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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Modifier and Type | Field and Description |
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static NeutralLoss |
NeutralLoss.C3H9N
C3H9N loss.
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static NeutralLoss |
NeutralLoss.CH4OS
CH4OS loss.
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static NeutralLoss |
NeutralLoss.H2O
H2O loss.
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static NeutralLoss |
NeutralLoss.H3PO4
H3PO4 loss.
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static NeutralLoss |
NeutralLoss.HCNO
HCNO loss.
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static NeutralLoss |
NeutralLoss.HPO3
H3PO3 loss.
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static NeutralLoss |
NeutralLoss.NH3
NH3 loss.
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Modifier and Type | Method and Description |
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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.
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NeutralLoss[] |
NeutralLossCombination.getNeutralLossCombination()
Returns the neutral losses in this combination.
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abstract NeutralLoss[] |
Ion.getNeutralLosses()
Returns the possible neutral losses of this ion type.
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Modifier and Type | Method and Description |
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static void |
NeutralLoss.addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss to the class static map.
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static Ion |
Ion.getGenericIon(Ion.IonType ionType,
int subType,
NeutralLoss[] neutralLosses)
Convenience method returning a generic ion based on the given ion type.
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static double |
IonFactory.getLossesMass(NeutralLoss[] neutralLosses)
Convenience summing the masses of various neutral losses.
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static String |
Ion.getNeutralLossesAsString(NeutralLoss[] neutralLosses)
Returns the neutral loss (if any), the empty string if no loss.
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boolean |
NeutralLoss.isSameAs(NeutralLoss anotherNeutralLoss)
Method indicating whether another neutral loss is the same as the one
considered.
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Constructor and Description |
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NeutralLossCombination(NeutralLoss[] neutralLossCombination)
Constructor.
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Modifier and Type | Method and Description |
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NeutralLoss[] |
TagFragmentIon.getNeutralLosses() |
NeutralLoss[] |
ReporterIon.getNeutralLosses() |
NeutralLoss[] |
RelatedIon.getNeutralLosses() |
NeutralLoss[] |
PrecursorIon.getNeutralLosses() |
NeutralLoss[] |
PeptideFragmentIon.getNeutralLosses() |
NeutralLoss[] |
ImmoniumIon.getNeutralLosses() |
NeutralLoss[] |
Glycan.getNeutralLosses() |
NeutralLoss[] |
ElementaryIon.getNeutralLosses() |
Constructor and Description |
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PeptideFragmentIon(int fragmentType,
int number,
double mass,
NeutralLoss[] neutralLosses)
Constructor.
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PeptideFragmentIon(int fragmentType,
NeutralLoss[] neutralLosses)
Constructor for a generic ion.
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PrecursorIon(double theoreticMass,
NeutralLoss[] neutralLosses)
Constructor.
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PrecursorIon(NeutralLoss[] neutralLosses)
Constructor for a generic ion.
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TagFragmentIon(int fragmentType,
int number,
int subNumber,
double mass,
NeutralLoss[] neutralLosses,
double massGap)
Constructor.
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TagFragmentIon(int fragmentType,
NeutralLoss[] neutralLosses)
Constructor for a generic ion.
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Modifier and Type | Method and Description |
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ArrayList<NeutralLoss> |
Modification.getNeutralLosses()
Returns the neutral losses possibly encountered with this modification.
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Modifier and Type | Method and Description |
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void |
Modification.addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss.
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Modifier and Type | Method and Description |
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void |
Modification.setNeutralLosses(ArrayList<NeutralLoss> neutralLosses)
Sets the neutral losses possibly encountered with this modification.
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Modifier and Type | Method and Description |
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ArrayList<NeutralLoss> |
AnnotationParameters.getNeutralLosses()
Returns the considered neutral losses.
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Modifier and Type | Method and Description |
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void |
SpecificAnnotationParameters.addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss.
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void |
AnnotationParameters.addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss.
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void |
NeutralLossesMap.addNeutralLoss(NeutralLoss neutralLoss,
int bStart,
int yStart)
Adds a new neutral loss to the map.
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boolean |
SpectrumAnnotator.isAccounted(NeutralLossesMap neutralLosses,
NeutralLoss neutralLoss,
Ion ion)
Returns a boolean indicating whether the neutral loss should be accounted
for.
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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,HashSet<Integer>> iontypes,
ArrayList<NeutralLoss> neutralLosses,
boolean singleChargeSelected,
boolean doubleChargeSelected,
boolean moreThanTwoChargesSelected)
Deprecated.
used only in demo classes
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