testsrc/compbio/runner/structure/RNAalifoldTester.java

   1 package compbio.runner.structure;
   2
   3
   4 import static org.testng.Assert.assertEquals;
   5 import static org.testng.Assert.assertFalse;
   6 import static org.testng.Assert.assertNotNull;
   7 import static org.testng.Assert.assertNull;
   8 import static org.testng.Assert.assertTrue;
   9 import static org.testng.Assert.fail;
  10
  11 import java.io.File;
  12 import java.io.FileInputStream;
  13 import java.io.FileNotFoundException;
  14 import java.io.IOException;
  15 import java.text.ParseException;
  16
  17 import javax.xml.bind.ValidationException;
  18
  19 import org.ggf.drmaa.DrmaaException;
  20 import org.ggf.drmaa.JobInfo;
  21 import org.testng.annotations.BeforeMethod;
  22 import org.testng.annotations.Test;
  23
  24 import compbio.data.sequence.Score;
  25 import compbio.data.sequence.ScoreManager;
  26 import compbio.data.sequence.ScoreManager.ScoreHolder;
  27 import compbio.data.sequence.SequenceUtil;
  28 import compbio.engine.AsyncExecutor;
  29 import compbio.engine.Configurator;
  30 import compbio.engine.SyncExecutor;
  31 import compbio.engine.client.ConfExecutable;
  32 import compbio.engine.client.ConfiguredExecutable;
  33 import compbio.engine.client.Executable;
  34 import compbio.engine.client.RunConfiguration;
  35 import compbio.engine.cluster.drmaa.ClusterUtil;
  36 import compbio.engine.cluster.drmaa.JobRunner;
  37 import compbio.engine.cluster.drmaa.StatisticManager;
  38 import compbio.engine.local.AsyncLocalRunner;
  39 import compbio.engine.local.LocalExecutorService;
  40 import compbio.engine.local.LocalRunner;
  41 import compbio.metadata.AllTestSuit;
  42 import compbio.metadata.JobExecutionException;
  43 import compbio.metadata.JobStatus;
  44 import compbio.metadata.JobSubmissionException;
  45 import compbio.metadata.LimitsManager;
  46 import compbio.metadata.PresetManager;
  47 import compbio.metadata.ResultNotAvailableException;
  48 import compbio.metadata.RunnerConfig;
  49 import compbio.runner.structure.RNAalifold;
  50
  51 public class RNAalifoldTester {
  52
  53         private RNAalifold rnaalifold;
  54
  55         public static String test_outfile = "rnaalifold.out";
  56
  57         public static void main(String[] args) throws JobSubmissionException,
  58                         JobExecutionException, InterruptedException {
  59
  60                 System.out.println("Run RNAalifold.main()");
  61
  62                 RNAalifold rnaalifold = new RNAalifold();
  63                 rnaalifold.setInput(AllTestSuit.test_input_rna).setOutput("test_outfile");
  64
  65                 ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator
  66                                         .configureExecutable(rnaalifold);
  67                 AsyncExecutor lr = new AsyncLocalRunner();
  68                 lr.submitJob(confRNAalifold);
  69                 Thread.sleep(3000);
  70                 LocalExecutorService.shutDown();
  71
  72         }
  73
  74 }