eu.isas.peptideshaker.stirred.modules

Class IdImporter

java.lang.Object

eu.isas.peptideshaker.stirred.modules.IdImporter

public class IdImporter
extends Object

This class imports the ids from a file.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
IdImporter(File searchEngineResultsFile, com.compomics.software.log.CliLogger cliLogger) Constructor.

Method Summary

Modifier and Type	Method and Description
com.compomics.util.experiment.io.identification.IdfileReader	getIdFileReader() Returns the identification file reader used.
ArrayList<com.compomics.util.experiment.identification.matches.SpectrumMatch>	loadSpectrumMatches(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.waiting.WaitingHandler waitingHandler) Parses the spectrum matches and returns them in an ArrayList.

Methods inherited from class java.lang.Object

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

Constructor Detail

IdImporter

public IdImporter(File searchEngineResultsFile,
                  com.compomics.software.log.CliLogger cliLogger)

Constructor.

Parameters:

searchEngineResultsFile - The search engine results file.

cliLogger - The logger to use for CLI report.

Method Detail

loadSpectrumMatches

public ArrayList<com.compomics.util.experiment.identification.matches.SpectrumMatch> loadSpectrumMatches(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                                                                                                         com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                                                                                                         com.compomics.util.waiting.WaitingHandler waitingHandler)

Parses the spectrum matches and returns them in an ArrayList.

Parameters:

identificationParameters - The identification parameters to use.

spectrumProvider - The spectrum provider to use.

waitingHandler - The waiting handler to use.

Returns:

The spectrum matches in an ArrayList.

getIdFileReader

public com.compomics.util.experiment.io.identification.IdfileReader getIdFileReader()

Returns the identification file reader used.

Returns:

The identification file reader.