AAConWS further work

[jabaws.git] / testsrc / compbio / ws / client / TestAAConWS.java

diff --git a/testsrc/compbio/ws/client/TestAAConWS.java b/testsrc/compbio/ws/client/TestAAConWS.java
index e0b002c..acaf57f 100644 (file)
--- a/testsrc/compbio/ws/client/TestAAConWS.java
+++ b/testsrc/compbio/ws/client/TestAAConWS.java
@@ -17,8 +17,8 @@ import org.testng.annotations.Test;
 \r
 import compbio.data.msa.Annotation;\r
 import compbio.data.msa.JABAService;\r
-import compbio.data.sequence.FastaSequence;\r
 import compbio.data.sequence.ConservationMethod;\r
+import compbio.data.sequence.FastaSequence;\r
 import compbio.data.sequence.Score;\r
 import compbio.data.sequence.SequenceUtil;\r
 import compbio.metadata.JobSubmissionException;\r
@@ -80,7 +80,8 @@ public class TestAAConWS {
                        HashSet<Score> result = msaws.getAnnotation(jobId);\r
                        assertNotNull(result);\r
                        assertEquals(result.size(), 1);\r
-                       assertEquals(result.iterator().next().getMethod(), ConservationMethod.SHENKIN);\r
+                       assertEquals(result.iterator().next().getMethod(),\r
+                                       ConservationMethod.SHENKIN);\r
                        List<Float> scores = result.iterator().next().getScores();\r
                        assertNotNull(scores);\r
                        assertEquals(scores.size(), 568);\r
@@ -192,6 +193,9 @@ public class TestAAConWS {
 \r
                try {\r
                        options.getArgument("Calculation method").setDefaultValue("SMERFS");\r
+                       // options.getArgument("SMERFS Column Scoring Method")\r
+                       // .setDefaultValue("MAX_SCORE");\r
+                       // options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");\r
                        String jobId = msaws.customAnalize(fsl, options.getArguments());\r
                        HashSet<Score> result = msaws.getAnnotation(jobId);\r
                        assertNotNull(result);\r