peptideShakerGUI.setDataSaved(false); // @TODO: this might not always be true, e.g., if nothing has changed, but better than not saving at all
boolean conversionCompleted;
try {
PrideXmlExport prideExport = new PrideXmlExport(PeptideShaker.getVersion(), peptideShakerGUI.getIdentification(), peptideShakerGUI.getProjectDetails(),
peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getPtmScoringPreferences(), peptideShakerGUI.getSpectrumCountingPreferences(),
peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSpectrumAnnotator(), peptideShakerGUI.getAnnotationPreferences(), peptideShakerGUI.getSequenceMatchingPreferences(),
selectedSample, selectedSample, selectedProtocol, selectedProtocol, referenceGroup, contactGroup, sample, protocol, instrument,
new File(outputFolderJTextField.getText()), outputFileName, progressDialog);
prideExport.createPrideXmlFile(progressDialog);
// validate the pride xml file
if (validatePrideXml && !projectExportDialog.progressCancelled()) {
progressDialog.setPrimaryProgressCounterIndeterminate(true);
progressDialog.setTitle("Validating PRIDE XML. Please Wait...");