Uses of Class
com.compomics.util.parameters.identification.IdentificationParameters

Packages that use IdentificationParameters

Package	Description
com.compomics.cli.identification_parameters	Command line for the handling of identification parameters.
com.compomics.cli.peptide_mapper	Command line for PeptideMapper.
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.identification_parameters	Parameters settings for the spectrum identification algorithms.
com.compomics.util.experiment.identification.modification.mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.modification.search_engine_mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.peptide_inference	Classes related to peptide inference.
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.identification.psm_scoring	Main PSM scoring class.
com.compomics.util.experiment.io.identification.writers	Writer for identification results.
com.compomics.util.gui.parameters.identification	GUI classes for parameters, settings and preferences used for identification.
com.compomics.util.parameters.identification	Identification parameters.

Uses of IdentificationParameters in com.compomics.cli.identification_parameters

Methods in com.compomics.cli.identification_parameters that return IdentificationParameters

Modifier and Type	Method	Description
IdentificationParameters	IdentificationParametersInputBean.getIdentificationParameters()	Returns the identification parameters.

Methods in com.compomics.cli.identification_parameters with parameters of type IdentificationParameters

Modifier and Type	Method	Description
void	IdentificationParametersInputBean.setIdentificationParameters(IdentificationParameters identificationParameters)	Sets the identification parameters.

Uses of IdentificationParameters in com.compomics.cli.peptide_mapper

Methods in com.compomics.cli.peptide_mapper with parameters of type IdentificationParameters

Modifier and Type	Method	Description
static void	PeptideMapperCLI.runMapping(File fastaFile, WaitingHandlerCLIImpl waitingHandlerCLIImpl, IdentificationParameters identificationParameters, String inputFilePath, String outputFilePath, int nCores, boolean peptideMapping)

Constructors in com.compomics.cli.peptide_mapper with parameters of type IdentificationParameters

Modifier	Constructor	Description
	MappingWorker(WaitingHandlerCLIImpl waitingHandlerCLIImpl, FastaMapper peptideMapper, IdentificationParameters identificationParameters, SimpleFileReader reader, SimpleSemaphore bufferMutex, SimpleFileWriter writer, boolean peptideMapping)

Uses of IdentificationParameters in com.compomics.util.experiment.identification.features

Methods in com.compomics.util.experiment.identification.features with parameters of type IdentificationParameters

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 IdentificationParameters

Modifier	Constructor	Description
	IdentificationFeaturesGenerator(Identification identification, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, Metrics metrics, SpectrumCountingParameters spectrumCountingPreferences)	Constructor.

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

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

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 IdentificationParameters in com.compomics.util.experiment.identification.identification_parameters

Methods in com.compomics.util.experiment.identification.identification_parameters that return IdentificationParameters

Modifier and Type	Method	Description
IdentificationParameters	IdentificationParametersFactory.getIdentificationParameters(String name)	Returns the identification parameters corresponding to the given name.

Methods in com.compomics.util.experiment.identification.identification_parameters with parameters of type IdentificationParameters

Modifier and Type	Method	Description
void	IdentificationParametersFactory.addIdentificationParameters(IdentificationParameters identificationParameters)	Adds the given identification parameters to the factory.
void	IdentificationParametersFactory.updateIdentificationParameters(IdentificationParameters oldParameters, IdentificationParameters newParameters)	Replaces old parameters by new.

Uses of IdentificationParameters in com.compomics.util.experiment.identification.modification.mapping

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

Modifier and Type	Method	Description
static void	ModificationLocalizationMapper.modificationLocalization(Peptide peptide, HashMap<Integer,ArrayList<String>> expectedNames, HashMap<ModificationMatch,ArrayList<String>> modNames, IdentificationParameters identificationParameters, IdfileReader idfileReader, ModificationProvider modificationProvider)	Makes an initial modification mapping based on the search engine results and the compatibility to the searched modifications.

Uses of IdentificationParameters in com.compomics.util.experiment.identification.modification.search_engine_mapping

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

Modifier and Type	Method	Description
static void	ModificationLocalizationMapper.modificationLocalization(Peptide peptide, IdentificationParameters identificationParameters, IdfileReader idfileReader, ModificationProvider modificationProvider, SequenceProvider sequenceProvider)	Makes an initial modification mapping based on the search engine results and the compatibility to the searched modifications.

Uses of IdentificationParameters in com.compomics.util.experiment.identification.peptide_inference

Methods in com.compomics.util.experiment.identification.peptide_inference with parameters of type IdentificationParameters

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 IdentificationParameters in com.compomics.util.experiment.identification.protein_inference.fm_index

Constructors in com.compomics.util.experiment.identification.protein_inference.fm_index with parameters of type IdentificationParameters

Modifier	Constructor	Description
	FMIndex(File fastaFile, FastaParameters fastaParameters, WaitingHandler waitingHandler, boolean displayProgress, IdentificationParameters identificationParameters)	Constructor.

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

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

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 IdentificationParameters in com.compomics.util.experiment.io.identification.writers

Constructors in com.compomics.util.experiment.io.identification.writers with parameters of type IdentificationParameters

Modifier	Constructor	Description
	SimpleMzIdentMLExporter(String softwareName, String softwareVersion, String softwareUrl, File tempFolder, File destinationFile, ArrayList<File> spectrumFiles, File searchEngineFile, HashMap<String,ArrayList<String>> searchEngines, File fastaFile, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider, ModificationProvider modificationProvider, FastaSummary fastaSummary, String contactFirstName, String contactLastName, String contactAddress, String contactEmail, String contactOrganizationName, String contactOrganizationAddress, String contactOrganizationEmail, boolean peptideInference)	Constructor.

Uses of IdentificationParameters in com.compomics.util.gui.parameters.identification

Methods in com.compomics.util.gui.parameters.identification that return IdentificationParameters

Modifier and Type	Method	Description
IdentificationParameters	IdentificationParametersEditionDialog.getIdentificationParameters()	Returns the identification parameters as set by the user.
IdentificationParameters	IdentificationParametersOverviewDialog.getIdentificationParameters()	Returns the selected identification parameters.

Methods in com.compomics.util.gui.parameters.identification with parameters of type IdentificationParameters

Modifier and Type	Method	Description
void	IdentificationParametersNameDialog.updateParameters(IdentificationParameters identificationParameters)	Updates the given identification parameters attributes.

Constructors in com.compomics.util.gui.parameters.identification with parameters of type IdentificationParameters

Modifier	Constructor	Description
	IdentificationParametersEditionDialog(Dialog owner, Frame parentFrame, IdentificationParameters identificationParameters, Image normalIcon, Image waitingIcon, LastSelectedFolder lastSelectedFolder, boolean editable)	Creates a new IdentificationParametersEditionDialog with a dialog as owner.
	IdentificationParametersEditionDialog(Frame parentFrame, IdentificationParameters identificationParameters, Image normalIcon, Image waitingIcon, LastSelectedFolder lastSelectedFolder, boolean editable)	Creates a new IdentificationParametersEditionDialog with a frame as owner.
	IdentificationParametersNameDialog(Dialog owner, Frame parentFrame, IdentificationParameters identificationParameters, boolean editable)	Creates a new IdentificationParametersNameDialog with a dialog as owner.
	IdentificationParametersNameDialog(Frame parentFrame, IdentificationParameters identificationParameters, boolean editable)	Creates a new IdentificationParametersNameDialog with a frame as owner.

Uses of IdentificationParameters in com.compomics.util.parameters.identification

Methods in com.compomics.util.parameters.identification that return IdentificationParameters

Modifier and Type	Method	Description
static IdentificationParameters	IdentificationParameters.getIdentificationParameters(File identificationParametersFile)	Loads the identification parameters from a file.

Methods in com.compomics.util.parameters.identification with parameters of type IdentificationParameters

Modifier and Type	Method	Description
boolean	IdentificationParameters.equals(IdentificationParameters otherIdentificationParameters)	Returns true if the identification parameter objects have identical settings.
static void	IdentificationParameters.saveIdentificationParameters(IdentificationParameters identificationParameters, File identificationParametersFile)	Saves the identification parameters to a file.