reportOutputFolder = new File(aLine.getOptionValue(ReportCLIParams.EXPORT_FOLDER.id));

        }

        if (aLine.hasOption(ReportCLIParams.REPORT_TYPE.id)) {

            ArrayList<Integer> options = CommandLineUtils.getIntegerListFromString(aLine.getOptionValue(ReportCLIParams.REPORT_TYPE.id), ",");

            for (int option : options) {

            }

        }

        if (aLine.hasOption(ReportCLIParams.DOCUMENTATION_TYPE.id)) {

            ArrayList<Integer> options = CommandLineUtils.getIntegerListFromString(aLine.getOptionValue(ReportCLIParams.DOCUMENTATION_TYPE.id), ",");

            for (int option : options) {

            }

        }

        pathSettingsCLIInputBean = new PathSettingsCLIInputBean(aLine);

    }

            PTMScoringPreferences ptmcoringPreferences, SpectrumCountingPreferences spectrumCountingPreferences, WaitingHandler waitingHandler)

            throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException,

            InterruptedException, MzMLUnmarshallerException, MathException {

        File reportFile = new File(reportCLIInputBean.getReportOutputFolder(), PSExportFactory.getDefaultReportName(experiment, sample, replicateNumber, reportType));

        //@TODO: allow format selection

        PSExportFactory.writeExport(exportScheme, reportFile, ExportFormat.text, experiment, sample, replicateNumber, projectDetails, identification, identificationFeaturesGenerator,

                searchParameters, null, null, null, null, nSurroundingAA, annotationPreferences, sequenceMatchingPreferences, idFilter, ptmcoringPreferences, spectrumCountingPreferences, waitingHandler);

     *

     * @throws IOException thrown of IOException occurs

     */

    public static void exportDocumentation(ReportCLIInputBean reportCLIInputBean, String reportType, WaitingHandler waitingHandler) throws IOException {

        File reportFile = new File(reportCLIInputBean.getReportOutputFolder(), PSExportFactory.getDefaultDocumentation(reportType));

        //@TODO: allow format selection

        PSExportFactory.writeDocumentation(exportScheme, ExportFormat.text, reportFile);

    }