new Thread("ProgenesisPsmThread") {
@Override
public void run() {
try {
if (psmSelectionComboBox.getSelectedIndex() == 4) {
ProgenesisExcelExport progenesisExcelExport = new ProgenesisExcelExport(
progressDialog,
peptideShakerGUI.getIdentification().getProteinIdentification(),
peptideShakerGUI.getSearchParameters().getEnzyme(),
peptideShakerGUI.getSequenceMatchingPreferences(),
peptideShakerGUI.getIdentification(),
finalOutputFile);
progenesisExcelExport.writeProgenesisExcelExport();
} else {
ProgenesisExport.writeProgenesisExport(finalOutputFile, peptideShakerGUI.getIdentification(),
ProgenesisExport.ExportType.getTypeFromIndex(userChoice), progressDialog, ptmSelection,
peptideShakerGUI.getSequenceMatchingPreferences());
}