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
    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.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 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 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.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.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      waitingHandler - The waiting handler.

    • 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 psbd 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