Uses of Class
com.compomics.util.experiment.identification.Identification
Package | Description |
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com.compomics.util.experiment.identification.features |
Classes for the generation of identification features.
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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_iterators |
Identification match iterators.
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com.compomics.util.experiment.identification.peptide_inference |
Classes related to peptide inference.
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com.compomics.util.experiment.identification.protein_inference |
Classes related to protein inference.
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com.compomics.util.experiment.quantification.spectrumcounting |
Experiment classes related to spectrum counting.
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com.compomics.util.gui.modification |
PTM GUI dialogs.
|
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Uses of Identification in com.compomics.util.experiment.identification.features
Methods in com.compomics.util.experiment.identification.features with parameters of type Identification Modifier and Type Method Description static double
IdentificationFeaturesGenerator. estimateSpectrumCounting(Identification identification, SequenceProvider sequenceProvider, long proteinMatchKey, SpectrumCountingParameters spectrumCountingPreferences, int maxPepLength, IdentificationParameters identificationParameters)
Returns the spectrum counting index based on the project settings.Constructors in com.compomics.util.experiment.identification.features with parameters of type Identification Constructor Description IdentificationFeaturesGenerator(Identification identification, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, Metrics metrics, SpectrumCountingParameters spectrumCountingPreferences)
Constructor. -
Uses of Identification in com.compomics.util.experiment.identification.filtering
Methods in com.compomics.util.experiment.identification.filtering with parameters of type Identification 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, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
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
MatchFilter. isValidated(long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
Tests whether a match is validated by this filter.abstract boolean
MatchFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.boolean
PeptideFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean
ProteinFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean
PsmFilter. isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
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Uses of Identification in com.compomics.util.experiment.identification.matches_iterators
Constructors in com.compomics.util.experiment.identification.matches_iterators with parameters of type Identification Constructor Description MatchesIterator(long[] keys, Class className, Identification identification, WaitingHandler waitingHandler, boolean displayProgress, String filters)
Constructor.MatchesIterator(Class className, Identification identification, WaitingHandler waitingHandler, boolean displayProgress)
Constructor.PeptideMatchesIterator(long[] keys, Identification identification, WaitingHandler waitingHandler, boolean displayProgress)
Constructor.PeptideMatchesIterator(Identification identification, WaitingHandler waitingHandler, boolean displayProgress)
Constructor.ProteinMatchesIterator(long[] keys, Identification identification, WaitingHandler waitingHandler, boolean displayProgress)
Constructor.ProteinMatchesIterator(Identification identification, WaitingHandler waitingHandler, boolean displayProgress)
Constructor.SpectrumMatchesIterator(long[] keys, Identification identification, WaitingHandler waitingHandler, boolean displayProgress)
Constructor.SpectrumMatchesIterator(long[] keys, Identification identification, WaitingHandler waitingHandler, boolean displayProgress, String filters)
Constructor.SpectrumMatchesIterator(Identification identification, WaitingHandler waitingHandler, boolean displayProgress)
Constructor. -
Uses of Identification in com.compomics.util.experiment.identification.peptide_inference
Methods in com.compomics.util.experiment.identification.peptide_inference with parameters of type Identification Modifier and Type Method Description void
PeptideInference. peptideInference(Identification identification, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider, WaitingHandler waitingHandler)
Infers the PTM localization and its confidence for the best match of every spectrum. -
Uses of Identification in com.compomics.util.experiment.identification.protein_inference
Constructors in com.compomics.util.experiment.identification.protein_inference with parameters of type Identification Constructor Description PeptideAndProteinBuilder(Identification identification)
Constructor. -
Uses of Identification in com.compomics.util.experiment.quantification.spectrumcounting
Methods in com.compomics.util.experiment.quantification.spectrumcounting with parameters of type Identification Modifier and Type Method Description void
ScalingFactorsEstimators. estimateScalingFactors(Identification identification, Metrics metrics, SequenceProvider sequenceProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, ProcessingParameters processingParameters)
Estimates the scaling factors and stores them in the given metrics. -
Uses of Identification in com.compomics.util.gui.modification
Constructors in com.compomics.util.gui.modification with parameters of type Identification Constructor Description ModificationTable(Identification identification, AnnotationParameters annotationParameters, PeptideMatch peptideMatch, Modification modification, boolean areaChart, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)
Constructor.