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