Uses of Class
com.compomics.util.experiment.identification.Identification

Packages that use Identification

Package	Description
com.compomics.util.experiment.identification.features	Classes for the generation of identification features.
com.compomics.util.experiment.identification.filtering	Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.matches_iterators	Identification match iterators.
com.compomics.util.experiment.identification.peptide_inference	Classes related to peptide inference.
com.compomics.util.experiment.identification.protein_inference	Classes related to protein inference.
com.compomics.util.experiment.quantification.spectrumcounting	Experiment classes related to spectrum counting.
com.compomics.util.gui.modification	PTM GUI dialogs.

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

Modifier	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)

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

Modifier	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

Modifier	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

Modifier	Constructor	Description
	ModificationTable(Identification identification, AnnotationParameters annotationParameters, PeptideMatch peptideMatch, Modification modification, boolean areaChart, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Constructor.