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 and Description
PercolatorUtils()

Method Summary

Modifier and Type	Method and Description
static String	getHeader(com.compomics.util.parameters.identification.search.SearchParameters searchParameters, Boolean rtPredictionsAvailable) Returns the header of the Percolator training file.
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 Detail

PercolatorUtils

public PercolatorUtils()

Method Detail

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.