+package compbio.runner.structure;
+
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.text.ParseException;
+
+import javax.xml.bind.ValidationException;
+
+import org.ggf.drmaa.DrmaaException;
+import org.ggf.drmaa.JobInfo;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
+import compbio.data.sequence.ScoreManager.ScoreHolder;
+import compbio.data.sequence.SequenceUtil;
+import compbio.engine.AsyncExecutor;
+import compbio.engine.Configurator;
+import compbio.engine.SyncExecutor;
+import compbio.engine.client.ConfExecutable;
+import compbio.engine.client.ConfiguredExecutable;
+import compbio.engine.client.Executable;
+import compbio.engine.client.RunConfiguration;
+import compbio.engine.cluster.drmaa.ClusterUtil;
+import compbio.engine.cluster.drmaa.JobRunner;
+import compbio.engine.cluster.drmaa.StatisticManager;
+import compbio.engine.local.AsyncLocalRunner;
+import compbio.engine.local.LocalExecutorService;
+import compbio.engine.local.LocalRunner;
+import compbio.metadata.AllTestSuit;
+import compbio.metadata.JobExecutionException;
+import compbio.metadata.JobStatus;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.LimitsManager;
+import compbio.metadata.PresetManager;
+import compbio.metadata.ResultNotAvailableException;
+import compbio.metadata.RunnerConfig;
+import compbio.runner.structure.RNAalifold;
+
+public class RNAalifoldTester {
+
+ private RNAalifold rnaalifold;
+
+ public static String test_outfile = "rnaalifold.out";
+
+ public static void main(String[] args) throws JobSubmissionException,
+ JobExecutionException, InterruptedException {
+
+ System.out.println("Run RNAalifold.main()");
+
+ RNAalifold rnaalifold = new RNAalifold();
+ rnaalifold.setInput(AllTestSuit.test_input_rna).setOutput("test_outfile");
+
+ ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
+ .configureExecutable(rnaalifold);
+ AsyncExecutor lr = new AsyncLocalRunner();
+ lr.submitJob(confRNAalifold);
+ Thread.sleep(3000);
+ LocalExecutorService.shutDown();
+
+ }
+
+}