Merge remote-tracking branch 'origin/develop' into

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

diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
index 30317f7..0743581 100644 (file)
--- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@ -77,6 +77,13 @@ public class JpredJabaStructExportImport
       }
     }
 
+    System.out.println("State of jpredws: " + jpredws);
+
+    if (jpredws == null)
+    {
+      System.exit(0);
+    }
+
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
 
     af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
@@ -105,8 +112,6 @@ public class JpredJabaStructExportImport
                     af.getViewport().getSelectionGroup().getSequenceAt(0),
                     false);
     af.hideSelSequences_actionPerformed(null);
-
-    assertNotNull(jpredws);
     jpredClient = new JPred301Client(jpredws, af, null, null);
 
     assertTrue(
@@ -152,7 +157,7 @@ public class JpredJabaStructExportImport
   @Test
   public void testJPredStructExport()
   {
-    assertNotNull(jpredws);
+
     jpredClient = new JPred301Client(jpredws, af, null, null);
 
     af.getViewport().getCalcManager().startWorker(jpredClient);
@@ -182,9 +187,8 @@ 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
@@ -246,8 +250,6 @@ public class JpredJabaStructExportImport
         opts.add(rg);
       }
     }
-
-    assertNotNull(jpredws);
     jpredClient = new JPred301Client(jpredws, af, null, opts);
 
     af.getViewport().getCalcManager().startWorker(jpredClient);
@@ -268,10 +270,10 @@ 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(