Package | Description |
---|---|
com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
|
com.compomics.util.experiment.identification.modification |
Modification mapping and localization.
|
com.compomics.util.experiment.identification.modification.scores |
PTM scores.
|
com.compomics.util.experiment.identification.psm_scoring |
Main PSM scoring class.
|
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.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
IonFactory.getFragmentIons(Peptide peptide,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
This method returns the theoretic ions expected from a peptide.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
ModificationtableContent.getModificationPlotData(Peptide peptide,
Modification modification,
int nMod,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationParameters,
SpecificAnnotationParameters specificAnnotationParameters,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the modification plot series in the JFreechart format for one
PSM.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<Modification> modifications,
ModificationParameters modificationParameters,
Spectrum spectrum,
SequenceProvider sequenceProvider,
AnnotationParameters annotationParameters,
SpecificAnnotationParameters specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingParameters sequenceMatchingParameters,
SequenceMatchingParameters modificationSequenceMatchingParameters,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the modification
possible locations.
|
Modifier and Type | Method and Description |
---|---|
double |
PsmScoresEstimator.getDecreasingScore(Peptide peptide,
int peptideCharge,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationParameters,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
double |
PsmScoresEstimator.getScore(Peptide peptide,
int peptideCharge,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationParameters,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
double |
PsmScoresEstimator.getScore(Peptide peptide,
int peptideCharge,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationParameters,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
PsmScore psmScore)
Scores the match between the given peptide and spectrum using the given
score.
|
Modifier and Type | Method and Description |
---|---|
double |
SnrScore.getScore(Peptide peptide,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the score.
|
double |
HyperScore.getScore(Peptide peptide,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the hyperscore.
|
Modifier and Type | Field and Description |
---|---|
protected SpecificAnnotationParameters |
SpectrumAnnotator.specificAnnotationSettings
If provided, the annotator will only look for the ions included in the
specific annotation settings.
|
Modifier and Type | Method and Description |
---|---|
SpecificAnnotationParameters |
SpecificAnnotationParameters.clone() |
SpecificAnnotationParameters |
AnnotationParameters.getSpecificAnnotationParameters(String spectrumFile,
String spectrumTitle,
SpectrumIdentificationAssumption spectrumIdentificationAssumption,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters,
SpectrumAnnotator spectrumAnnotator)
Returns the annotation preferences specific to a spectrum and an
identification assumption.
|
Modifier and Type | Method and Description |
---|---|
IonMatch[] |
SpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the currently matched ions with the given settings using the
intensity filter.
|
abstract IonMatch[] |
SpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter)
Returns the currently matched ions with the given settings.
|
protected HashMap<Integer,ArrayList<Ion>> |
SpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings)
Returns the expected ions in a map indexed by the possible charges.
|
protected ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(SpecificAnnotationParameters specificAnnotationSettings,
double peakMz,
double peakIntensity)
This method matches the potential fragment ions of a given peptide with a
given peak.
|
Modifier and Type | Method and Description |
---|---|
Map<Integer,ArrayList<IonMatch>> |
PeptideSpectrumAnnotator.getCoveredAminoAcids(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
|
IonMatch[] |
TagSpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
IonMatch[] |
PeptideSpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the expected ions in a map indexed by the possible charges.
|
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)
Returns the expected ions in a map indexed by the possible charges.
|
IonMatch[] |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Tag tag)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using an intensity filter.
|
IonMatch[] |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Tag tag,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
IonMatch[] |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
|
IonMatch[] |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
IonMatch[] |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in an array of IonMatches.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
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,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a stream of IonMatches.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.matchPeak(Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings,
double peakMz,
double peakIntensity)
This method matches the potential fragment ions of a given peptide with a
given peak according to the annotation settings.
|
void |
PeptideSpectrumAnnotator.setPeptide(Peptide peptide,
int precursorCharge,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
SpecificAnnotationParameters specificAnnotationSettings)
Sets a new peptide to annotate.
|
void |
PeptideSpectrumAnnotator.setPeptide(Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons,
int precursorCharge,
SpecificAnnotationParameters specificAnnotationSettings)
Sets a new peptide to annotate.
|
Copyright © 2021. All rights reserved.