eu.isas.peptideshaker.followup

Class DeepLcExport

java.lang.Object

eu.isas.peptideshaker.followup.DeepLcExport

public class DeepLcExport
extends Object

Export for RT prediction using DeepLC.

Author:

Marc Vaudel, Dafni Skiadopoulou

Constructor Summary

Constructors

Constructor and Description
DeepLcExport()

Method Summary

Modifier and Type	Method and Description
static void	deepLcExport(File destinationFile, File confidentHitsDestinationFile, HashSet<Long> keys, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, 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 DeepLC training file for the given spectrum file.
static ArrayList<File>	deepLcExport(String destinationStem, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler) Exports DeepLC training files for each of the spectrum files.
static File	getConfidentHitsDestinationFile(String destinationStem, String spectrumFile, boolean addSuffix) Returns the file where to write the export for confident hits.
static File	getDestinationFile(String destinationStem, String spectrumFile, boolean addSuffix) Returns the file where to write the export.
static ArrayList<File>	getExportedFiles(String destinationStem, com.compomics.util.experiment.identification.Identification identification) Returns an ArrayList of all the files that will be written by the export.

Methods inherited from class java.lang.Object

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

Constructor Detail

DeepLcExport

public DeepLcExport()

Method Detail

deepLcExport

public static ArrayList<File> deepLcExport(String destinationStem,
                                           com.compomics.util.experiment.identification.Identification identification,
                                           com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters,
                                           com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
                                           com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider,
                                           com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                           com.compomics.util.waiting.WaitingHandler waitingHandler)

Exports DeepLC training files for each of the spectrum files. Returns an ArrayList of the files exported.

Parameters:

destinationStem - The stem to use for the path.

identification - The identification object containing the matches.

modificationParameters - The modification parameters.

sequenceMatchingParameters - The sequence matching parameters.

sequenceProvider - The sequence provider.

spectrumProvider - The spectrum provider.

waitingHandler - The waiting handler.

Returns:

An ArrayList of the files exported.

getExportedFiles

public static ArrayList<File> getExportedFiles(String destinationStem,
                                               com.compomics.util.experiment.identification.Identification identification)

Returns an ArrayList of all the files that will be written by the export.

Parameters:

destinationStem - The stem to use for the path.

identification - The identification object containing the matches.

Returns:

An ArrayList of all the files that will be written by the export.

getDestinationFile

public static File getDestinationFile(String destinationStem,
                                      String spectrumFile,
                                      boolean addSuffix)

Returns the file where to write the export.

Parameters:

destinationStem - The stem to use for the path.

spectrumFile - The name of the spectrum file.

addSuffix - A boolean indicating whehter the name of the spectrum file should be appended to the stem.

Returns:

The file where to write the export.

getConfidentHitsDestinationFile

public static File getConfidentHitsDestinationFile(String destinationStem,
                                                   String spectrumFile,
                                                   boolean addSuffix)

Returns the file where to write the export for confident hits.

Parameters:

destinationStem - The stem to use for the path.

spectrumFile - The name of the spectrum file.

addSuffix - A boolean indicating whehter the name of the spectrum file should be appended to the stem.

Returns:

The file where to write the export.

deepLcExport

public static void deepLcExport(File destinationFile,
                                File confidentHitsDestinationFile,
                                HashSet<Long> keys,
                                com.compomics.util.experiment.identification.Identification identification,
                                com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters,
                                com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters,
                                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 DeepLC training file for the given spectrum file.

Parameters:

destinationFile - The file where to write the export.

confidentHitsDestinationFile - The file where to write the export for confident hits.

keys - The keys of the spectrum matches.

identification - The identification object containing the matches.

modificationParameters - The modification parameters.

sequenceMatchingParameters - The sequence matching parameters.

sequenceProvider - The sequence provider.

spectrumProvider - The spectrum provider.

waitingHandler - The waiting handler.