From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 15 Jun 2015 13:03:22 +0000 (+0100)
Subject: JAL-1775 test demonstrating bug
X-Git-Tag: Jalview_2_9~20
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=420357044cf67b53c45aa7274dc29b8e0077c8a7

JAL-1775 test demonstrating bug
---

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 36b3196..9398c55 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -102,6 +102,38 @@ 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()
   {