Package | Description |
---|---|
com.compomics.util.experiment.identification.modification |
Additional PSM scoring classes.
|
com.compomics.util.experiment.identification.modification.scores |
PTM scores.
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com.compomics.util.experiment.identification.psm_scoring.psm_scores |
Main PTM scoring classes.
|
com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
|
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators |
This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
|
com.compomics.util.gui.modification |
PTM GUI dialogs.
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com.compomics.util.gui.parameters.identification.advanced |
Dialogs for advanced identification parameters.
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com.compomics.util.parameters.identification |
Identification parameters.
|
Modifier and Type | Method and Description |
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static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
ModificationtableContent.getModificationPlotData(Peptide peptide,
Modification modification,
int nMod,
Spectrum spectrum,
AnnotationParameters annotationPreferences,
SpecificAnnotationParameters specificAnnotationPreferences)
Returns the modification plot series in the JFreechart format for one
PSM.
|
static ModificationtableContent |
ModificationtableContent.getModificationTableContent(PeptideAssumption peptideAssumption,
Modification modification,
int nMod,
Spectrum spectrum,
AnnotationParameters annotationParameters)
Get the table content.
|
Modifier and Type | Method and Description |
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static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<Modification> modifications,
Spectrum spectrum,
SequenceProvider sequenceProvider,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceMatchingParameters modificationSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the modification
possible locations.
|
Modifier and Type | Method and Description |
---|---|
double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Returns the score.
|
double |
HyperScore.getScore(Peptide peptide,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Returns the hyperscore.
|
Modifier and Type | Method and Description |
---|---|
AnnotationParameters |
AnnotationParameters.clone()
Clones the settings.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings)
Returns the currently matched ions with the given settings using the intensity filter.
|
abstract ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean useIntensityFilter)
Returns the currently matched ions with the given settings.
|
boolean |
AnnotationParameters.isSameAs(AnnotationParameters annotationSettings)
Returns a boolean indicating whether the given annotation settings are
the same as these ones.
|
Modifier and Type | Method and Description |
---|---|
Map<Integer,ArrayList<IonMatch>> |
PeptideSpectrumAnnotator.getCoveredAminoAcids(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getCurrentAnnotation(Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean useIntensityFilter) |
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getCurrentAnnotation(Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean useIntensityFilter) |
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Tag tag)
Returns the spectrum annotations of a spectrum in a list of IonMatches using an intensity filter.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Tag tag,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
Constructor and Description |
---|
SimplePeptideAnnotator(Peptide peptide,
int charge,
AnnotationParameters annotationSettings)
Constructor.
|
Constructor and Description |
---|
ModificationTable(Identification identification,
AnnotationParameters annotationParameters,
PeptideMatch peptideMatch,
Modification ptm,
boolean areaChart)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
AnnotationParameters |
AnnotationParametersDialog.getAnnotationSettings()
Returns the annotation settings as set by the user.
|
Constructor and Description |
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AnnotationParametersDialog(Dialog owner,
Frame parentFrame,
AnnotationParameters annotationSettings,
double maxFragmentIonAccuracy,
ArrayList<NeutralLoss> possibleNeutralLosses,
ArrayList<Integer> reporterIons,
boolean editable)
Creates a new AnnotationPreferencesDialog with a dialog as owner.
|
AnnotationParametersDialog(Frame parentFrame,
AnnotationParameters annotationSettings,
double maxFragmentIonAccuracy,
ArrayList<NeutralLoss> possibleNeutralLosses,
ArrayList<Integer> reporterIons,
boolean editable)
Creates a new AnnotationPreferencesDialog with a frame as owner.
|
Modifier and Type | Method and Description |
---|---|
AnnotationParameters |
IdentificationParameters.getAnnotationParameters()
Returns the annotation parameters used for identification.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationParameters.setAnnotationParameters(AnnotationParameters annotationParameters)
Sets the annotation parameters used for identification.
|
Constructor and Description |
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IdentificationParameters(String name,
String description,
SearchParameters searchParameters,
AnnotationParameters annotationParameters,
SequenceMatchingParameters sequenceMatchingParameters,
PeptideVariantsParameters peptideVariantsParameters,
GeneParameters geneParameters,
PsmScoringParameters psmScoringParameters,
PeptideAssumptionFilter peptideAssumptionFilter,
ModificationLocalizationParameters ModificationLocalizationParameters,
ProteinInferenceParameters proteinInferenceParameters,
IdMatchValidationParameters idValidationParameters,
FractionParameters fractionParameters)
Constructor.
|
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