Uses of Enum
com.compomics.util.experiment.biology.ions.Ion.IonType

Packages that use Ion.IonType

Package	Description
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
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 Ion.IonType in com.compomics.util.experiment.biology.ions

Fields in com.compomics.util.experiment.biology.ions declared as Ion.IonType

Modifier and Type	Field	Description
protected Ion.IonType	Ion.type	Type of ion.

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

Modifier and Type	Method	Description
Ion.IonType	Ion.getType()	Returns the ion type.
static Ion.IonType	Ion.IonType.valueOf(String name)	Returns the enum constant of this type with the specified name.
static Ion.IonType[]	Ion.IonType.values()	Returns an array containing the constants of this enum type, in the order they are declared.

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

Modifier and Type	Method	Description
static ArrayList<Ion.IonType>	Ion.getImplementedIonTypes()	Returns the implemented ion types.

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

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.
static int[]	Ion.getPossibleSubtypes(Ion.IonType ionType)	Returns an array of possible subtypes.
static HashSet<Integer>	Ion.getPossibleSubtypesAsSet(Ion.IonType ionType)	Returns a hashset of possible subtypes.
static String	Ion.getTypeAsString(Ion.IonType type)	Returns the type of ion as string.

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

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

Modifier and Type	Method	Description
HashMap<Ion.IonType,HashSet<Integer>>	AnnotationParameters.getIonTypes()	Returns the type of ions annotated.
HashMap<Ion.IonType,HashSet<Integer>>	SpecificAnnotationParameters.getIonTypes()	Returns the map of ions to annotate.

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

Modifier and Type	Method	Description
void	AnnotationParameters.addIonType(Ion.IonType ionType)	Adds a new ion type to annotate.
void	AnnotationParameters.addIonType(Ion.IonType ionType, int subType)	Adds a new ion type and subtype to annotate.
void	SpecificAnnotationParameters.addIonType(Ion.IonType ionType)	Adds a new ion type to annotate.
void	SpecificAnnotationParameters.addIonType(Ion.IonType ionType, int subType)	Adds a new ion type and subtype to annotate.

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

Modifier and Type	Method	Description
void	SpecificAnnotationParameters.setSelectedIonsMap(HashMap<Ion.IonType,HashSet<Integer>> selectedIonsMap)	Sets the map of ions to annotate.

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

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

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

Constructor parameters in com.compomics.util.gui.spectrum with type arguments of type Ion.IonType

Modifier	Constructor	Description
	IonLabelColorTableModel(HashMap<Ion.IonType,HashSet<Integer>> iontypes, HashSet<String> neutralLosses)	Constructor which sets a new table.