Fixes to test cases

[jabaws.git] / testsrc / compbio / runner / conservation / AAConTester.java

diff --git a/testsrc/compbio/runner/conservation/AAConTester.java b/testsrc/compbio/runner/conservation/AAConTester.java
index edf637b..1dc0b77 100644 (file)
--- 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;\r
 import java.text.ParseException;\r
 import java.util.Arrays;\r
+import java.util.HashSet;\r
 \r
 import javax.xml.bind.ValidationException;\r
 \r
@@ -37,8 +38,8 @@ import org.ggf.drmaa.JobInfo;
 import org.testng.annotations.BeforeMethod;\r
 import org.testng.annotations.Test;\r
 \r
-import compbio.data.sequence.Method;\r
-import compbio.data.sequence.MultiAnnotatedSequence;\r
+import compbio.data.sequence.Score;\r
+import compbio.data.sequence.ScoreManager;\r
 import compbio.engine.AsyncExecutor;\r
 import compbio.engine.Configurator;\r
 import compbio.engine.FilePuller;\r
@@ -188,9 +189,9 @@ public class AAConTester {
                        lr.executeJob();\r
                        ConfiguredExecutable<?> al1 = lr.waitForResult();\r
                        assertNotNull(al1.getResults());\r
-                       MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
+                       ScoreManager annotations = confAAcon.getResults();\r
                        assertNotNull(annotations);\r
-                       assertEquals(annotations.getAnnotations().size(), 1);\r
+                       assertEquals(annotations.asSet().size(), 18);\r
                        assertEquals(al1.getResults(), annotations);\r
                } catch (JobSubmissionException e) {\r
                        e.printStackTrace();\r
@@ -219,9 +220,9 @@ public class AAConTester {
                        lr.executeJob();\r
                        ConfiguredExecutable<?> al1 = lr.waitForResult();\r
                        assertNotNull(al1.getResults());\r
-                       MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
+                       ScoreManager annotations = confAAcon.getResults();\r
                        assertNotNull(annotations);\r
-                       assertEquals(annotations.getAnnotations().size(), 13);\r
+                       assertEquals(annotations.asSet().size(), 13);\r
                        assertEquals(al1.getResults(), annotations);\r
                } catch (JobSubmissionException e) {\r
                        e.printStackTrace();\r
@@ -252,9 +253,9 @@ public class AAConTester {
                        lr.executeJob();\r
                        ConfiguredExecutable<?> al1 = lr.waitForResult();\r
                        assertNotNull(al1.getResults());\r
-                       MultiAnnotatedSequence<Method> annotations = confAAcon.getResults();\r
+                       ScoreManager annotations = confAAcon.getResults();\r
                        assertNotNull(annotations);\r
-                       assertEquals(annotations.getAnnotations().size(), 3);\r
+                       assertEquals(annotations.asSet().size(), 3);\r
                        assertEquals(al1.getResults(), annotations);\r
 \r
                } catch (JobSubmissionException e) {\r