eu.isas.peptideshaker.followup

Class PepXmlExport

java.lang.Object

eu.isas.peptideshaker.followup.PepXmlExport

public class PepXmlExport
extends Object

Export to PepXML.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor and Description
PepXmlExport() Constructor.

Method Summary

Modifier and Type

Method and Description

void

writePepXmlFile(com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, File destinationFile, String peptideShakerVersion, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler) Writes the PSM results to the given file in the PepXML format.

Methods inherited from class java.lang.Object

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

Constructor Detail

PepXmlExport

public PepXmlExport()

Constructor.

Method Detail

writePepXmlFile

public void writePepXmlFile(com.compomics.util.experiment.identification.Identification identification,
                            com.compomics.util.parameters.identification.IdentificationParameters identificationParameters,
                            com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider,
                            File destinationFile,
                            String peptideShakerVersion,
                            com.compomics.util.waiting.WaitingHandler waitingHandler,
                            com.compomics.util.exceptions.ExceptionHandler exceptionHandler)
                     throws IOException

Writes the PSM results to the given file in the PepXML format.

Parameters:

identification - the identification object containing the identification results

identificationParameters - the identification parameters

spectrumProvider - the spectrum provider

destinationFile - the file where to write

peptideShakerVersion - the PeptideShaker version

waitingHandler - a waiting handler to display progress and allow interrupting the process

exceptionHandler - a handler for exceptions

Throws:

IOException - exception thrown whenever an error is encountered while reading or writing a file