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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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ArrayList<NeutralLoss> |
NeutralLossesMap.getAccountedNeutralLosses()
Returns an arraylist of implemented neutral losses |
Methods in com.compomics.util.experiment.identification with parameters of type NeutralLoss | |
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void |
NeutralLossesMap.addNeutralLoss(NeutralLoss neutralLoss,
int bStart,
int yStart)
Adds a new neutral loss to the map |
boolean |
NeutralLossesMap.containsLoss(NeutralLoss neutralLoss)
Returns a boolean indicating whether a loss is implemented in the mapping |
int |
NeutralLossesMap.getBStart(NeutralLoss neutralLoss)
Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1) |
int |
NeutralLossesMap.getYStart(NeutralLoss neutralLoss)
Returns the amino acid where a neutral loss should start being accounted for when predicting b ions (counting from N-terminus, first aa is 1) |
boolean |
SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses,
NeutralLoss neutralLoss,
PeptideFragmentIon fragmentIon,
Peptide peptide)
Returns a boolean indicating whether the neutral loss should be accounted for. |
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)
Filters the annotations and returns the annotations matching the currently selected types. |
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