Package | Description |
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
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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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Modifier and Type | Field and Description |
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protected Ion.IonType |
Ion.type
Type of ion.
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Modifier and Type | Method and Description |
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Ion.IonType |
Ion.getType()
Returns the ion type.
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static Ion.IonType |
Ion.IonType.valueOf(String name)
Returns the enum constant of this type with the specified name.
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static Ion.IonType[] |
Ion.IonType.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
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Modifier and Type | Method and Description |
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static ArrayList<Ion.IonType> |
Ion.getImplementedIonTypes()
Returns the implemented ion types.
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Modifier and Type | Method and Description |
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static Ion |
Ion.getGenericIon(Ion.IonType ionType,
int subType)
Convenience method returning a generic ion based on the given ion type
without neutral losses.
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static Ion |
Ion.getGenericIon(Ion.IonType ionType,
int subType,
ArrayList<NeutralLoss> neutralLosses)
Convenience method returning a generic ion based on the given ion type.
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static ArrayList<Integer> |
Ion.getPossibleSubtypes(Ion.IonType ionType)
Returns an arraylist of possible subtypes.
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static String |
Ion.getTypeAsString(Ion.IonType type)
Returns the type of ion as string.
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Modifier and Type | Method and Description |
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HashMap<Ion.IonType,HashSet<Integer>> |
SpecificAnnotationSettings.getIonTypes()
Returns the map of ions to annotate.
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HashMap<Ion.IonType,HashSet<Integer>> |
AnnotationSettings.getIonTypes()
Returns the type of ions annotated.
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Modifier and Type | Method and Description |
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void |
SpecificAnnotationSettings.addIonType(Ion.IonType ionType)
Adds a new ion type to annotate.
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void |
AnnotationSettings.addIonType(Ion.IonType ionType)
Adds a new ion type to annotate.
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void |
SpecificAnnotationSettings.addIonType(Ion.IonType ionType,
int subType)
Adds a new ion type and subtype to annotate.
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void |
AnnotationSettings.addIonType(Ion.IonType ionType,
int subType)
Adds a new ion type and subtype to annotate.
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Modifier and Type | Method and Description |
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void |
SpecificAnnotationSettings.setSelectedIonsMap(HashMap<Ion.IonType,HashSet<Integer>> selectedIonsMap)
Sets the map of ions to annotate.
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Modifier and Type | Method and Description |
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static Vector<SpectrumAnnotation> |
SpectrumPanel.filterAnnotations(Vector<SpectrumAnnotation> annotations,
HashMap<Ion.IonType,ArrayList<Integer>> iontypes,
ArrayList<NeutralLoss> neutralLosses,
boolean singleChargeSelected,
boolean doubleChargeSelected,
boolean moreThanTwoChargesSelected)
Deprecated.
don't use method based on the peak labels but on the data
type
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Constructor and Description |
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IonLabelColorTableModel(HashMap<Ion.IonType,HashSet<Integer>> iontypes,
ArrayList<NeutralLoss> neutralLosses)
Constructor which sets a new table.
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