ion is the same as another ion.

Uses of Ion in com.compomics.util.experiment.biology.ions.impl

Subclasses of Ion in com.compomics.util.experiment.biology.ions.impl

Modifier and Type	Class	Description
class	ElementaryIon	This class represents an elementary ion.
class	Glycan	This class represents a glycan.
class	ImmoniumIon	Represents an immonium ion.
class	PeptideFragmentIon	This class models a peptide fragment ion.
class	PrecursorIon	A precursor ion.
class	RelatedIon	Represents a related ion, i.e., an ion that is related to a given amino acid, and is its own factory.
class	ReporterIon	This class models a reporter ion and is its own factory.
class	TagFragmentIon	A fragment ion obtained from a tag.

Methods in com.compomics.util.experiment.biology.ions.impl with parameters of type Ion

Modifier and Type	Method	Description
boolean	ElementaryIon.isSameAs(Ion anotherIon)
boolean	Glycan.isSameAs(Ion anotherIon)
boolean	ImmoniumIon.isSameAs(Ion anotherIon)
boolean	PeptideFragmentIon.isSameAs(Ion anotherIon)
boolean	PrecursorIon.isSameAs(Ion anotherIon)
boolean	RelatedIon.isSameAs(Ion anotherIon)
boolean	ReporterIon.isSameAs(Ion anotherIon)
boolean	TagFragmentIon.isSameAs(Ion anotherIon)

Uses of Ion in com.compomics.util.experiment.identification.matches

Fields in com.compomics.util.experiment.identification.matches declared as Ion

Modifier and Type	Field	Description
Ion	IonMatch.ion	The matching ion.

Methods in com.compomics.util.experiment.identification.matches with parameters of type Ion

Modifier and Type	Method	Description
static String	IonMatch.getMatchKey(Ion ion, int charge)	Returns the key for the ion match uniquely representing a peak annotation.
static String	IonMatch.getMatchKey(Ion ion, int charge, IonMatchKeysCache ionMatchKeysCache)	Returns the key for the ion match uniquely representing a peak annotation.
static String	IonMatch.getPeakAnnotation(boolean html, Ion ion, int charge)	Returns the annotation to use for a given ion and charge as a String.
static String	IonMatch.getPeakAnnotation(Ion ion, int charge)	Returns the annotation to use for a given ion and charge as a String.

Constructors in com.compomics.util.experiment.identification.matches with parameters of type Ion

Modifier	Constructor	Description
	IonMatch(double peakMz, double peakIntensity, Ion ion, int charge)	Constructor for an ion match.

Uses of Ion in com.compomics.util.experiment.identification.peptide_fragmentation

Methods in com.compomics.util.experiment.identification.peptide_fragmentation with parameters of type Ion

Modifier and Type	Method	Description
Double	FragmentItensityPredictor.getIntentisy(Ion ion)	Returns the intensity expected for the given peak.

Uses of Ion in com.compomics.util.experiment.identification.peptide_fragmentation.models

Methods in com.compomics.util.experiment.identification.peptide_fragmentation.models with parameters of type Ion

Modifier and Type	Method	Description
static Double	SequestFragmentationModel.getIntensity(Ion ion)	Returns the intensity expected for the given ion.

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

Fields in com.compomics.util.experiment.identification.spectrum_annotation with type parameters of type Ion

Modifier and Type	Field	Description
protected HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>	SpectrumAnnotator.theoreticalFragmentIons	The theoretic fragment ions.

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

Modifier and Type	Method	Description
protected HashMap<Integer,ArrayList<Ion>>	SpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings)	Returns the expected ions in a map indexed by the possible charges.

Methods in com.compomics.util.experiment.identification.spectrum_annotation with parameters of type Ion

Modifier and Type	Method	Description
boolean	SpectrumAnnotator.chargeValidated(Ion theoreticIon, int charge, int precursorCharge)	Returns a boolean indicating whether the given charge can be found on the given fragment ion.
String	IonMatchKeysCache.getMatchKey(Ion ion, int charge)	Returns the key for the ion match uniquely representing a peak annotation.
boolean	SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses, NeutralLoss neutralLoss, Ion ion)	Returns a boolean indicating whether the neutral loss should be accounted for.
boolean	SpectrumAnnotator.lossesValidated(NeutralLossesMap neutralLosses, Ion theoreticIon)	Returns a boolean indicating whether the neutral losses of the given fragment ion fit the requirement of the given neutral losses map.
protected IonMatch	SpectrumAnnotator.matchInSpectrum(double[] spectrumMz, double[] spectrumIntensity, Ion theoreticIon, int inspectedCharge)	Matches a theoretic ion in the spectrum.
static ArrayList<IonMatch>	SpectrumAnnotator.matchReporterIon(Ion theoreticIon, int charge, Spectrum spectrum, double massTolerance)	Convenience method to match a reporter ion in a spectrum.

Uses of Ion in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

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

Modifier and Type	Method	Description
HashMap<Integer,ArrayList<Ion>>	PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the expected ions in a map indexed by the possible charges.
HashMap<Integer,ArrayList<Ion>>	PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)	Returns the expected ions in a map indexed by the possible charges.

Method parameters in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators with type arguments of type Ion

Modifier and Type	Method	Description
HashMap<Integer,ArrayList<Ion>>	PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)	Returns the expected ions in a map indexed by the possible charges.
IonMatch[]	PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments, boolean useIntensityFilter)	Returns the spectrum annotations of a spectrum in an array of IonMatches.
java.util.stream.Stream<IonMatch>	PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments, boolean useIntensityFilter)	Returns the spectrum annotations of a spectrum in a stream of IonMatches.
void	PeptideSpectrumAnnotator.setPeptide(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons, int precursorCharge, SpecificAnnotationParameters specificAnnotationSettings)	Sets a new peptide to annotate.

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

Methods in com.compomics.util.gui.spectrum that return Ion

Modifier and Type	Method	Description
Ion	IonLabelColorTableModel.getIonAtRow(int rowIndex)	Returns the ion type at the given row.

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

Modifier and Type	Method	Description
static Color	SpectrumPanel.determineDefaultFragmentIonColor(Ion ion, boolean isSpectrum)	Returns the peak color to be used for the given peak label.
static Color	SpectrumPanel.determineFragmentIonColor(Ion ion, boolean isSpectrum)	Returns the peak color to be used for the given peak label according to the color map.
static void	SpectrumPanel.setIonColor(Ion ion, Color color)	Sets an annotation color for the given ion.