X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=testsrc%2Fcompbio%2Frunner%2Fconservation%2FAAConTester.java;h=1dc0b7766b057a765ed9cba81140318cc18351b1;hb=3644426ec0e9e9ceb798bd426085d8d9dd8dbb56;hp=edf637bede858687e8a4a5b7b93696f826155417;hpb=27e1fc31d6e3cc48e5abddcc939f3c73b11fcd55;p=jabaws.git

diff --git a/testsrc/compbio/runner/conservation/AAConTester.java b/testsrc/compbio/runner/conservation/AAConTester.java
index edf637b..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.data.sequence.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();
@@ -252,9 +253,9 @@ 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) {