Examples of org.bioinfo.ngs.qc.qualimap.process.EpiAnalysis


        initOutputDir();


        AnalysisResultManager resultManager = new AnalysisResultManager(AnalysisType.CLUSTERING);


        EpiAnalysis epiAnalysis = new EpiAnalysis(resultManager,homePath,cfg);


        LoggerThread loggerThread = new LoggerThread() {
            public void logLine(String msg) {
                System.out.println(msg);
            }
        };
        epiAnalysis.setOutputParsingThread(loggerThread);


        try {
            epiAnalysis.run();
        } catch (Exception e) {
            System.err.println("Failed to run analysis\n" + e.getMessage());
            e.printStackTrace();
            System.exit(-1);
        }

        cfg.fragmentLength  = Integer.parseInt(settingsDialog.getReadSmoothingLength());
        cfg.clusters = settingsDialog.getClusterNumbers();
        cfg.vizType = settingsDialog.getVisuzliationType();


        String homePath = settingsDialog.getHomeFrame().getQualimapFolder();
        EpiAnalysis epiAnalysis = new EpiAnalysis(tabProperties, homePath, cfg);


        OutputParsingThread outputParsingThread= new OutputParsingThread( settingsDialog ) ;
        epiAnalysis.setOutputParsingThread(outputParsingThread);


        epiAnalysis.setProgressStream(settingsDialog.getProgressStream());




        try {


            epiAnalysis.run();


        } catch (Exception e)  {
            JOptionPane.showMessageDialog(settingsDialog, e.getMessage(),
                    "Epigenetics analysis", JOptionPane.ERROR_MESSAGE );
            e.printStackTrace();

Related Classes of org.bioinfo.ngs.qc.qualimap.process.EpiAnalysis

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