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

            System.err.println("The input file " + inputFile + " does not contain any samples. " +
                    "Please check file format.");
            System.exit(-1);
        }


        CountsQcAnalysis countsAnalysis =
                new CountsQcAnalysis(resultManager, homePath, samples);




        countsAnalysis.setInputFilePath(inputFile);


        Map<Integer,String> cMap = new HashMap<Integer, String>();
        for (int i = 0; i < conditionNames.size(); ++i) {
            cMap.put(i + 1, conditionNames.get(i));
        }
        countsAnalysis.setConditionNames(cMap);


        countsAnalysis.setThreshold( k );


        if (compareConditions) {
            countsAnalysis.activateComparison();
        }


        if (!infoFile.isEmpty()) {
            countsAnalysis.setInfoFilePath(infoFile);
        }


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




        countsAnalysis.run();


        logger.println("\nPreparing result report");
        exportResult(resultManager);


        logger.println("Finished");


        settingsDlg.setUiEnabled(false);


        String homePath = settingsDlg.getHomeFrame().getQualimapFolder() + File.separator;


        CountsQcAnalysis countsAnalysis = new CountsQcAnalysis(tabProperties, homePath,
                settingsDlg.getDataItems());


        countsAnalysis.setThreshold( settingsDlg.getCountsThreshold() );
        countsAnalysis.setConditionNames(  settingsDlg.getConditionsMap() );


        if (settingsDlg.performComparison()) {
            countsAnalysis.activateComparison();
        }


        boolean  includeInfoFile = settingsDlg.annotationIsProvided();
        if (includeInfoFile) {
            String infoFilePath;
            if (settingsDlg.infoFileIsProvided())  {
                infoFilePath = settingsDlg.getInfoFilePath();
            } else {
                infoFilePath =  homePath + "species" + File.separator + settingsDlg.getSelectedSpecies();
            }
            countsAnalysis.setInfoFilePath(infoFilePath);
        }


        AnalysisDialogLoggerThread outputParsingThread= new AnalysisDialogLoggerThread( settingsDlg ) ;
        countsAnalysis.setOutputParsingThread(outputParsingThread);


        try {
            countsAnalysis.run();
        } catch (Exception e) {
            JOptionPane.showMessageDialog(settingsDlg, "Failed to analyze counts data. " + e.getMessage(),
                    settingsDlg.getTitle(), JOptionPane.ERROR_MESSAGE);
            settingsDlg.setUiEnabled(true);
            //settingsDlg.resetUi();

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

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