From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 19 Jun 2013 14:42:50 +0000 (+0100)
Subject: JWS-50 patch AAConWS test for refactoring of calculation parameters to a series of... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=08c0c578427def351c7fe3cb6bc1f9cc3eb1bce7;p=jabaws.git

JWS-50 patch AAConWS test for refactoring of calculation parameters to a series of options
---

diff --git a/testsrc/compbio/ws/client/TestAAConWS.java b/testsrc/compbio/ws/client/TestAAConWS.java
index b6be0d7..d54e67f 100644
--- a/testsrc/compbio/ws/client/TestAAConWS.java
+++ b/testsrc/compbio/ws/client/TestAAConWS.java
@@ -9,6 +9,7 @@ import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.net.ConnectException;
+import java.util.ArrayList;
 import java.util.List;
 
 import javax.xml.ws.WebServiceException;
@@ -213,21 +214,23 @@ public class TestAAConWS {
 		// System.out.println(options.getArguments());
 
 		try {
-			options.getArgument("Calculation method").setDefaultValue("SMERFS");
+			List<Option<AACon>> args = new ArrayList<Option<AACon>>();
+			Option<AACon> arg,normarg;
+			args.add(arg=options.getArgument("SMERFS"));
+			args.add(normarg=options.getArgument("Normalize"));
+			arg.setValue(arg.getPossibleValues().get(0));
 			// options.getArgument("SMERFS Column Scoring Method")
 			// .setDefaultValue("MAX_SCORE");
 			// options.getArgument("SMERFS Gap Threshhold").setDefaultValue("1");
-			String jobId = msaws.customAnalize(fsl, options.getArguments());
+			String jobId = msaws.customAnalize(fsl, args);
 			ScoreManager result = msaws.getAnnotation(jobId);
 			assertNotNull(result);
 			assertEquals(result.asSet().size(), 1);
 			assertEquals(result.asSet().iterator().next().getScores().get(0),
 					0.698f);
-
-			options.getArgument("Calculation method").setDefaultValue("SMERFS");
-			options.removeArgument("Normalize");
-			System.out.println(options);
-			jobId = msaws.customAnalize(fsl, options.getArguments());
+			args.remove(normarg); // remove normalization argument
+			// System.out.println(options);
+			jobId = msaws.customAnalize(fsl, args);
 			result = msaws.getAnnotation(jobId);
 			assertNotNull(result);
 			assertEquals(result.asSet().size(), 1);