PSMaps pSMaps = new PSMaps();
pSMaps = (PSMaps) peptideShakerGUI.getIdentification().getUrParam(pSMaps);
PeptideShaker miniShaker = new PeptideShaker(peptideShakerGUI.getExperiment(), peptideShakerGUI.getSample(), peptideShakerGUI.getReplicateNumber(), pSMaps);
try {
miniShaker.spectrumMapChanged(peptideShakerGUI.getIdentification(), progressDialog, peptideShakerGUI.getProcessingPreferences(), peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getSequenceMatchingPreferences());
} catch (Exception e) {
JOptionPane.showMessageDialog(peptideShakerGUI, JOptionEditorPane.getJOptionEditorPane(
"An identification conflict occured. If you can reproduce the error <br>"
+ "Please <a href=\"http://code.google.com/p/peptide-shaker/issues/list\">contact the developers</a>."),
"Identification Conflict", JOptionPane.ERROR_MESSAGE);