eu.isas.peptideshaker.followup

Class Ms2PipExport

java.lang.Object

eu.isas.peptideshaker.followup.Ms2PipExport

public class Ms2PipExport
extends Object

Export training files for ms2pip.

Author:

Marc Vaudel, Dafni Skiadopoulou

Constructor Summary

Constructors

Constructor and Description
Ms2PipExport()

Method Summary

Modifier and Type	Method and Description
static void	ms2pipExport(File peprecFile, 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 ms2pip training file for the given spectrum file.
static ArrayList<File>	ms2pipExport(File peprecFile, String[] models, 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.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler) Exports ms2pip config and peprec files.
static void	writeConfigFile(File configFile, String model, com.compomics.util.parameters.identification.search.SearchParameters searchParameters) Writes a config file for a given model.

Methods inherited from class java.lang.Object

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

Constructor Detail

Ms2PipExport

public Ms2PipExport()

Method Detail

ms2pipExport

public static ArrayList<File> ms2pipExport(File peprecFile,
                                           String[] models,
                                           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.io.biology.protein.SequenceProvider sequenceProvider,
                                           com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                           com.compomics.util.waiting.WaitingHandler waitingHandler)

Exports ms2pip config and peprec files. Returns an ArrayList of the files written.

Parameters:

peprecFile - The file where to write the peptides.

models - The names of the models to write config files for.

identification - The identification object containing the matches.

searchParameters - The search 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.

writeConfigFile

public static void writeConfigFile(File configFile,
                                   String model,
                                   com.compomics.util.parameters.identification.search.SearchParameters searchParameters)

Writes a config file for a given model.

Parameters:

configFile - The file where to write.

model - The name of the model.

searchParameters - The search parameters.

ms2pipExport

public static void ms2pipExport(File peprecFile,
                                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 ms2pip training file for the given spectrum file.

Parameters:

peprecFile - The file where to write the export.

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.