Examples of run()

Examples of org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis.run()

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            BamQCRegionReporter bamQcReporter = new BamQCRegionReporter(false, true);


            try {
                bamQc.run();
                bamQcReporter.loadReportData(bamQc.getBamStats());
                bamQcReporter.computeChartsBuffers(bamQc.getBamStats(), bamQc.getLocator(), bamQc.isPairedData());
            } catch (Exception e) {
                assertTrue("Error calculating stats. " + e.getMessage(), false);
                e.printStackTrace();
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Examples of org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.run()

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                }
            }


            try {
                computeCountsTask.run();
                Map<String,Double> readCounts = computeCountsTask.getReadCounts();

                /*List<String> geneNames = asSortedList(readCounts.keySet());

                for (String key : geneNames) {
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Examples of org.bioinfo.ngs.qc.qualimap.process.CountsQcAnalysis.run()

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            }
        };
        countsAnalysis.setOutputParsingThread(loggerThread);


        countsAnalysis.run();

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

        logger.println("Finished");
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Examples of org.bioinfo.ngs.qc.qualimap.process.EpiAnalysis.run()

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            }
        };
        epiAnalysis.setOutputParsingThread(loggerThread);

        try {
            epiAnalysis.run();
        } catch (Exception e) {
            System.err.println("Failed to run analysis\n" + e.getMessage());
            e.printStackTrace();
            System.exit(-1);
        }
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Examples of org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.run()

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        if (settingsDlg.runBamQcFirst()) {
            multiBamQcAnalysis.setRunBamQcFirst( settingsDlg.getBamQcConfig() );
        }

        try {
            multiBamQcAnalysis.run();
        } catch (Exception e) {
            JOptionPane.showMessageDialog(settingsDlg, "Failed to run multi-sample BAM QC!\n" + e.getMessage(),
                    settingsDlg.getTitle(), JOptionPane.ERROR_MESSAGE);
            settingsDlg.setUiEnabled(true);
            //settingsDlg.resetUi();
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Examples of org.bioinfo.ngs.qc.qualimap.process.RNASeqQCAnalysis.run()

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            String countsPath = settingsDlg.getCountsOutputPath();
            rnaSeqQCAnalysis.setCountsFilePath(countsPath);
        }

        try {
            rnaSeqQCAnalysis.run();
        } catch (Exception e) {
            JOptionPane.showMessageDialog(settingsDlg, "Failed to analyze counts data. " + e.getMessage(),
                    settingsDlg.getTitle(), JOptionPane.ERROR_MESSAGE);
            settingsDlg.setUiEnabled(true);
            return;
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Examples of org.boris.xlloop.FunctionServer.run()

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                });
        cfh.add(fifh);
        fsw.setPauseMillis(1000);
        fsw.start();
        fs.setFunctionHandler(new DebugFunctionHandler(cfh));
        fs.run();
    }

    private static void registerAddin(File f,
            FunctionInformationHandler fifh,
            CompositeFunctionHandler cfh) {
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Examples of org.broad.igv.batch.BatchRunner.run()

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                SwingWorker worker = new SwingWorker() {

                    @Override
                    protected Object doInBackground() throws Exception {
                        bRun.run();
                        return null;
                    }
                };

                worker.execute();
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Examples of org.broad.igv.dev.api.batch.Command.run()

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        List<String> subArgs = Collections.emptyList();
        if (args.size() > 1) subArgs = args.subList(1, args.size());
        try {
            Object ocmmand = RuntimeUtils.loadInstanceForName(cmd, null);
            Command command = (Command) ocmmand;
            return command.run(subArgs);
        } catch (ClassNotFoundException e) {
            return null;
        } catch (Exception e) {
            return e.getMessage();
        }
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Examples of org.broad.igv.tools.sort.Sorter.run()

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        }

        sorter.setMaxRecords(maxRecords);

        try {
            sorter.run();
        } catch (Exception e) {
            e.printStackTrace();
            // Delete output file as its probably corrupt
            if (writeStdOut && outputFile.exists()) {
                outputFile.delete();
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