Examples of BatchRunner

Examples of org.broad.igv.batch.BatchRunner

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                    mainFrame.setVisible(true);
                    if (igvArgs.getLocusString() != null) {
                        goToLocus(igvArgs.getLocusString());
                    }
                    if (runningBatch) {
                        LongRunningTask.submit(new BatchRunner(igvArgs.getBatchFile()));
                    }

                }
            });
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Examples of org.broad.igv.batch.BatchRunner

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    public void actionPerformed(ActionEvent e) {

        if (e.getActionCommand().equalsIgnoreCase("run batch script...")) {
            File script = chooseScriptFile();
            if (script != null && script.isFile()) {
                final BatchRunner bRun = new BatchRunner(script.getPath());

                SwingWorker worker = new SwingWorker() {

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

                worker.execute();
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Examples of org.mitre.medfacts.i2b2.cli.BatchRunner

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    for (RunConfiguration currentRunConfiguration : runConfigurationList)
    {
      int size = currentRunConfiguration.getFileList().size();
      logger.info(String.format("====== BEGIN RUN # %d WITH %d FILES IN TRAINING SET =====", i, size));

      BatchRunner b = new BatchRunner();
      b.setMode(Mode.EVAL);

      ScopeParser scopeParser = new ScopeParser(scopeFile.getAbsolutePath(), cueFile.getAbsolutePath());
      b.setScopeParser(scopeParser);

      b.setBaseDirectoryString(baseDirectoryString);
      b.setTrainingDirectory(trainDirectory.getAbsolutePath());
      b.setDecodeDirectory(evalDirectory.getAbsolutePath());

      b.setFileNameSuffix(String.format("%03d", currentRunConfiguration.getFileList().size()));

      String featuresFileString = "featureFile11d_with_class";
      File featuresFile = new File(baseDirectory, featuresFileString);

      b.processEnabledFeaturesFile(featuresFile);

      b.setRunConfiguration(currentRunConfiguration);

      b.execute();

      logger.info(String.format("====== END RUN # %d WITH %d FILES IN TRAINING SET =====", i, size));
      i++;
    }
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