X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=testsrc%2Fcompbio%2Fws%2Fclient%2FTestAAConWS.java;fp=testsrc%2Fcompbio%2Fws%2Fclient%2FTestAAConWS.java;h=acaf57f129a61d44139ccb8e47924d2e52d5497f;hb=eee7bbead2d812ef1aa67389ae2d1c4884c47458;hp=e0b002c3c9d72aca514d7424db62bcc9a0e581d4;hpb=6adca61e46b4daf4136621f942f313c74e44e61d;p=jabaws.git

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