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

Packages that use NeutralLoss

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.biology.modifications
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 NeutralLoss in com.compomics.util.experiment.biology.ions

Fields in com.compomics.util.experiment.biology.ions declared as NeutralLoss

Modifier and Type	Field	Description
static final NeutralLoss	NeutralLoss.C3H9N	C3H9N loss.
static final NeutralLoss	NeutralLoss.CH4OS	CH4OS loss.
static final NeutralLoss	NeutralLoss.H2O	H2O loss.
static final NeutralLoss	NeutralLoss.H3PO4	H3PO4 loss.
static final NeutralLoss	NeutralLoss.HCNO	HCNO loss.
static final NeutralLoss	NeutralLoss.HPO3	H3PO3 loss.
static final NeutralLoss	NeutralLoss.NH3	NH3 loss.

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

Modifier and Type	Method	Description
NeutralLoss	NeutralLoss.clone()
static NeutralLoss	NeutralLoss.getNeutralLoss(String name)	Returns the neutral loss associated to the given name in the static map of the class.
NeutralLoss[]	NeutralLossCombination.getNeutralLossCombination()	Returns the neutral losses in this combination.
abstract NeutralLoss[]	Ion.getNeutralLosses()	Returns the possible neutral losses of this ion type.

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

Modifier and Type	Method	Description
static void	NeutralLoss.addNeutralLoss(NeutralLoss neutralLoss)	Adds a neutral loss to the class static map.
static Ion	Ion.getGenericIon(Ion.IonType ionType, int subType, NeutralLoss[] neutralLosses)	Convenience method returning a generic ion based on the given ion type.
static double	IonFactory.getLossesMass(NeutralLoss[] neutralLosses)	Convenience summing the masses of various neutral losses.
static String	Ion.getNeutralLossesAsString(NeutralLoss[] neutralLosses)	Returns the neutral loss (if any), the empty string if no loss.
boolean	NeutralLoss.isSameAs(NeutralLoss anotherNeutralLoss)	Method indicating whether another neutral loss is the same as the one considered.

Constructors in com.compomics.util.experiment.biology.ions with parameters of type NeutralLoss

Modifier	Constructor	Description
	NeutralLossCombination(NeutralLoss[] neutralLossCombination)	Constructor.

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

Methods in com.compomics.util.experiment.biology.ions.impl that return NeutralLoss

Modifier and Type	Method	Description
NeutralLoss[]	ElementaryIon.getNeutralLosses()
NeutralLoss[]	Glycan.getNeutralLosses()
NeutralLoss[]	ImmoniumIon.getNeutralLosses()
NeutralLoss[]	PeptideFragmentIon.getNeutralLosses()
NeutralLoss[]	PrecursorIon.getNeutralLosses()
NeutralLoss[]	RelatedIon.getNeutralLosses()
NeutralLoss[]	ReporterIon.getNeutralLosses()
NeutralLoss[]	TagFragmentIon.getNeutralLosses()

Constructors in com.compomics.util.experiment.biology.ions.impl with parameters of type NeutralLoss

Modifier	Constructor	Description
	PeptideFragmentIon(int fragmentType, int number, double mass, NeutralLoss[] neutralLosses)	Constructor.
	PeptideFragmentIon(int fragmentType, NeutralLoss[] neutralLosses)	Constructor for a generic ion.
	PrecursorIon(double theoreticMass, NeutralLoss[] neutralLosses)	Constructor.
	PrecursorIon(NeutralLoss[] neutralLosses)	Constructor for a generic ion.
	TagFragmentIon(int fragmentType, int number, int subNumber, double mass, NeutralLoss[] neutralLosses, double massGap)	Constructor.
	TagFragmentIon(int fragmentType, NeutralLoss[] neutralLosses)	Constructor for a generic ion.

Uses of NeutralLoss in com.compomics.util.experiment.biology.modifications

Methods in com.compomics.util.experiment.biology.modifications that return types with arguments of type NeutralLoss

Modifier and Type	Method	Description
ArrayList<NeutralLoss>	Modification.getNeutralLosses()	Returns the neutral losses possibly encountered with this modification.

Methods in com.compomics.util.experiment.biology.modifications with parameters of type NeutralLoss

Modifier and Type	Method	Description
void	Modification.addNeutralLoss(NeutralLoss neutralLoss)	Adds a neutral loss.

Method parameters in com.compomics.util.experiment.biology.modifications with type arguments of type NeutralLoss

Modifier and Type	Method	Description
void	Modification.setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)	Sets the neutral losses possibly encountered with this modification.

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

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

Modifier and Type	Method	Description
ArrayList<NeutralLoss>	AnnotationParameters.getNeutralLosses()	Returns the considered neutral losses.

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

Modifier and Type	Method	Description
void	AnnotationParameters.addNeutralLoss(NeutralLoss neutralLoss)	Adds a neutral loss.
void	NeutralLossesMap.addNeutralLoss(NeutralLoss neutralLoss, int bStart, int yStart)	Adds a new neutral loss to the map.
void	SpecificAnnotationParameters.addNeutralLoss(NeutralLoss neutralLoss)	Adds a neutral loss.
boolean	SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses, NeutralLoss neutralLoss, Ion ion)	Returns a boolean indicating whether the neutral loss should be accounted for.

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

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

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