JAL-1775 test demonstrating bug

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index c1c3357..665d9c8 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -119,6 +119,38 @@ public class RNAStructExportImport
   }
 
   @Test
+  public void testRNAAliFoldValidStructure()
+  {
+
+    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+
+    af.getViewport().getCalcManager().startWorker(alifoldClient);
+
+    do
+    {
+      try
+      {
+        Thread.sleep(50);
+      } catch (InterruptedException x)
+      {
+      }
+      ;
+    } while (af.getViewport().getCalcManager().isWorking());
+
+    AlignmentI orig_alig = af.getViewport().getAlignment();
+    for (AlignmentAnnotation aa:orig_alig.getAlignmentAnnotation())
+    {
+      if (alifoldClient.involves(aa))
+      {
+        if (aa.isRNA())
+        {
+          Assert.assertTrue("Did not create valid structure from RNAALiFold prediction", aa.isValidStruc());
+        }
+      }
+    }
+  }
+
+  @Test
   public void testRNAStructExport()
   {