public static List<AnalyteSettings> createAnalyteSettings() { Scanner scan = new Scanner(System.in); List<AnalyteSettings> analyteSettings = new ArrayList(); AnalyteSettings analyte = new AnalyteSettings(); GlycanSettings gSettings = new GlycanSettings(); gSettings.setAllowInnerFragments(false); gSettings.setPerDerivatisationType(getPerDerivatisationType()); System.out.println("Set the max number of cleaveges: "); String maxClvg = scan.nextLine(); gSettings.setMaxNumOfCleavages(Integer.parseInt(maxClvg)); System.out.println("Set the max number of Cross Ring cleaveges: "); String maxCRClvg = scan.nextLine(); gSettings.setMaxNumOfCrossRingCleavages(Integer.parseInt(maxCRClvg)); gSettings.setGlycanFragments(FragmentFactory.createFragments()); gSettings.setReducingEnd(ReducingEndFactory.createReducingEnd()); analyte.setGlycanSettings(gSettings); analyteSettings.add(analyte); return analyteSettings; }