Uses of Class
eu.isas.peptideshaker.scoring.maps.InputMap

Packages that use InputMap

Package	Description
eu.isas.peptideshaker.fileimport	Import of search results.
eu.isas.peptideshaker.processing	Classes used to create PeptideShaker projects.
eu.isas.peptideshaker.scoring	Identification scoring.
eu.isas.peptideshaker.scoring.psm_scoring	PSM scoring.
eu.isas.peptideshaker.validation	Matches validation.

Uses of InputMap in eu.isas.peptideshaker.fileimport

Methods in eu.isas.peptideshaker.fileimport that return InputMap

Modifier and Type	Method and Description
InputMap	FileImporter.getInputMap() Returns the input map.

Methods in eu.isas.peptideshaker.fileimport with parameters of type InputMap

Modifier and Type

Method and Description

void

PsmImporter.importPsms(ArrayList<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatches, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, InputMap inputMap, com.compomics.util.experiment.io.identification.IdfileReader fileReader, File idFile, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.protein_inference.FastaMapper fastaMapper, int nThreads, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Imports PSMs.

Constructors in eu.isas.peptideshaker.fileimport with parameters of type InputMap

Constructor and Description

PsmFirstHitRunnable(ConcurrentLinkedQueue<com.compomics.util.experiment.identification.matches.SpectrumMatch> spectrumMatchQueue, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, InputMap inputMap, HashMap<String,Integer> proteinCount, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Constructor.

Uses of InputMap in eu.isas.peptideshaker.processing

Methods in eu.isas.peptideshaker.processing with parameters of type InputMap

Modifier and Type

Method and Description

void

PsmProcessor.processPsms(InputMap inputMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, MatchesValidator matchesValidator, ModificationLocalizationScorer modificationLocalizationScorer, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider, HashMap<String,Integer> proteinCount, int nThreads, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Iterates the spectrum matches and saves assumption probabilities, selects best hits, scores modification localization, and refines protein mapping accordingly.

Constructors in eu.isas.peptideshaker.processing with parameters of type InputMap

Constructor and Description

PsmProcessorRunnable(ConcurrentLinkedQueue<Long> spectrumMatchKeysIterator, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, InputMap inputMap, MatchesValidator matchesValidator, ModificationLocalizationScorer modificationLocalizationScorer, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.biology.modifications.ModificationProvider modificationProvider, HashMap<String,Integer> proteinCount, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Constructor.

Uses of InputMap in eu.isas.peptideshaker.scoring

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

Modifier and Type	Method and Description
InputMap	PSMaps.getInputMap() Returns the target decoy map of all search engine scores.

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

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

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

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

Modifier and Type	Method and Description
void	PsmScorer.estimateIntermediateScoreProbabilities(com.compomics.util.experiment.identification.Identification identification, InputMap inputMap, com.compomics.util.parameters.tools.ProcessingParameters processingPreferences, com.compomics.util.waiting.WaitingHandler waitingHandler) Estimates the probabilities associated to the intermediate PSM scores.
void	PsmScorer.estimateIntermediateScores(com.compomics.util.experiment.identification.Identification identification, InputMap inputMap, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Scores the PSMs contained in an identification object.
ArrayList<Integer>	PsmScorer.estimateIntermediateScores(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, InputMap inputMap, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator peptideSpectrumAnnotator, com.compomics.util.experiment.identification.psm_scoring.psm_scores.HyperScore hyperScore, com.compomics.util.waiting.WaitingHandler waitingHandler) Scores the PSMs contained in an identification object.
void	PsmScorer.scorePsms(com.compomics.util.experiment.identification.Identification identification, InputMap inputMap, com.compomics.util.parameters.tools.ProcessingParameters processingPreferences, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler) Attaches a score to the PSMs.
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 InputMap in eu.isas.peptideshaker.validation

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

Modifier and Type	Method and Description
static void	MatchesValidator.updatePeptideAssumptionValidationLevel(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.parameters.identification.IdentificationParameters identificationParameters, InputMap inputMap, long spectrumMatchKey, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, boolean applyQCFilters) Updates the validation status of a peptide assumption.
void	MatchesValidator.validateIdentifications(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, InputMap inputMap, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, 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, com.compomics.util.parameters.peptide_shaker.ProjectType projectType, com.compomics.util.parameters.tools.ProcessingParameters processingParameters) This method validates the identification matches of an identification object.