-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();
-
- }
-
-}
+package compbio.runner.structure;\r
+\r
+\r
+import static org.testng.Assert.assertEquals;\r
+import static org.testng.Assert.assertFalse;\r
+import static org.testng.Assert.assertNotNull;\r
+import static org.testng.Assert.assertNull;\r
+import static org.testng.Assert.assertTrue;\r
+import static org.testng.Assert.fail;\r
+\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.text.ParseException;\r
+\r
+import javax.xml.bind.ValidationException;\r
+\r
+import org.apache.log4j.*;\r
+import org.ggf.drmaa.DrmaaException;\r
+import org.ggf.drmaa.JobInfo;\r
+import org.testng.annotations.BeforeMethod;\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.data.sequence.RNAStructScoreManager;\r
+import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\r
+import compbio.data.sequence.ScoreManager.ScoreHolder;\r
+import compbio.data.sequence.SequenceUtil;\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.SyncExecutor;\r
+import compbio.engine.client.ConfExecutable;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.Executable;\r
+import compbio.engine.client.RunConfiguration;\r
+import compbio.engine.cluster.drmaa.ClusterEngineUtil;\r
+import compbio.engine.cluster.drmaa.ClusterRunner;\r
+import compbio.engine.cluster.drmaa.StatisticManager;\r
+import compbio.engine.local.AsyncLocalRunner;\r
+import compbio.engine.local.LocalExecutorService;\r
+import compbio.engine.local.LocalRunner;\r
+import compbio.metadata.AllTestSuit;\r
+import compbio.metadata.JobExecutionException;\r
+import compbio.metadata.JobStatus;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.LimitsManager;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
+import compbio.runner.msa.ClustalW;\r
+import compbio.runner.structure.RNAalifold;\r
+\r
+public class RNAalifoldTester {\r
+\r
+ private static Logger log = Logger\r
+ .getLogger(AllTestSuit.RUNNER_TEST_LOGGER);\r
+ \r
+ \r
+ private RNAalifold rnaalifold;\r
+ \r
+ static final String rnaalifoldConfigFile = AllTestSuit.TEST_DATA_PATH\r
+ + "RNAalifoldParameters.xml";\r
+ public static String test_outfile = "rnaalifold.out";\r
+ \r
+ \r
+ @Test(groups = { AllTestSuit.test_group_runner })\r
+ public void testRunLocally() {\r
+ RNAalifold rnaalifold = new RNAalifold();\r
+ rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput(test_outfile);\r
+ try{\r
+ \r
+ ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator\r
+ .configureExecutable(rnaalifold, Executable.ExecProvider.Local);\r
+ LocalRunner lr = new LocalRunner(confRNAalifold);\r
+ lr.executeJob();\r
+ confRNAalifold = (ConfiguredExecutable<RNAalifold>) lr.waitForResult();\r
+ \r
+ System.out.println("TEST");\r
+ System.out.println(((RNAStructScoreManager) confRNAalifold.getResults()).toString());\r
+ \r
+ assertNotNull(confRNAalifold.getResults()); \r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+ \r
+ \r
+ public static void main(String[] args) throws JobSubmissionException,\r
+ JobExecutionException, InterruptedException, ResultNotAvailableException {\r
+\r
+ \r
+ log.warn("Logger test :- Run RNAalifold.main()");\r
+\r
+ RNAalifold rnaalifold = new RNAalifold();\r
+ rnaalifold.setInput(AllTestSuit.test_input_aln).setOutput("test_outfile.txt");\r
+ \r
+ ConfiguredExecutable<RNAalifold> confRNAalifold = Configurator\r
+ .configureExecutable(rnaalifold);\r
+ AsyncExecutor lr = new AsyncLocalRunner();\r
+ lr.submitJob(confRNAalifold);\r
+ \r
+ \r
+ System.out.println(((RNAStructScoreManager) confRNAalifold.getResults()).toString());\r
+\r
+ \r
+ Thread.sleep(3000);\r
+ LocalExecutorService.shutDown();\r
+ \r
+ }\r
+ \r
+}\r
git://source.jalview.org / jabaws.git / blobdiff