Uses of Class
com.compomics.util.experiment.biology.ions.Ion.IonType
Package | Description |
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com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
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com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
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com.compomics.util.gui.spectrum |
Spectrum and Chromatogram visualization GUI classes.
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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 classesConstructor parameters in com.compomics.util.gui.spectrum with type arguments of type Ion.IonType Constructor Description IonLabelColorTableModel(HashMap<Ion.IonType,HashSet<Integer>> iontypes, HashSet<String> neutralLosses)
Constructor which sets a new table.