Uses of Class
com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters

Packages that use SpecificAnnotationParameters

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.

Uses of SpecificAnnotationParameters in com.compomics.util.experiment.biology.ions

Methods in com.compomics.util.experiment.biology.ions with parameters of type SpecificAnnotationParameters

Modifier and Type	Method	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.

Uses of SpecificAnnotationParameters in com.compomics.util.experiment.identification.modification

Methods in com.compomics.util.experiment.identification.modification with parameters of type SpecificAnnotationParameters

Modifier and Type	Method	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.

Uses of SpecificAnnotationParameters in com.compomics.util.experiment.identification.modification.scores

Methods in com.compomics.util.experiment.identification.modification.scores with parameters of type SpecificAnnotationParameters

Modifier and Type	Method	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, ModificationProvider modificationProvider)	Returns the PhosphoRS sequence probabilities for the modification possible locations.

Uses of SpecificAnnotationParameters in com.compomics.util.experiment.identification.psm_scoring

Methods in com.compomics.util.experiment.identification.psm_scoring with parameters of type SpecificAnnotationParameters

Modifier and Type	Method	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.

Uses of SpecificAnnotationParameters in com.compomics.util.experiment.identification.psm_scoring.psm_scores

Methods in com.compomics.util.experiment.identification.psm_scoring.psm_scores with parameters of type SpecificAnnotationParameters

Modifier and Type	Method	Description
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.
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.

Uses of SpecificAnnotationParameters in com.compomics.util.experiment.identification.spectrum_annotation

Fields in com.compomics.util.experiment.identification.spectrum_annotation declared as SpecificAnnotationParameters

Modifier and Type	Field	Description
protected SpecificAnnotationParameters	SpectrumAnnotator.specificAnnotationSettings	If provided, the annotator will only look for the ions included in the specific annotation settings.

Methods in com.compomics.util.experiment.identification.spectrum_annotation that return SpecificAnnotationParameters

Modifier and Type	Method	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.

Methods in com.compomics.util.experiment.identification.spectrum_annotation with parameters of type SpecificAnnotationParameters

Modifier and Type	Method	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.

Uses of SpecificAnnotationParameters in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators with parameters of type SpecificAnnotationParameters

Modifier and Type	Method	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[]	PeptideSpectrumAnnotator.getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
IonMatch[]	TagSpectrumAnnotator.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[]	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.
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.
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.