Merge remote-tracking branch 'origin/develop' into

[jalview.git] / test / jalview / ws / jabaws / RNAStructExportImport.java

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 2c6fd0c..5eeff50 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -77,6 +77,11 @@ 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);
 
     af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
@@ -128,9 +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
@@ -191,8 +195,6 @@ public class RNAStructExportImport
         opts.add(rg);
       }
     }
-
-    assertNotNull(rnaalifoldws);
     alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);
@@ -213,10 +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(