Package | Description |
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com.compomics.util.experiment.biology |
Experiment classes related to biological entities.
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com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
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com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
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com.compomics.util.gui.parameters.identification_parameters |
GUI classes for parameters, settings and preferences used for identification.
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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.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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Modifier and Type | Method and Description |
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static ArrayList<ArrayList<NeutralLoss>> |
IonFactory.getAccountedNeutralLosses(ArrayList<NeutralLoss> possibleNeutralLosses)
Convenience method returning the possible neutral losses combination as
accounted by the factory, i.e., for now up to two neutral losses per
peak.
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static ArrayList<NeutralLoss> |
IonFactory.getDefaultNeutralLosses()
Returns the default neutral losses.
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ArrayList<NeutralLoss> |
PTM.getNeutralLosses()
Returns the neutral losses possibly encountered with this modification.
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abstract ArrayList<NeutralLoss> |
Ion.getNeutralLosses()
Returns the possible neutral losses of this ion type.
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static ArrayList<NeutralLoss> |
IonFactory.getNeutralLosses(PtmSettings ptmSettings)
Returns a list containing the default neutral losses and the losses found
in the given modifications.
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Modifier and Type | Method and Description |
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void |
PTM.addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss.
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static void |
NeutralLoss.addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss to the class static map.
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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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Modifier and Type | Method and Description |
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static ArrayList<ArrayList<NeutralLoss>> |
IonFactory.getAccountedNeutralLosses(ArrayList<NeutralLoss> possibleNeutralLosses)
Convenience method returning the possible neutral losses combination as
accounted by the factory, i.e., for now up to two neutral losses per
peak.
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static Ion |
Ion.getGenericIon(Ion.IonType ionType,
int subType,
ArrayList<NeutralLoss> neutralLosses)
Convenience method returning a generic ion based on the given ion type.
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static double |
IonFactory.getLossesMass(ArrayList<NeutralLoss> neutralLosses)
Convenience summing the masses of various neutral losses.
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static String |
Ion.getNeutralLossesAsString(ArrayList<NeutralLoss> neutralLosses)
Returns the neutral loss (if any), the empty string if no loss.
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void |
PTM.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> |
TagFragmentIon.getNeutralLosses() |
ArrayList<NeutralLoss> |
ReporterIon.getNeutralLosses() |
ArrayList<NeutralLoss> |
RelatedIon.getNeutralLosses() |
ArrayList<NeutralLoss> |
PrecursorIon.getNeutralLosses() |
ArrayList<NeutralLoss> |
PeptideFragmentIon.getNeutralLosses() |
ArrayList<NeutralLoss> |
ImmoniumIon.getNeutralLosses() |
ArrayList<NeutralLoss> |
Glycan.getNeutralLosses() |
ArrayList<NeutralLoss> |
ElementaryIon.getNeutralLosses() |
Constructor and Description |
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PeptideFragmentIon(int fragmentType,
ArrayList<NeutralLoss> neutralLosses)
Constructor for a generic ion.
|
PeptideFragmentIon(int fragmentType,
int number,
double mass,
ArrayList<NeutralLoss> neutralLosses)
Constructor.
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PrecursorIon(ArrayList<NeutralLoss> neutralLosses)
Constructor for a generic ion.
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PrecursorIon(double theoreticMass,
ArrayList<NeutralLoss> neutralLosses)
Constructor.
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TagFragmentIon(int fragmentType,
ArrayList<NeutralLoss> neutralLosses)
Constructor for a generic ion.
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TagFragmentIon(int fragmentType,
int number,
int subNumber,
double mass,
ArrayList<NeutralLoss> neutralLosses,
double massGap)
Constructor.
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Modifier and Type | Method and Description |
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ArrayList<NeutralLoss> |
AnnotationSettings.getNeutralLosses()
Returns the considered neutral losses.
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Modifier and Type | Method and Description |
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void |
SpecificAnnotationSettings.addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss.
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void |
AnnotationSettings.addNeutralLoss(NeutralLoss neutralLoss)
Adds a neutral loss.
|
void |
NeutralLossesMap.addNeutralLoss(NeutralLoss neutralLoss,
Integer bStart,
Integer 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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Constructor and Description |
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AnnotationSettingsDialog(Dialog owner,
Frame parentFrame,
AnnotationSettings annotationSettings,
double maxFragmentIonAccuracy,
ArrayList<NeutralLoss> possibleNeutralLosses,
ArrayList<Integer> reporterIons,
boolean editable)
Creates a new AnnotationPreferencesDialog with a dialog as owner.
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AnnotationSettingsDialog(Frame parentFrame,
AnnotationSettings annotationSettings,
double maxFragmentIonAccuracy,
ArrayList<NeutralLoss> possibleNeutralLosses,
ArrayList<Integer> reporterIons,
boolean editable)
Creates a new AnnotationPreferencesDialog with a frame as owner.
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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,ArrayList<Integer>> iontypes,
ArrayList<NeutralLoss> neutralLosses,
boolean singleChargeSelected,
boolean doubleChargeSelected,
boolean moreThanTwoChargesSelected)
Deprecated.
don't use method based on the peak labels but on the data
type
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Constructor and Description |
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IonLabelColorTableModel(HashMap<Ion.IonType,HashSet<Integer>> iontypes,
ArrayList<NeutralLoss> neutralLosses)
Constructor which sets a new table.
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