JAL-3070 pull up hostURL and postURL to UIinfo and getter for action ext

[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 6cd32c7..089c29f 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -89,6 +89,12 @@ public class RNAStructExportImport
     Cache.initLogger();
     disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
 
+    while (disc.isRunning())
+    {
+      // don't get services until discoverer has finished
+      Thread.sleep(100);
+    }
+
     for (Jws2Instance svc : disc.getServices())
     {
 
@@ -196,12 +202,14 @@ public class RNAStructExportImport
     } while (af.getViewport().getCalcManager().isWorking());
 
     AlignmentI orig_alig = af.getViewport().getAlignment();
-
-    testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
+    // JBPNote: this assert fails (2.10.2) because the 'Reference Positions'
+    // annotation is mistakenly recognised as an RNA annotation row when read in
+    // as an annotation file.
+    verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
 
   }
 
-  public static void testAnnotationFileIO(String testname, AlignmentI al)
+  static void verifyAnnotationFileIO(String testname, AlignmentI al)
   {
     try
     {
@@ -236,7 +244,8 @@ public class RNAStructExportImport
                       DataSourceType.PASTE));
 
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+              false);
       return;
     } catch (Exception e)
     {