private boolean dataSaved = true;
private double bubbleScale = 1;
private static boolean useLogFile = true;
private LastSelectedFolder lastSelectedFolder;
private PTMFactory ptmFactory;
<BUG>private EnzymeFactory enzymeFactory = EnzymeFactory.getInstance();
private UtilitiesUserPreferences utilitiesUserPreferences;</BUG>
private ProcessingPreferences processingPreferences = new ProcessingPreferences();
private ProgressDialogX progressDialog;
private OverviewPanel overviewPanel;

private boolean dataSaved = true;
private double bubbleScale = 1;
private static boolean useLogFile = true;
private LastSelectedFolder lastSelectedFolder;
private PTMFactory ptmFactory;
private EnzymeFactory enzymeFactory;
private UtilitiesUserPreferences utilitiesUserPreferences;
private ProcessingPreferences processingPreferences = new ProcessingPreferences();
private ProgressDialogX progressDialog;
private OverviewPanel overviewPanel;
