Fix bug in category class and use Jim's test as a test case

[jabaws.git] / testsrc / compbio / runner / disorder / JronnTester.java

diff --git a/testsrc/compbio/runner/disorder/JronnTester.java b/testsrc/compbio/runner/disorder/JronnTester.java
index d784387..4635d10 100644 (file)
--- a/testsrc/compbio/runner/disorder/JronnTester.java
+++ b/testsrc/compbio/runner/disorder/JronnTester.java
@@ -40,6 +40,7 @@ import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;\r
 \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
@@ -186,9 +187,9 @@ public class JronnTester {
                        lr.executeJob();\r
                        ConfiguredExecutable<?> al1 = lr.waitForResult();\r
                        assertNotNull(al1.getResults());\r
-                       Map<String, Score> al2 = confJronn.getResults();\r
+                       ScoreManager al2 = confJronn.getResults();\r
                        assertNotNull(al2);\r
-                       assertEquals(al2.size(), 3);\r
+                       assertEquals(al2.asMap().size(), 3);\r
                        assertEquals(al1.getResults(), al2);\r
                } catch (JobSubmissionException e) {\r
                        e.printStackTrace();\r
@@ -214,9 +215,9 @@ public class JronnTester {
                        lr.executeJob();\r
                        ConfiguredExecutable<?> al1 = lr.waitForResult();\r
                        assertNotNull(al1.getResults());\r
-                       Map<String, Score> al2 = confJronn.getResults();\r
+                       ScoreManager al2 = confJronn.getResults();\r
                        assertNotNull(al2);\r
-                       assertEquals(al2.size(), 3);\r
+                       assertEquals(al2.asMap().size(), 3);\r
                        assertEquals(al1.getResults(), al2);\r
                } catch (JobSubmissionException e) {\r
                        e.printStackTrace();\r
@@ -352,8 +353,8 @@ public class JronnTester {
                try {\r
                        RunnerConfig<Jronn> jronnConfig = ConfExecutable\r
                                        .getRunnerOptions(Jronn.class);\r
-                       assertNotNull(jronnConfig);\r
-                       assertTrue(jronnConfig.getArguments().size() > 0);\r
+                       // There is not supported parameters for Jronn\r
+                       assertNull(jronnConfig);\r
 \r
                        PresetManager<Jronn> jronnPresets = ConfExecutable\r
                                        .getRunnerPresets(Jronn.class);\r