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Packages that use NeutralLoss | |
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com.compomics.util.experiment.biology | This package contains experiement classes related to biological entities. |
com.compomics.util.experiment.biology.ions | This package contains experiment classes related to ions. |
com.compomics.util.experiment.biology.neutrallosses | |
com.compomics.util.experiment.identification | This package contains experiment classes related to identifications. |
com.compomics.util.gui.spectrum | This package contains GUI classes related to Spectrum and Chromatogram visualization. |
Uses of NeutralLoss in com.compomics.util.experiment.biology |
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Fields in com.compomics.util.experiment.biology declared as NeutralLoss | |
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static NeutralLoss |
NeutralLoss.CH4OS
CH4OS loss |
static NeutralLoss |
NeutralLoss.H2O
H2O loss |
static NeutralLoss |
NeutralLoss.H3PO4
H3PO4 loss |
static NeutralLoss |
NeutralLoss.HPO3
H3PO3 loss |
static NeutralLoss |
NeutralLoss.NH3
NH3 loss |
Methods in com.compomics.util.experiment.biology with parameters of type NeutralLoss | |
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boolean |
NeutralLoss.isSameAs(NeutralLoss anotherNeutralLoss)
Method indicating whether another neutral loss is the same as the one considered |
Uses of NeutralLoss in com.compomics.util.experiment.biology.ions |
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Methods in com.compomics.util.experiment.biology.ions that return types with arguments of type NeutralLoss | |
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ArrayList<NeutralLoss> |
PeptideFragmentIon.getNeutralLosses()
Returns the neutral losses for this fragment ion |
Constructor parameters in com.compomics.util.experiment.biology.ions with type arguments of type NeutralLoss | |
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PeptideFragmentIon(PeptideFragmentIon.PeptideFragmentIonType type,
int number,
double mass,
ArrayList<NeutralLoss> neutralLosses)
Construction for a peptide fragment with neutral loss. |
Uses of NeutralLoss in com.compomics.util.experiment.biology.neutrallosses |
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Subclasses of NeutralLoss in com.compomics.util.experiment.biology.neutrallosses | |
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class |
CH4OS
Neutral loss CH4OS, likely to be encountered on fragment from peptides containing an oxidized methionine. |
class |
H2O
A water loss, likely to be found on fragments from peptides containing the amino-acid D, E, S or T |
class |
H3PO4
A phosphorylation loss, likely to be found on fragments from phosphorylated peptides on Y. |
class |
HPO3
A phosphorylation loss, likely to be found on fragments from phosphorylated peptides on S or T. |
class |
NH3
A nitrium loss, likely to be found on fragments from peptides containing the amino-acid K, N, Q or R. |
Uses of NeutralLoss in com.compomics.util.experiment.identification |
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Methods in com.compomics.util.experiment.identification that return types with arguments of type NeutralLoss | |
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static HashMap<NeutralLoss,Integer> |
SpectrumAnnotator.getDefaultLosses(Peptide peptide)
Returns the possible neutral losses expected by default for a given peptide. |
static HashMap<NeutralLoss,Integer> |
SpectrumAnnotator.getDefaultLosses(Peptide peptide,
ArrayList<NeutralLoss> imposedNeutralLosses)
Returns the neutral losses map by default for a given peptide and a given list of neutral losses. |
Methods in com.compomics.util.experiment.identification with parameters of type NeutralLoss | |
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boolean |
SpectrumAnnotator.isAccounted(HashMap<NeutralLoss,Integer> neutralLosses,
NeutralLoss neutralLoss,
PeptideFragmentIon fragmentIon,
Peptide peptide)
Returns a boolean indicating whether the neutral loss should be accounted for |
Method parameters in com.compomics.util.experiment.identification with type arguments of type NeutralLoss | |
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ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
HashMap<NeutralLoss,Integer> neutralLosses,
ArrayList<Integer> charges)
Returns the currently matched ions with the given settings |
static HashMap<NeutralLoss,Integer> |
SpectrumAnnotator.getDefaultLosses(Peptide peptide,
ArrayList<NeutralLoss> imposedNeutralLosses)
Returns the neutral losses map by default for a given peptide and a given list of neutral losses. |
ArrayList<IonMatch> |
SpectrumAnnotator.getSpectrumAnnotation(ArrayList<PeptideFragmentIon.PeptideFragmentIonType> expectedFragmentIons,
HashMap<NeutralLoss,Integer> neutralLosses,
ArrayList<Integer> charges,
MSnSpectrum spectrum,
Peptide peptide,
double intensityLimit,
double mzTolerance)
Returns the spectrum annotations of a spectrum in a list of IonMatches Note that, except for +1 precursors, fragments ions will be expected to have a charge strictly smaller than the precursor ion charge. |
boolean |
SpectrumAnnotator.isAccounted(HashMap<NeutralLoss,Integer> neutralLosses,
NeutralLoss neutralLoss,
PeptideFragmentIon fragmentIon,
Peptide peptide)
Returns a boolean indicating whether the neutral loss should be accounted for |
boolean |
SpectrumAnnotator.lossesValidated(HashMap<NeutralLoss,Integer> neutralLosses,
PeptideFragmentIon fragmentIon,
Peptide peptide)
Returns a boolean indicating whether the neutral losses of the given fragment ion are fit the requirement of the given neutral losses map |
ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(Peptide peptide,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> iontypes,
ArrayList<Integer> charges,
HashMap<NeutralLoss,Integer> neutralLosses,
Peak peak,
double massTolerance)
This method matches the potential fragment ions of a given peptide with a given peak. |
Uses of NeutralLoss in com.compomics.util.gui.spectrum |
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Method parameters in com.compomics.util.gui.spectrum with type arguments of type NeutralLoss | |
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static Vector<DefaultSpectrumAnnotation> |
SpectrumPanel.filterAnnotations(Vector<DefaultSpectrumAnnotation> annotations,
ArrayList<PeptideFragmentIon.PeptideFragmentIonType> fragmentIonTypes,
ArrayList<NeutralLoss> neutralLosses,
boolean singleChargeSelected,
boolean doubleChargeSelected,
boolean moreThanTwoChargesSelected)
Deprecated. Filtering of annotations should not be necessary anymore. |
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