X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FJpredJabaStructExportImport.java;h=c522bc39b69e17afab2ce7eab709219adfadf78d;hb=bc12a8c2d3727216f12bbf9ffd49cd137d19ad9a;hp=f0b8f99e7f2e769ae6fa10ecce78475cc37e7aa0;hpb=8fae74e850aa0446371370d0eed2c0be2a417001;p=jalview.git

diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
index f0b8f99..c522bc3 100644
--- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,18 +23,6 @@ package jalview.ws.jabaws;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
-import jalview.datamodel.AlignmentI;
-import jalview.gui.Jalview2XML;
-import jalview.io.AnnotationFile;
-import jalview.io.FormatAdapter;
-import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.JPred301Client;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.AutoCalcSetting;
 
 import java.awt.Component;
 import java.util.ArrayList;
@@ -50,6 +38,18 @@ import org.junit.Test;
 import compbio.metadata.Argument;
 import compbio.metadata.WrongParameterException;
 
+import jalview.datamodel.AlignmentI;
+import jalview.gui.Jalview2XML;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.JPred301Client;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.SequenceAnnotationWSClient;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
 public class JpredJabaStructExportImport
 {
   public static String testseqs = "examples/uniref50.fa";
@@ -81,7 +81,9 @@ public class JpredJabaStructExportImport
     System.out.println("State of jpredws: " + jpredws);
 
     if (jpredws == null)
-      System.exit(0);
+    {
+      fail("jpredws is null");
+    }
 
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
 
@@ -186,9 +188,8 @@ public class JpredJabaStructExportImport
       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
@@ -270,10 +271,10 @@ public class JpredJabaStructExportImport
     // 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,
                     "testJPredWS_param.jar", "trial parameter writeout"));
     assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
-            false).LoadJalviewAlign("testJpredWS_param.jar")) != null);
+            false).loadJalviewAlign("testJpredWS_param.jar")) != null);
     if (nalf != null)
     {
       AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(