public ProteinMapper(XTandemMain app) { super(app); ScoringModifications scoringMods = app.getScoringMods(); PeptideModification[] modifications = scoringMods.getModifications(); m_Modifications = modifications; setGenerateDecoysForModifiedPeptides( app.getBooleanParameter( XTandemUtilities.CREATE_DECOY_FOR_MODIFIED_PEPTIDES_PROPERTY, Boolean.FALSE)); // hard code modifications of cystein }