Package eu.isas.peptideshaker.cmd

Class CLIExportMethods

java.lang.Object
eu.isas.peptideshaker.cmd.CLIExportMethods
public class CLIExportMethods extends Object
This class groups standard methods used by the different command line interfaces.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Summary

    Constructors
    Constructor
    Description
    CLIExportMethods()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static File
    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>
    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 void
    exportDocumentation(ReportCLIInputBean reportCLIInputBean, String reportType, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Writes the documentation corresponding to an export given the command line arguments.
    static File
    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>
    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
    exportMzId(MzidCLIInputBean mzidCLIInputBean, PsdbParent psbdParent, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Exports the project in the mzIdentML format.
    static void
    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
    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
    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
    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
    exportProteoforms(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Exports proteoforms.
    static void
    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 File
    exportReport(ReportCLIInputBean reportCLIInputBean, String reportType, String experiment, ProjectDetails projectDetails, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, 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.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, int nSurroundingAA, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Writes an export according to the command line settings contained in the reportCLIInputBean.
    static void
    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>
    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>
    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.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • CLIExportMethods

      public CLIExportMethods()

  • Method Details

    • recalibrateSpectra

      public static ArrayList<File> 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) throws IOException
      Recalibrates spectra as specified in the follow-up input bean.
      Parameters:
      followUpCLIInputBean - the follow up input bean
      identification - the identification
      sequenceProvider - the sequence provider
      spectrumProvider - The spectrum provider.
      identificationParameters - the identification parameters
      waitingHandler - a waiting handler to display progress
      Returns:
      ArrayList files containing the recalibrated spectra
      Throws:
      IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

    • exportSpectra

      public static ArrayList<File> 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) throws IOException, SQLException, ClassNotFoundException, InterruptedException
      Exports the spectra as specified in the follow-up input bean.
      Parameters:
      followUpCLIInputBean - the follow up input bean
      identification - the identification
      spectrumProvider - The spectrum provider.
      waitingHandler - a waiting handler to display progress
      sequenceMatchingPreferences - the sequence matching preferences
      Returns:
      ArrayList files containing the spectra
      Throws:
      IOException - exception thrown whenever an IO exception occurred while reading or writing to a file
      InterruptedException - exception thrown whenever a threading issue occurred while interacting with the database
      SQLException - exception thrown whenever an SQL exception occurred while interacting with the database
      ClassNotFoundException - exception thrown whenever an exception occurred while deserializing an object

    • exportAccessions

      public static File 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) throws IOException
      Exports the accessions as specified in the follow-up input bean.
      Parameters:
      followUpCLIInputBean - the follow up input bean
      identification - the identification
      sequenceProvider - the FASTA sequence provider
      waitingHandler - a waiting handler to display progress
      filteringPreferences - the filtering preferences
      Returns:
      File file containing accessions
      Throws:
      IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

    • exportProteinSequences

      public static File 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) throws IOException
      Exports the protein details in FASTA format as specified in the follow-up input bean.
      Parameters:
      followUpCLIInputBean - the follow up input bean
      identification - the identification
      sequenceProvider - the FASTA sequence provider
      waitingHandler - a waiting handler to display progress
      filteringPreferences - the filtering preferences
      Returns:
      File file containing the protein details in FASTA format
      Throws:
      IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

    • exportProgenesis

      public static File 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) throws IOException
      Exports the identification in a Progenesis compatible format.
      Parameters:
      followUpCLIInputBean - the follow up input bean
      identification - the identification
      waitingHandler - a waiting handler to display progress
      sequenceProvider - the sequence provider
      proteinDetailsProvider - the protein details provider
      sequenceMatchingPreferences - the sequence matching preferences
      Returns:
      File file containing the identification data in a Progenesis compatible format
      Throws:
      IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

    • exportProteoforms

      public static File exportProteoforms(FollowUpCLIInputBean followUpCLIInputBean, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.waiting.WaitingHandler waitingHandler)
      Exports proteoforms.
      Parameters:
      followUpCLIInputBean - the follow up input bean
      identification - the identification
      waitingHandler - a waiting handler to display progress
      Returns:
      File file containing the proteoforms data

    • exportDeepLC

      public static ArrayList<File> 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.
      Parameters:
      followUpCLIInputBean - the follow up input bean
      identification - the identification
      modificationParameters - The modification parameters.
      sequenceMatchingParameters - The sequence matching parameters.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      waitingHandler - The waiting handler.
      Returns:
      The files created by the export.

    • exportMs2pip

      public static ArrayList<File> 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.
      Parameters:
      followUpCLIInputBean - the follow up input bean
      identification - the identification
      searchParameters - The search parameters.
      sequenceMatchingParameters - The sequence matching parameters.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      waitingHandler - The waiting handler.
      Returns:
      The files created by the export.

    • exportPercolator

      public static void 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.
      Parameters:
      followUpCLIInputBean - the follow up input bean
      identification - the identification
      searchParameters - The search parameters.
      sequenceMatchingParameters - The sequence matching parameters.
      annotationParameters - The annotation parameters.
      modificationLocalizationParameters - The modification localization parameters.
      modificationParameters - The modification parameters.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      waitingHandler - The waiting handler.

    • exportPeaksIntensities

      public static void 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).
      Parameters:
      followUpCLIInputBean - the follow up input bean
      identification - the identification
      searchParameters - the search parameters
      sequenceMatchingParameters - the sequence matching parameters
      annotationParameters - the annotation parameters
      modificationLocalizationParameters - the modification localization parameters
      modificationParameters - the modification parameters
      sequenceProvider - the sequence provider
      spectrumProvider - the spectrum provider
      waitingHandler - the waiting handler

    • exportRTValues

      public static void 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).
      Parameters:
      followUpCLIInputBean - the follow up input bean
      identification - the identification
      searchParameters - The search parameters.
      sequenceMatchingParameters - The sequence matching parameters.
      annotationParameters - The annotation parameters.
      modificationLocalizationParameters - The modification localization parameters.
      modificationParameters - The modification parameters.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      waitingHandler - The waiting handler.

    • exportPSMIdentifiers

      public static void 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)

    • exportInclusionList

      public static File 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) throws IOException
      Exports an inclusion list of the validated hits.
      Parameters:
      followUpCLIInputBean - the follow up input bean
      identification - the identification
      identificationFeaturesGenerator - the identification features generator
      spectrumProvider - The spectrum provider.
      searchParameters - the search parameters
      waitingHandler - a waiting handler to display progress
      filterPreferences - the filter preferences
      Returns:
      File file containing the inclusion list
      Throws:
      IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

    • exportReport

      public static File exportReport(ReportCLIInputBean reportCLIInputBean, String reportType, String experiment, ProjectDetails projectDetails, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator, 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.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, int nSurroundingAA, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Writes an export according to the command line settings contained in the reportCLIInputBean.
      Parameters:
      reportCLIInputBean - the command line settings
      reportType - the report type
      experiment - the experiment of the project
      projectDetails - the project details of the project
      identification - the identification of the project
      geneMaps - the gene maps
      identificationFeaturesGenerator - the identification features generator
      identificationParameters - the identification parameters used
      sequenceProvider - the sequence provider
      proteinDetailsProvider - the protein details provider
      spectrumProvider - The spectrum provider.
      nSurroundingAA - the number of amino acids to export on the side of peptide sequences
      spectrumCountingPreferences - the spectrum counting preferences
      waitingHandler - waiting handler displaying feedback to the user
      Returns:
      File file containing the exported report
      Throws:
      IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

    • exportDocumentation

      public static void exportDocumentation(ReportCLIInputBean reportCLIInputBean, String reportType, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Writes the documentation corresponding to an export given the command line arguments.
      Parameters:
      reportCLIInputBean - the command line arguments
      reportType - the type of report of interest
      waitingHandler - waiting handler displaying feedback to the user
      Throws:
      IOException - exception thrown whenever an IO exception occurred while reading or writing to a file

    • exportMzId

      public static void exportMzId(MzidCLIInputBean mzidCLIInputBean, PsdbParent psbdParent, com.compomics.util.waiting.WaitingHandler waitingHandler) throws IOException
      Exports the project in the mzIdentML format.
      Parameters:
      mzidCLIInputBean - the user input
      psbdParent - a PSDB file parent allowing accessing the information it contains
      waitingHandler - a waiting handler allowing display of progress and interruption of the export
      Throws:
      IOException - exception thrown whenever an IO exception occurred while reading or writing to a file