Package eu.isas.peptideshaker.followup

Class DeepLcExport

java.lang.Object
eu.isas.peptideshaker.followup.DeepLcExport
public class DeepLcExport extends Object
Export for RT prediction using DeepLC.
Author:
Marc Vaudel, Dafni Skiadopoulou

  • Constructor Summary

    Constructors
    Constructor
    Description
    DeepLcExport()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    deepLcExport(File destinationFile, File confidentHitsDestinationFile, HashMap<String,Double> confidenceScores, HashSet<Long> keys, 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 a DeepLC training file for the given spectrum file.
    static ArrayList<File>
    deepLcExport(String destinationStem, File percolatorBenchmarkResultsFile, 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 DeepLC training files for each of the spectrum files.Returns an ArrayList of the files exported.
    static File
    getConfidentHitsDestinationFile(String destinationStem, String spectrumFile, boolean addSuffix)
    Returns the file where to write the export for confident hits.
    static File
    getDestinationFile(String destinationStem, String spectrumFile, boolean addSuffix)
    Returns the file where to write the export.
    static ArrayList<File>
    getExportedFiles(String destinationStem, com.compomics.util.experiment.identification.Identification identification)
    Returns an ArrayList of all the files that will be written by the export.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • DeepLcExport

      public DeepLcExport()

  • Method Details

    • deepLcExport

      public static ArrayList<File> deepLcExport(String destinationStem, File percolatorBenchmarkResultsFile, 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 DeepLC training files for each of the spectrum files.Returns an ArrayList of the files exported.
      Parameters:
      destinationStem - The stem to use for the path.
      percolatorBenchmarkResultsFile - The file containing Percolator results for all PSMs.
      identification - The identification object containing the matches.
      modificationParameters - The modification parameters.
      sequenceMatchingParameters - The sequence matching parameters.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      waitingHandler - The waiting handler.
      Returns:
      An ArrayList of the files exported.

    • getExportedFiles

      public static ArrayList<File> getExportedFiles(String destinationStem, com.compomics.util.experiment.identification.Identification identification)
      Returns an ArrayList of all the files that will be written by the export.
      Parameters:
      destinationStem - The stem to use for the path.
      identification - The identification object containing the matches.
      Returns:
      An ArrayList of all the files that will be written by the export.

    • getDestinationFile

      public static File getDestinationFile(String destinationStem, String spectrumFile, boolean addSuffix)
      Returns the file where to write the export.
      Parameters:
      destinationStem - The stem to use for the path.
      spectrumFile - The name of the spectrum file.
      addSuffix - A boolean indicating whether the name of the spectrum file should be appended to the stem.
      Returns:
      The file where to write the export.

    • getConfidentHitsDestinationFile

      public static File getConfidentHitsDestinationFile(String destinationStem, String spectrumFile, boolean addSuffix)
      Returns the file where to write the export for confident hits.
      Parameters:
      destinationStem - The stem to use for the path.
      spectrumFile - The name of the spectrum file.
      addSuffix - A boolean indicating whether the name of the spectrum file should be appended to the stem.
      Returns:
      The file where to write the export.

    • deepLcExport

      public static void deepLcExport(File destinationFile, File confidentHitsDestinationFile, HashMap<String,Double> confidenceScores, HashSet<Long> keys, 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 a DeepLC training file for the given spectrum file.
      Parameters:
      destinationFile - The file where to write the export.
      confidentHitsDestinationFile - The file where to write the export for confident hits.
      confidenceScores - Confidence score for each PSM.
      keys - The keys of the spectrum matches.
      identification - The identification object containing the matches.
      modificationParameters - The modification parameters.
      sequenceMatchingParameters - The sequence matching parameters.
      sequenceProvider - The sequence provider.
      spectrumProvider - The spectrum provider.
      waitingHandler - The waiting handler.