Package eu.isas.peptideshaker.followup

Class PercolatorExport

java.lang.Object
eu.isas.peptideshaker.followup.PercolatorExport
public class PercolatorExport extends Object
Export for Percolator.
Author:
Marc Vaudel, Dafni Skiadopoulou

  • Constructor Summary

    Constructors
    Constructor
    Description
    PercolatorExport()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static void
    percolatorExport​(File destinationFile, File deepLcFile, File ms2pipFile, 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 a Percolator training file for each of the spectrum files.
    static void
    percolatorExport​(File destinationFile, HashMap<String,​ArrayList<Double>> rtPrediction, HashMap<String,​ArrayList<com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum>> fragmentationPrediction, 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 a Percolator training file.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • PercolatorExport

      public PercolatorExport()

  • Method Details

    • percolatorExport

      public static void percolatorExport​(File destinationFile, File deepLcFile, File ms2pipFile, 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 a Percolator training file for each of the spectrum files. Returns an ArrayList of the files exported.
      Parameters:
      destinationFile - The file to use to write the file.
      deepLcFile - The deepLC results.
      ms2pipFile - The ms2pip results.
      identification - The identification object containing the matches.
      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.

    • percolatorExport

      public static void percolatorExport​(File destinationFile, HashMap<String,​ArrayList<Double>> rtPrediction, HashMap<String,​ArrayList<com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum>> fragmentationPrediction, 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 a Percolator training file.
      Parameters:
      destinationFile - The file where to write the export.
      rtPrediction - The retention time prediction.
      fragmentationPrediction - The fragmentation prediction.
      identification - The identification object containing the matches.
      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.