X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FDisorderAnnotExportImport.java;h=6076dec6f6bd102f1c5d1b21f22f8086a6dd7c73;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=bd743e0e1f786c23615e8931a8c79ed30721b9b7;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
index bd743e0..6076dec 100644
--- a/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
+++ b/test/jalview/ws/jabaws/DisorderAnnotExportImport.java
@@ -1,28 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.jabaws;
 
-import static org.junit.Assert.*;
-
-import java.util.ArrayList;
-import java.util.List;
-
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.io.AnnotationFile;
@@ -32,6 +32,9 @@ import jalview.ws.jws2.AADisorderClient;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 
+import java.util.ArrayList;
+import java.util.List;
+
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -98,16 +101,17 @@ public class DisorderAnnotExportImport
       ;
     } while (af.getViewport().getCalcManager().isWorking());
     AlignmentI orig_alig = af.getViewport().getAlignment();
-    // NOTE: Consensus annotation row cannot be exported and reimported faithfully - so we remove them
+    // NOTE: Consensus annotation row cannot be exported and reimported
+    // faithfully - so we remove them
     List<AlignmentAnnotation> toremove = new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation aa:orig_alig.getAlignmentAnnotation())
+    for (AlignmentAnnotation aa : orig_alig.getAlignmentAnnotation())
     {
       if (aa.autoCalculated)
       {
         toremove.add(aa);
       }
     }
-    for (AlignmentAnnotation aa:toremove)
+    for (AlignmentAnnotation aa : toremove)
     {
       orig_alig.deleteAnnotation(aa);
     }
@@ -121,9 +125,8 @@ public class DisorderAnnotExportImport
     {
       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