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