Uses of Class
com.compomics.util.experiment.biology.ions.NeutralLoss
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.biology.ions.impl |
Ion implementations.
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com.compomics.util.experiment.biology.modifications | |
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 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 NeutralLoss
NeutralLoss. C3H9N
C3H9N loss.static NeutralLoss
NeutralLoss. CH4OS
CH4OS loss.static NeutralLoss
NeutralLoss. H2O
H2O loss.static NeutralLoss
NeutralLoss. H3PO4
H3PO4 loss.static NeutralLoss
NeutralLoss. HCNO
HCNO loss.static NeutralLoss
NeutralLoss. HPO3
H3PO3 loss.static 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 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 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