JOptionPane.QUESTION_MESSAGE);
if (value == JOptionPane.YES_OPTION) {
addShortcutAtDeskTop();
}
}
<BUG>loadEnzymes();</BUG>
PeptideShaker.instantiateFacories(utilitiesUserPreferences);
<BUG>ptmFactory = PTMFactory.getInstance();
spectrumFactory = SpectrumFactory.getInstance();</BUG>
sequenceFactory = SequenceFactory.getInstance();

JOptionPane.QUESTION_MESSAGE);
if (value == JOptionPane.YES_OPTION) {
addShortcutAtDeskTop();
}
}
PeptideShaker.instantiateFacories(utilitiesUserPreferences);
ptmFactory = PTMFactory.getInstance();
enzymeFactory = EnzymeFactory.getInstance();
spectrumFactory = SpectrumFactory.getInstance();
sequenceFactory = SequenceFactory.getInstance();
