Examples of PSExportFactory

Examples of eu.isas.peptideshaker.export.PSExportFactory

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        if (aLine.hasOption(ReportCLIParams.EXPORT_FOLDER.id)) {
            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), ",");
            PSExportFactory exportFactory = PSExportFactory.getInstance();
            for (int option : options) {
                reportTypes.add(exportFactory.getExportTypeFromCommandLineOption(option));
            }
        }
        if (aLine.hasOption(ReportCLIParams.DOCUMENTATION_TYPE.id)) {
            ArrayList<Integer> options = CommandLineUtils.getIntegerListFromString(aLine.getOptionValue(ReportCLIParams.DOCUMENTATION_TYPE.id), ",");
            PSExportFactory exportFactory = PSExportFactory.getInstance();
            for (int option : options) {
                documentationTypes.add(exportFactory.getExportTypeFromCommandLineOption(option));
            }
        }
        pathSettingsCLIInputBean = new PathSettingsCLIInputBean(aLine);
    }
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Examples of eu.isas.peptideshaker.export.PSExportFactory

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            SearchParameters searchParameters, AnnotationPreferences annotationPreferences, SequenceMatchingPreferences sequenceMatchingPreferences, int nSurroundingAA, IdFilter idFilter,
            PTMScoringPreferences ptmcoringPreferences, SpectrumCountingPreferences spectrumCountingPreferences, WaitingHandler waitingHandler)
            throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException,
            InterruptedException, MzMLUnmarshallerException, MathException {

        PSExportFactory exportFactory = PSExportFactory.getInstance();
        ExportScheme exportScheme = exportFactory.getExportScheme(reportType);
        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);
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Examples of eu.isas.peptideshaker.export.PSExportFactory

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     * @param waitingHandler waiting handler displaying feedback to the user
     *
     * @throws IOException thrown of IOException occurs
     */
    public static void exportDocumentation(ReportCLIInputBean reportCLIInputBean, String reportType, WaitingHandler waitingHandler) throws IOException {
        PSExportFactory exportFactory = PSExportFactory.getInstance();
        ExportScheme exportScheme = exportFactory.getExportScheme(reportType);
        File reportFile = new File(reportCLIInputBean.getReportOutputFolder(), PSExportFactory.getDefaultDocumentation(reportType));

        //@TODO: allow format selection
        PSExportFactory.writeDocumentation(exportScheme, ExportFormat.text, reportFile);
    }
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