X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=testsrc%2Fcompbio%2Frunner%2Fconservation%2FAAConTester.java;h=1dc0b7766b057a765ed9cba81140318cc18351b1;hb=b52b03d3fd8606731fa620350a389ee7dc37d9e9;hp=fbb972095f11c26b29ef0759e80232a48b1c571e;hpb=8dbcae11b8d2b3d12223bfa5b7d44c08f7d3dd82;p=jabaws.git

diff --git a/testsrc/compbio/runner/conservation/AAConTester.java b/testsrc/compbio/runner/conservation/AAConTester.java
index fbb9720..1dc0b77 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;
@@ -188,9 +189,9 @@ 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();
@@ -219,9 +220,9 @@ 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();
@@ -252,10 +253,11 @@ 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) {
 			e.printStackTrace();
 			fail(e.getLocalizedMessage());