Uses of Class
eu.isas.peptideshaker.scoring.targetdecoy.TargetDecoyMap

Packages that use TargetDecoyMap

Package	Description
eu.isas.peptideshaker.gui	GUI dialogs and helper classes.
eu.isas.peptideshaker.protein_inference	Protein inference classes.
eu.isas.peptideshaker.scoring	Identification scoring.
eu.isas.peptideshaker.scoring.maps	Target decoy maps.
eu.isas.peptideshaker.scoring.psm_scoring	PSM scoring.
eu.isas.peptideshaker.scoring.targetdecoy	Target/decoy related classes.
eu.isas.peptideshaker.validation	Matches validation.

Uses of TargetDecoyMap in eu.isas.peptideshaker.gui

Constructors in eu.isas.peptideshaker.gui with parameters of type TargetDecoyMap

Modifier	Constructor	Description
	MatchValidationDialog(Frame parent, com.compomics.util.experiment.identification.Identification identification, TargetDecoyMap targetDecoyMap, long matchKey, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, String fastaFile, MatchValidationDialog.MatchType matchType)	Constructor for a protein match validation dialog.

Uses of TargetDecoyMap in eu.isas.peptideshaker.protein_inference

Methods in eu.isas.peptideshaker.protein_inference with parameters of type TargetDecoyMap

Modifier and Type	Method	Description
void	ProteinInference.inferPiStatus(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, TargetDecoyMap proteinMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)	Selects the leading protein of protein groups and infers PI status of peptide and proteins.
void	ProteinInference.inferPiStatus(com.compomics.util.experiment.identification.matches.ProteinMatch proteinMatch, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, TargetDecoyMap proteinMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)	Selects the leading protein of protein groups and infers PI status of peptide and proteins.

Uses of TargetDecoyMap in eu.isas.peptideshaker.scoring

Methods in eu.isas.peptideshaker.scoring that return TargetDecoyMap

Modifier and Type	Method	Description
TargetDecoyMap	PSMaps.getPeptideMap()	Returns the target decoy map at the peptide level.
TargetDecoyMap	PSMaps.getProteinMap()	Returns the target decoy map at the protein level.
TargetDecoyMap	PSMaps.getPsmMap()	Returns the target decoy map at the psm level.

Constructors in eu.isas.peptideshaker.scoring with parameters of type TargetDecoyMap

Modifier	Constructor	Description
	PSMaps(InputMap inputMap, TargetDecoyMap psmMap, TargetDecoyMap peptideMap, TargetDecoyMap proteinMap)	Constructor for the PSMaps.

Uses of TargetDecoyMap in eu.isas.peptideshaker.scoring.maps

Fields in eu.isas.peptideshaker.scoring.maps with type parameters of type TargetDecoyMap

Modifier and Type	Field	Description
protected final HashMap<Integer,HashMap<String,TargetDecoyMap>>	SpecificTargetDecoyMap.fileSpecificMaps	The map of the target decoy maps indexed by file and category.
protected final HashMap<Integer,TargetDecoyMap>	SpecificTargetDecoyMap.groupedMaps	The map of the target decoy maps indexed by category.

Methods in eu.isas.peptideshaker.scoring.maps that return TargetDecoyMap

Modifier and Type	Method	Description
TargetDecoyMap	InputMap.getIntermediateScoreMap(String fileName, int advocateIndex, int scoreIndex)	Returns the target decoy map associated to a given spectrum file, advocate and score type.
TargetDecoyMap	InputMap.getMap()	Returns the first target/decoy map of the input map in case a single algorithm was used.
TargetDecoyMap	InputMap.getTargetDecoyMap(int algorithm)	Returns the target decoy map attached to the given algorithm.
TargetDecoyMap	InputMap.getTargetDecoyMap(int algorithm, String fileName)	Returns the target decoy map attached to the given algorithm for a specific spectrum file.
TargetDecoyMap	SpecificTargetDecoyMap.getTargetDecoyMap(int category, String spectrumFile)	Returns the desired target decoy map.

Methods in eu.isas.peptideshaker.scoring.maps that return types with arguments of type TargetDecoyMap

Modifier and Type	Method	Description
ArrayList<TargetDecoyMap>	InputMap.getTargetDecoyMaps()	Returns a list of all target decoy maps contained in this mapping.
ArrayList<TargetDecoyMap>	SpecificTargetDecoyMap.getTargetDecoyMaps()	Returns a list of the target decoy maps used for scoring.

Uses of TargetDecoyMap in eu.isas.peptideshaker.scoring.psm_scoring

Methods in eu.isas.peptideshaker.scoring.psm_scoring with parameters of type TargetDecoyMap

Modifier and Type	Method	Description
void	BestMatchSelection.selectBestHit(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, InputMap inputMap, TargetDecoyMap psmTargetDecoyMap, com.compomics.util.experiment.identification.Identification identification)	Selects the best hit.

Uses of TargetDecoyMap in eu.isas.peptideshaker.scoring.targetdecoy

Methods in eu.isas.peptideshaker.scoring.targetdecoy with parameters of type TargetDecoyMap

Modifier and Type	Method	Description
void	TargetDecoyMap.addAll(TargetDecoyMap anOtherMap)	Adds all the points from another target/decoy map.

Uses of TargetDecoyMap in eu.isas.peptideshaker.validation

Methods in eu.isas.peptideshaker.validation that return TargetDecoyMap

Modifier and Type	Method	Description
TargetDecoyMap	MatchesValidator.getPeptideMap()	Returns the peptide scoring specific map.
TargetDecoyMap	MatchesValidator.getProteinMap()	Returns the protein scoring map.
TargetDecoyMap	MatchesValidator.getPsmMap()	Returns the PSM scoring specific map.

Methods in eu.isas.peptideshaker.validation with parameters of type TargetDecoyMap

Modifier and Type	Method	Description
void	MatchesValidator.setPeptideMap(TargetDecoyMap peptideMap)	Sets the peptide scoring specific map.
void	MatchesValidator.setProteinMap(TargetDecoyMap proteinMap)	Sets the protein scoring map.
void	MatchesValidator.setPsmMap(TargetDecoyMap psmMap)	Sets the PSM scoring specific map.
static void	MatchesValidator.updatePeptideMatchValidationLevel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, TargetDecoyMap peptideMap, long peptideKey)	Updates the validation status of a peptide match.
static void	MatchesValidator.updateProteinMatchValidationLevel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, TargetDecoyMap targetDecoyMap, double scoreThreshold, double nTargetLimit, double confidenceThreshold, boolean noValidated, long proteinKey)	Updates the validation status of a protein match.
static void	MatchesValidator.updateProteinMatchValidationLevel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, TargetDecoyMap proteinMap, long proteinKey)	Updates the validation status of a protein match.
static void	MatchesValidator.updateSpectrumMatchValidationLevel(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, TargetDecoyMap psmMap, long spectrumMatchKey, boolean applyQCFilters)	Updates the validation status of a spectrum match.

Constructors in eu.isas.peptideshaker.validation with parameters of type TargetDecoyMap

Modifier	Constructor	Description
	MatchesValidator(TargetDecoyMap psmMap, TargetDecoyMap peptideMap, TargetDecoyMap proteinMap)	Constructor.