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 StringBuilder
    calculateSpectraDistances(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, String ionSpectrum)
    Returns the spectra metrics.
    static double
    findMatchedPeaksRatio(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, int alignedPeaksNum)
    Returns the ratio of matched predicted peaks.
    static int
    findTerminiCoverage(ArrayList<ArrayList<Integer>> aligned_peaks, String ion)
    Returns the ratio of matched predicted peaks.
    static ArrayList<ArrayList<Integer>>
    getAlignedPeaks(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum)
    Returns the indices of the predicted peaks and their measured matches (measuredIndex = -1 if predicted peak unmatched).
    static double
    getCrossEntropy(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, double matchedPeaksRatio)
    Returns the cross entropy between the measured and predicted mass spectrum.
    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, Boolean spectraPredictionsAvailable)
    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, ArrayList<Double> peptideRTs, ArrayList<com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum> predictedSpectra, 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, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters)
    Gets the peptide data to provide to percolator.
    static long
    getPeptideKey(String peptideData)
    Returns a unique key corresponding to the given peptide.
    static ArrayList<Double>
    getPeptideObservedPredictedRT(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, ArrayList<Double> predictedRts, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)
     
    static String
    getPeptideRTData(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, ArrayList<Double> peptideRTs, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory)
     
    static long
    getPsmKey(String psmData)
    Returns a unique key corresponding to the given PSM.
    static String
    getRTValuesHeader()
    Returns the header of the file with the RT observed and predicted values.
    static String
    getSequenceWithModifications(com.compomics.util.experiment.biology.proteins.Peptide peptide, 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.biology.modifications.ModificationFactory modificationFactory)
    Returns the sequence of the peptides with modifications encoded as required by Percolator.
    static double
    getSpectraCosine(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, ArrayList<ArrayList<Integer>> alignedPeaks)
    Returns the cosine distance between the measured and predicted mass spectrum.
    static double
    getSpectraLogDist(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, ArrayList<ArrayList<Integer>> alignedPeaks, double matchedPeaksRatio)
    Returns the log distance between the measured and predicted mass spectrum.
    static ArrayList<com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum>
    normalizeIntensities(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, ArrayList<ArrayList<Integer>> alignedPeaks)
    Normalize the intensities of the observed and predicted spectra, as probability distributions for cross entropy computation.
    static ArrayList<com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum>
    scaleIntensities(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, ArrayList<ArrayList<Integer>> alignedPeaks)
    Scale the intensities of the observed and predicted spectra.

    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, Boolean spectraPredictionsAvailable)
      Returns the header of the Percolator training file.
      Parameters:
      searchParameters - The parameters of the search.
      rtPredictionsAvailable - Flag indicating whether RT predictions are given.
      spectraPredictionsAvailable - Flag indicating whether spectra predictions are given.
      Returns:
      The header of the Percolator training file.

    • getRTValuesHeader

      public static String getRTValuesHeader()
      Returns the header of the file with the RT observed and predicted values.
      Returns:
      The header of the file with the RT observed and predicted values.

    • getPeptideData

      public static String getPeptideData(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, ArrayList<Double> peptideRTs, ArrayList<com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum> predictedSpectra, 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, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters)
      Gets the peptide data to provide to percolator.
      Parameters:
      spectrumMatch - The spectrum match where the peptide was found.
      peptideAssumption - The peptide assumption.
      peptideRTs - The retention time predictions for this peptide.
      predictedSpectra - The predicted mass spectra 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.
      modificationParameters - The modification parameters
      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.

    • calculateSpectraDistances

      public static StringBuilder calculateSpectraDistances(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, String ionSpectrum)
      Returns the spectra metrics.
      Parameters:
      measuredSpectrum - The measured spectrum.
      predictedSpectrum - The predicted spectrum.
      ionSpectrum - String showing whether the spectrum consists of only B or Y ions.
      Returns:
      String builder with the spectra distances.

    • findTerminiCoverage

      public static int findTerminiCoverage(ArrayList<ArrayList<Integer>> aligned_peaks, String ion)
      Returns the ratio of matched predicted peaks.
      Parameters:
      aligned_peaks - The indices of aligned peaks.
      ion - "B" or "Y" ion.
      Returns:
      #mathced peaks / #predicted peaks

    • findMatchedPeaksRatio

      public static double findMatchedPeaksRatio(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, int alignedPeaksNum)
      Returns the ratio of matched predicted peaks.
      Parameters:
      predictedSpectrum - The predicted spectrum.
      alignedPeaksNum - The number of matched peaks.
      Returns:
      #mathced peaks / #predicted peaks

    • scaleIntensities

      public static ArrayList<com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum> scaleIntensities(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, ArrayList<ArrayList<Integer>> alignedPeaks)
      Scale the intensities of the observed and predicted spectra.
      Parameters:
      measuredSpectrum - The measured spectrum.
      predictedSpectrum - The predicted spectrum.
      alignedPeaks - The indices of the matched peaks.
      Returns:
      ArrayList(ScaledObservedSpectrum, ScaledPredictedSpectrum)

    • normalizeIntensities

      public static ArrayList<com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum> normalizeIntensities(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, ArrayList<ArrayList<Integer>> alignedPeaks)
      Normalize the intensities of the observed and predicted spectra, as probability distributions for cross entropy computation.
      Parameters:
      measuredSpectrum - The measured spectrum.
      predictedSpectrum - The predicted spectrum.
      alignedPeaks - The indices of the matched peaks.
      Returns:
      ArrayList(NormalizedObservedSpectrum, NormalizedPredictedSpectrum)

    • getCrossEntropy

      public static double getCrossEntropy(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, double matchedPeaksRatio)
      Returns the cross entropy between the measured and predicted mass spectrum.
      Parameters:
      measuredSpectrum - The measured spectrum.
      predictedSpectrum - The predicted spectrum.
      matchedPeaksRatio - The ratio of matched predicted peaks. //@param alignedPeaks The indices of the matched peaks.
      Returns:
      spectra cross entropy

    • getSpectraCosine

      public static double getSpectraCosine(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, ArrayList<ArrayList<Integer>> alignedPeaks)
      Returns the cosine distance between the measured and predicted mass spectrum.
      Parameters:
      measuredSpectrum - The measured spectrum.
      predictedSpectrum - The predicted spectrum.
      alignedPeaks - The indices of the matched peaks.
      Returns:
      spectra cosine similarity

    • getSpectraLogDist

      public static double getSpectraLogDist(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum, ArrayList<ArrayList<Integer>> alignedPeaks, double matchedPeaksRatio)
      Returns the log distance between the measured and predicted mass spectrum.
      Parameters:
      measuredSpectrum - The measured spectrum.
      predictedSpectrum - The predicted spectrum.
      alignedPeaks - The indices of the matched peaks.
      matchedPeaksRatio - The ratio of matched predicted peaks.
      Returns:
      spectra log distance

    • getAlignedPeaks

      public static ArrayList<ArrayList<Integer>> getAlignedPeaks(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum measuredSpectrum, com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum predictedSpectrum)
      Returns the indices of the predicted peaks and their measured matches (measuredIndex = -1 if predicted peak unmatched).
      Parameters:
      measuredSpectrum - The measured spectrum.
      predictedSpectrum - The predicted spectrum.
      Returns:
      [ [measuredMatchedPeakIndex_1, predictedMatchedPeakIndex_1], ... [] [measuredMatchedPeakIndex_n, predictedMatchedPeakIndex_n]]

    • getSequenceWithModifications

      public static String getSequenceWithModifications(com.compomics.util.experiment.biology.proteins.Peptide peptide, 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.biology.modifications.ModificationFactory modificationFactory)
      Returns the sequence of the peptides with modifications encoded as required by Percolator.
      Parameters:
      peptide - The peptide.
      modificationParameters - The modification parameters of the search.
      sequenceProvider - The sequence provider.
      sequenceMatchingParameters - The sequence matching parameters.
      modificationFactory - The factory containing the modification details
      Returns:
      the modifications of the peptides encoded as required by DeepLc.

    • getPeptideRTData

      public static String getPeptideRTData(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption peptideAssumption, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, ArrayList<Double> peptideRTs, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory)

    • getPeptideObservedPredictedRT

      public static ArrayList<Double> getPeptideObservedPredictedRT(com.compomics.util.experiment.identification.matches.SpectrumMatch spectrumMatch, ArrayList<Double> predictedRts, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider)

    • 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.

    • getPsmKey

      public static long getPsmKey(String psmData)
      Returns a unique key corresponding to the given PSM.
      Parameters:
      psmData - The psm data as string.
      Returns:
      The unique key corresponding to the PSM data.