X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=testsrc%2Fcompbio%2Frunner%2Fconservation%2FAAConTester.java;h=fbb972095f11c26b29ef0759e80232a48b1c571e;hb=8dbcae11b8d2b3d12223bfa5b7d44c08f7d3dd82;hp=033555a3eb91ec97fe0725c4f9fec1d4ca0ec16f;hpb=9ebd9109c7b762a91f50d2a5eac0ed2bdd0b2a4b;p=jabaws.git

diff --git a/testsrc/compbio/runner/conservation/AAConTester.java b/testsrc/compbio/runner/conservation/AAConTester.java
index 033555a..fbb9720 100644
--- a/testsrc/compbio/runner/conservation/AAConTester.java
+++ b/testsrc/compbio/runner/conservation/AAConTester.java
@@ -20,7 +20,6 @@ package compbio.runner.conservation;
 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;
 
@@ -29,6 +28,7 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.text.ParseException;
+import java.util.Arrays;
 
 import javax.xml.bind.ValidationException;
 
@@ -56,9 +56,11 @@ import compbio.metadata.JobExecutionException;
 import compbio.metadata.JobStatus;
 import compbio.metadata.JobSubmissionException;
 import compbio.metadata.LimitsManager;
+import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.ResultNotAvailableException;
 import compbio.metadata.RunnerConfig;
+import compbio.runner.Util;
 import compbio.util.FileWatcher;
 import compbio.util.SysPrefs;
 
@@ -188,7 +190,38 @@ public class AAConTester {
 			assertNotNull(al1.getResults());
 			MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();
 			assertNotNull(annotations);
-			assertEquals(annotations.getAnnotations().size(), 18);
+			assertEquals(annotations.getAnnotations().size(), 1);
+			assertEquals(al1.getResults(), annotations);
+		} catch (JobSubmissionException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (ResultNotAvailableException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		} catch (JobExecutionException e) {
+			e.printStackTrace();
+			fail(e.getLocalizedMessage());
+		}
+	}
+
+	@Test()
+	public void testRunLocallyWithPreset() {
+		try {
+			PresetManager<AACon> aaconPresets = Util.getPresets(AACon.class);
+			assert aaconPresets != null;
+			ConfiguredExecutable<AACon> confAAcon = Configurator
+					.configureExecutable(aacon, Executable.ExecProvider.Local);
+			Preset<AACon> quick = aaconPresets
+					.getPresetByName("Quick conservation");
+			confAAcon.addParameters(quick.getOptions());
+			// For local execution use relative
+			LocalRunner lr = new LocalRunner(confAAcon);
+			lr.executeJob();
+			ConfiguredExecutable<?> al1 = lr.waitForResult();
+			assertNotNull(al1.getResults());
+			MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();
+			assertNotNull(annotations);
+			assertEquals(annotations.getAnnotations().size(), 13);
 			assertEquals(al1.getResults(), annotations);
 		} catch (JobSubmissionException e) {
 			e.printStackTrace();
@@ -205,18 +238,23 @@ public class AAConTester {
 	@Test()
 	public void testRunLocallyOnTwoCpu() {
 		try {
+			aacon = new AACon();
+			aacon.setInput(test_alignment_input).setOutput(test_outfile);
+
 			aacon.setNCore(2);
 			ConfiguredExecutable<AACon> confAAcon = Configurator
 					.configureExecutable(aacon, Executable.ExecProvider.Local);
-
+			confAAcon.addParameters(Arrays.asList("-m=KABAT,JORES"));
+			confAAcon.addParameters(Arrays.asList("-m=TAYLOR_GAPS"));
 			// For local execution use relative
 			LocalRunner lr = new LocalRunner(confAAcon);
+
 			lr.executeJob();
 			ConfiguredExecutable<?> al1 = lr.waitForResult();
 			assertNotNull(al1.getResults());
 			MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();
 			assertNotNull(annotations);
-			assertEquals(annotations.getAnnotations().size(), 18);
+			assertEquals(annotations.getAnnotations().size(), 3);
 			assertEquals(al1.getResults(), annotations);
 		} catch (JobSubmissionException e) {
 			e.printStackTrace();
@@ -229,7 +267,6 @@ public class AAConTester {
 			fail(e.getLocalizedMessage());
 		}
 	}
-
 	@Test()
 	public void readStatistics() {
 		try {
@@ -358,7 +395,7 @@ public class AAConTester {
 
 			PresetManager<AACon> aaconPresets = ConfExecutable
 					.getRunnerPresets(AACon.class);
-			assertNull(aaconPresets); // there is no presets
+			assertNotNull(aaconPresets);
 
 			LimitsManager<AACon> jronnLimits = ConfExecutable
 					.getRunnerLimits(AACon.class);