Uses of Class
eu.isas.peptideshaker.cmd.FollowUpCLIInputBean

Packages that use FollowUpCLIInputBean

Package	Description
eu.isas.peptideshaker.cmd	Command line usage.

Uses of FollowUpCLIInputBean in eu.isas.peptideshaker.cmd

Methods in eu.isas.peptideshaker.cmd that return FollowUpCLIInputBean

Modifier and Type	Method	Description
FollowUpCLIInputBean	PeptideShakerCLIInputBean.getFollowUpCLIInputBean()	Returns the follow-up options required.

Methods in eu.isas.peptideshaker.cmd with parameters of type FollowUpCLIInputBean

Modifier and Type	Method	Description
static File	CLIExportMethods.exportAccessions(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.gui.filtering.FilterParameters filteringPreferences)	Exports the accessions as specified in the follow-up input bean.
static ArrayList<File>	CLIExportMethods.exportDeepLC(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)	Exports files needed by DeepLC.
static File	CLIExportMethods.exportInclusionList(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.gui.filtering.FilterParameters filterPreferences)	Exports an inclusion list of the validated hits.
static ArrayList<File>	CLIExportMethods.exportMs2pip(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)	Exports the files needed by ms2pip.
static void	CLIExportMethods.exportPeaksIntensities(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters annotationParameters, com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters modificationLocalizationParameters, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)	Exports the peaks intensities (observed).
static void	CLIExportMethods.exportPercolator(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters annotationParameters, com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters modificationLocalizationParameters, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)	Exports the files needed by Percolator.
static File	CLIExportMethods.exportProgenesis(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences)	Exports the identification in a Progenesis compatible format.
static File	CLIExportMethods.exportProteinSequences(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.gui.filtering.FilterParameters filteringPreferences)	Exports the protein details in FASTA format as specified in the follow-up input bean.
static File	CLIExportMethods.exportProteoforms(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler)	Exports proteoforms.
static void	CLIExportMethods.exportPSMIdentifiers(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)
static void	CLIExportMethods.exportRTValues(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters annotationParameters, com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters modificationLocalizationParameters, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)	Exports the RT values (observed,predicted).
static ArrayList<File>	CLIExportMethods.exportSpectra(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingPreferences)	Exports the spectra as specified in the follow-up input bean.
static ArrayList<File>	CLIExportMethods.recalibrateSpectra(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler)	Recalibrates spectra as specified in the follow-up input bean.

Constructors in eu.isas.peptideshaker.cmd with parameters of type FollowUpCLIInputBean

Modifier	Constructor	Description
	FollowUpCLI(FollowUpCLIInputBean followUpCLIInputBean)	Construct a new FollowUpCLI runnable from a FollowUpCLI Bean.