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 HashMap<String,ArrayList<com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum>>	getIntensitiesPrediction(File ms2pipFile)	Parses the peaks intensities prediction from MS2PIP.
static void	percolatorExport(File destinationFile, File deepLcFile, File rtObsPredsFile, 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.parameters.identification.search.ModificationParameters modificationParameters, 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, File rtObsPredsFile, 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.parameters.identification.search.ModificationParameters modificationParameters, 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.
static void	RTValuesExport(File deepLcFile, File rtObsPredsFile, 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.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler)

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 rtObsPredsFile,
 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.parameters.identification.search.ModificationParameters modificationParameters,
 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.

rtObsPredsFile - The file to write RT observed and predicted values per PSM.

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

modificationParameters - The modification parameters

sequenceProvider - The sequence provider.

spectrumProvider - The spectrum provider.

waitingHandler - The waiting handler.

getIntensitiesPrediction

public static HashMap<String,ArrayList<com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum>> getIntensitiesPrediction(File ms2pipFile)

Parses the peaks intensities prediction from MS2PIP. Expected format: predicted_spectrum_key,charge,ion,ionnumber,mz,prediction 2238942014911164193,3,B,1,138.066,0

Parameters:

ms2pipFile - File with spectra fragmentation predictions from MS2PIP.

Returns:

Map with pairs (Ms2PipKey, [Spectrum, bSpectrum, ySpectrum])

percolatorExport

public static void percolatorExport(File destinationFile,
 File rtObsPredsFile,
 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.parameters.identification.search.ModificationParameters modificationParameters,
 com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
 com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
 com.compomics.util.waiting.WaitingHandler waitingHandler)
                             throws InterruptedException,
ExecutionException

Exports a Percolator training file.

Parameters:

destinationFile - The file where to write the export.

rtObsPredsFile - The file to write RT observed and predicted values per PSM.

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

modificationParameters - The modification parameters

sequenceProvider - The sequence provider.

spectrumProvider - The spectrum provider.

waitingHandler - The waiting handler.

Throws:

InterruptedException - Exception thrown if the execution is interrupted.

ExecutionException - Exception thrown if an error occurred during concurrent execution.

RTValuesExport

public static void RTValuesExport(File deepLcFile,
 File rtObsPredsFile,
 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.parameters.identification.search.ModificationParameters modificationParameters,
 com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
 com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
 com.compomics.util.waiting.WaitingHandler waitingHandler)

Parameters:

deepLcFile - The deepLC results.

rtObsPredsFile - The file to write RT observed and predicted values per PSM.

identification - The identification object containing the matches.

searchParameters - The search parameters.

sequenceMatchingParameters - The sequence matching parameters.

annotationParameters - The annotation parameters.

modificationLocalizationParameters - The modification localization.

modificationParameters - The modification parameters

sequenceProvider - The sequence provider.

spectrumProvider - The spectrum provider.

waitingHandler - The waiting handler.