X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=eb987324e8376617b23235e98b3d88121be567c3;hb=25aaaa87042b3f507ad4348120df7dd073182759;hp=61e078248657e4dbf9f8834fe13d82910b88c963;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 61e0782..eb98732 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -20,33 +20,27 @@
  */
 package jalview.ws.jabaws;
 
-import static org.junit.Assert.*;
-
-import java.awt.Component;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-
-import jalview.api.AlignCalcManagerI;
-import jalview.datamodel.AlignmentAnnotation;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
 import jalview.gui.Jalview2XML;
 import jalview.io.AnnotationFile;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.AADisorderClient;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.RNAalifoldClient;
 import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.dm.JabaOption;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.AutoCalcSetting;
 
+import java.awt.Component;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -70,7 +64,7 @@ public class RNAStructExportImport
   {
 
     jalview.bin.Cache.initLogger();
-    disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+    disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
 
     for (Jws2Instance svc : disc.getServices())
     {
@@ -84,7 +78,9 @@ public class RNAStructExportImport
     System.out.println("State of rnaalifoldws: " + rnaalifoldws);
 
     if (rnaalifoldws == null)
+    {
       System.exit(0);
+    }
 
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
 
@@ -137,9 +133,8 @@ public class RNAStructExportImport
       String aligfileout = new FormatAdapter().formatSequences("PFAM",
               al.getSequencesArray());
 
-      String anfileout = new AnnotationFile().printAnnotations(
-              al.getAlignmentAnnotation(), al.getGroups(),
-              al.getProperties());
+      String anfileout = new AnnotationFile()
+              .printAnnotationsForAlignment(al);
       assertTrue(
               "Test "
                       + testname
@@ -220,10 +215,10 @@ public class RNAStructExportImport
     // write out parameters
     jalview.gui.AlignFrame nalf = null;
     assertTrue("Couldn't write out the Jar file",
-            new Jalview2XML(false).SaveAlignment(af,
+            new Jalview2XML(false).saveAlignment(af,
                     "testRnalifold_param.jar", "trial parameter writeout"));
     assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
-            false).LoadJalviewAlign("testRnalifold_param.jar")) != null);
+            false).loadJalviewAlign("testRnalifold_param.jar")) != null);
     if (nalf != null)
     {
       AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(