X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=testsrc%2Fcompbio%2Frunner%2Fconservation%2FAAConTester.java;h=353509a70c14b9461eb1ac5d2be7099f1eef820a;hb=0ec796d8e2a97d2c006a88522010cd2fff5a0d96;hp=da924f0bc261d7ef03cd578c74d1025561bcd5ec;hpb=a66674ad9520261789bbfe8401f88b37ae2a71a2;p=jabaws.git

diff --git a/testsrc/compbio/runner/conservation/AAConTester.java b/testsrc/compbio/runner/conservation/AAConTester.java
index da924f0..353509a 100644
--- a/testsrc/compbio/runner/conservation/AAConTester.java
+++ b/testsrc/compbio/runner/conservation/AAConTester.java
@@ -29,6 +29,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.text.ParseException;
 import java.util.Arrays;
+import java.util.HashSet;
 
 import javax.xml.bind.ValidationException;
 
@@ -37,8 +38,8 @@ import org.ggf.drmaa.JobInfo;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-import compbio.conservation.Method;
-import compbio.data.sequence.MultiAnnotatedSequence;
+import compbio.data.sequence.Score;
+import compbio.data.sequence.ScoreManager;
 import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
 import compbio.engine.FilePuller;
@@ -51,6 +52,7 @@ import compbio.engine.cluster.drmaa.ClusterUtil;
 import compbio.engine.cluster.drmaa.JobRunner;
 import compbio.engine.cluster.drmaa.StatisticManager;
 import compbio.engine.local.LocalRunner;
+import compbio.metadata.AllTestSuit;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobExecutionException;
 import compbio.metadata.JobStatus;
@@ -80,7 +82,7 @@ public class AAConTester {
 		aacon.setInput(test_alignment_input).setOutput(test_outfile);
 	}
 
-	@Test()
+	@Test(groups = {AllTestSuit.test_group_runner})
 	public void testRunOnCluster() {
 		assertFalse(SysPrefs.isWindows,
 				"Cluster execution can only be in unix environment");
@@ -136,7 +138,7 @@ public class AAConTester {
 	 * This tests fails from time to time depending on the cluster load or some
 	 * other factors. Any client code has to adjust for this issue
 	 */
-	@Test()
+	@Test(groups = {AllTestSuit.test_group_runner, AllTestSuit.test_group_cluster})
 	public void testRunOnClusterAsync() {
 		assertFalse(SysPrefs.isWindows,
 				"Cluster execution can only be in unix environment");
@@ -177,7 +179,7 @@ public class AAConTester {
 		}
 	}
 
-	@Test()
+	@Test(groups = {AllTestSuit.test_group_runner})
 	public void testRunLocally() {
 		try {
 			ConfiguredExecutable<AACon> confAAcon = Configurator
@@ -188,9 +190,9 @@ public class AAConTester {
 			lr.executeJob();
 			ConfiguredExecutable<?> al1 = lr.waitForResult();
 			assertNotNull(al1.getResults());
-			MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();
+			ScoreManager annotations = confAAcon.getResults();
 			assertNotNull(annotations);
-			assertEquals(annotations.getAnnotations().size(), 1);
+			assertEquals(annotations.asSet().size(), 18);
 			assertEquals(al1.getResults(), annotations);
 		} catch (JobSubmissionException e) {
 			e.printStackTrace();
@@ -204,7 +206,7 @@ public class AAConTester {
 		}
 	}
 
-	@Test()
+	@Test(groups = {AllTestSuit.test_group_runner})
 	public void testRunLocallyWithPreset() {
 		try {
 			PresetManager<AACon> aaconPresets = Util.getPresets(AACon.class);
@@ -219,9 +221,9 @@ public class AAConTester {
 			lr.executeJob();
 			ConfiguredExecutable<?> al1 = lr.waitForResult();
 			assertNotNull(al1.getResults());
-			MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();
+			ScoreManager annotations = confAAcon.getResults();
 			assertNotNull(annotations);
-			assertEquals(annotations.getAnnotations().size(), 13);
+			assertEquals(annotations.asSet().size(), 13);
 			assertEquals(al1.getResults(), annotations);
 		} catch (JobSubmissionException e) {
 			e.printStackTrace();
@@ -235,7 +237,7 @@ public class AAConTester {
 		}
 	}
 
-	@Test()
+	@Test(groups = {AllTestSuit.test_group_runner})
 	public void testRunLocallyOnTwoCpu() {
 		try {
 			aacon = new AACon();
@@ -252,9 +254,9 @@ public class AAConTester {
 			lr.executeJob();
 			ConfiguredExecutable<?> al1 = lr.waitForResult();
 			assertNotNull(al1.getResults());
-			MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();
+			ScoreManager annotations = confAAcon.getResults();
 			assertNotNull(annotations);
-			assertEquals(annotations.getAnnotations().size(), 3);
+			assertEquals(annotations.asSet().size(), 3);
 			assertEquals(al1.getResults(), annotations);
 
 		} catch (JobSubmissionException e) {
@@ -268,7 +270,8 @@ public class AAConTester {
 			fail(e.getLocalizedMessage());
 		}
 	}
-	@Test()
+	
+	@Test(groups = {AllTestSuit.test_group_runner})
 	public void readStatistics() {
 		try {
 			ConfiguredExecutable<AACon> confAAcon = Configurator
@@ -318,7 +321,7 @@ public class AAConTester {
 		}
 	}
 
-	@Test()
+	@Test(groups = {AllTestSuit.test_group_runner})
 	public void testPersistance() {
 		try {
 			AACon aacon = new AACon();
@@ -386,7 +389,7 @@ public class AAConTester {
 		}
 	}
 
-	@Test()
+	@Test(groups = {AllTestSuit.test_group_runner})
 	public void testConfigurationLoading() {
 		try {
 			RunnerConfig<AACon> aaconConfig = ConfExecutable