Uses of Class
com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption

Packages that use PeptideAssumption

Package	Description
com.compomics.util.experiment.identification.filtering	Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
com.compomics.util.experiment.identification.modification	Modification mapping and localization.
com.compomics.util.experiment.io.identification.writers	Writer for identification results.

Uses of PeptideAssumption in com.compomics.util.experiment.identification.filtering

Methods in com.compomics.util.experiment.identification.filtering with parameters of type PeptideAssumption

Modifier and Type	Method	Description
boolean	AssumptionFilter.isValidated(long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)	Tests whether a match is validated by this filter.
boolean	AssumptionFilter.isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)	Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.
boolean	PeptideAssumptionFilter.validatePrecursor(PeptideAssumption assumption, String spectrumFile, String spectrumTitle, SpectrumProvider spectrumProvider, SearchParameters searchParameters)	Validates the mass deviation of a peptide assumption.

Uses of PeptideAssumption in com.compomics.util.experiment.identification.matches

Methods in com.compomics.util.experiment.identification.matches that return PeptideAssumption

Modifier and Type	Method	Description
PeptideAssumption	SpectrumMatch.getBestPeptideAssumption()	Getter for the best peptide assumption.

Methods in com.compomics.util.experiment.identification.matches that return types with arguments of type PeptideAssumption

Modifier and Type	Method	Description
java.util.stream.Stream<PeptideAssumption>	SpectrumMatch.getAllPeptideAssumptions()	Returns a stream of all peptide assumptions
TreeMap<Double,ArrayList<PeptideAssumption>>	SpectrumMatch.getAllPeptideAssumptions(int advocateId)	Returns all peptide assumptions for the specified search engine indexed by their score.
HashMap<Integer,TreeMap<Double,ArrayList<PeptideAssumption>>>	SpectrumMatch.getPeptideAssumptionsMap()	Returns the peptide assumptions map: advocate id > score > list of assumptions.

Methods in com.compomics.util.experiment.identification.matches with parameters of type PeptideAssumption

Modifier and Type	Method	Description
void	SpectrumMatch.addPeptideAssumption(int advocateId, PeptideAssumption peptideAssumption)	Add a hit.
void	SpectrumMatch.removePeptideAssumption(PeptideAssumption peptideAssumption)	Removes an assumption from the mapping.
void	SpectrumMatch.setBestPeptideAssumption(PeptideAssumption bestPeptideAssumption)	Setter for the best peptide assumption.

Method parameters in com.compomics.util.experiment.identification.matches with type arguments of type PeptideAssumption

Modifier and Type	Method	Description
void	SpectrumMatch.setPeptideAssumptionMap(HashMap<Integer,TreeMap<Double,ArrayList<PeptideAssumption>>> peptideAssumptionsMap)	Sets the peptide assumption map.

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

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

Modifier and Type	Method	Description
static ModificationtableContent	ModificationtableContent.getModificationTableContent(PeptideAssumption peptideAssumption, Modification modification, int nMod, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Get the table content.

Uses of PeptideAssumption in com.compomics.util.experiment.io.identification.writers

Method parameters in com.compomics.util.experiment.io.identification.writers with type arguments of type PeptideAssumption

Modifier and Type	Method	Description
void	SimpleMzIdentMLExporter.addSpectrum(String spectrumFile, String spectrumTitle, ArrayList<PeptideAssumption> peptideAssumptions, ArrayList<TreeMap<Double,HashMap<Integer,Double>>> modificationLocalizationScores, PeptideSpectrumAnnotator peptideSpectrumAnnotator)	Adds a peptide-spectrum match to the file.