Package eu.isas.peptideshaker.utils

Class PercolatorUtils

java.lang.Object
eu.isas.peptideshaker.utils.PercolatorUtils
public class PercolatorUtils extends Object
Utils for the export and import of Percolator results.
Author:
Marc Vaudel, Dafni Skiadopoulou

  • Constructor Summary

    Constructors
    Constructor
    Description
    PercolatorUtils()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static boolean[]
    getEnzymaticityFeature​(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)
    Computes the value for the enzymaticity feature.
    static String
    getHeader​(com.compomics.util.parameters.identification.search.SearchParameters searchParameters, Boolean rtPredictionsAvailable)
    Returns the header of the Percolator training file.
    static double
    getIntensityCoverageFeature​(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, 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)
    Computes the value for the intensity coverage feature.
    static double[]
    getMeasuredAndDeltaMzFeature​(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)
    Computes the value for the measured and delta mass feature.
    static String
    getPeptideData​(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, Boolean rtPredictionsAvailable, ArrayList<Double> predictedRts, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, 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.biology.modifications.ModificationFactory modificationFactory, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)
    Gets the peptide data to provide to percolator.
    static long
    getPeptideKey​(String peptideData)
    Returns a unique key corresponding to the given peptide.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • PercolatorUtils

      public PercolatorUtils()

  • Method Details

    • getHeader

      public static String getHeader​(com.compomics.util.parameters.identification.search.SearchParameters searchParameters, Boolean rtPredictionsAvailable)
      Returns the header of the Percolator training file.
      Parameters:
      searchParameters - The parameters of the search.
      rtPredictionsAvailable - Flag indicating whether RT predictions are given.
      Returns:
      The header of the Percolator training file.

    • getPeptideData

      public static String getPeptideData​(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, Boolean rtPredictionsAvailable, ArrayList<Double> predictedRts, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, 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.biology.modifications.ModificationFactory modificationFactory, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)
      Gets the peptide data to provide to percolator.
      Parameters:
      spectrumMatch - The spectrum match where the peptide was found.
      peptideAssumption - The peptide assumption.
      rtPredictionsAvailable - Flag indicating whether retention time predictions are given.
      predictedRts - The retention time predictions for this peptide.
      searchParameters - The parameters of the search.
      sequenceProvider - The sequence provider.
      sequenceMatchingParameters - The sequence matching parameters.
      annotationParameters - The annotation parameters.
      modificationLocalizationParameters - The modification localization parameters.
      modificationFactory - The factory containing the modification details.
      spectrumProvider - The spectrum provider.
      Returns:
      The peptide data as string.

    • getPeptideKey

      public static long getPeptideKey​(String peptideData)
      Returns a unique key corresponding to the given peptide.
      Parameters:
      peptideData - The peptide data as string.
      Returns:
      The unique key corresponding to the peptide data.

    • getEnzymaticityFeature

      public static boolean[] getEnzymaticityFeature​(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)
      Computes the value for the enzymaticity feature.
      Parameters:
      peptideAssumption - The peptide assumption object.
      searchParameters - The search parameters.
      sequenceProvider - The sequence provider to use for protein sequences.
      Returns:
      The value of the given feature as object.

    • getMeasuredAndDeltaMzFeature

      public static double[] getMeasuredAndDeltaMzFeature​(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)
      Computes the value for the measured and delta mass feature.
      Parameters:
      spectrumMatch - The spectrum match object.
      peptideAssumption - The peptide assumption object.
      searchParameters - The search parameters.
      spectrumProvider - The spectrum provider to use for spectra.
      Returns:
      The value of the given feature as object.

    • getIntensityCoverageFeature

      public static double getIntensityCoverageFeature​(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, 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)
      Computes the value for the intensity coverage feature.
      Parameters:
      spectrumMatch - The spectrum match object.
      peptideAssumption - The peptide assumption object.
      searchParameters - The search parameters.
      annotationParameters - The annotation parameters.
      modificationLocalizationParameters - The modification localization parameters.
      sequenceProvider - The sequence provider to use for protein sequences.
      spectrumProvider - The spectrum provider to use for spectra.
      Returns:
      The value of the given feature as object.