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 and Description
PercolatorExport()

Method Summary

Modifier and Type	Method and 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 Detail

PercolatorExport

public PercolatorExport()

Method Detail

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.