X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=ee07335b84b7eec22aa40a505410fbae1cd65034;hb=7692386ccfe778075dd83a753d30a7a27fe507be;hp=23c775137d3d04d3c1b0b3304b3c22e756089431;hpb=dfa39e09cf3ffa44cc1e764bfa72900bab96136d;p=jalview.git

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 23c7751..ee07335 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -98,7 +98,7 @@ public class RNAStructExportImport
     for (Jws2Instance svc : disc.getServices())
     {
 
-      if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
+      if (svc.getNameURI().toLowerCase().contains("rnaalifoldws"))
       {
         rnaalifoldws = svc;
       }
@@ -118,7 +118,7 @@ public class RNAStructExportImport
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
 
     // remove any existing annotation
-    List<AlignmentAnnotation> aal = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> aal = new ArrayList<>();
     for (AlignmentAnnotation rna : af.getViewport().getAlignment()
             .getAlignmentAnnotation())
     {
@@ -202,12 +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
     {
@@ -242,7 +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)
     {
@@ -256,7 +259,7 @@ public class RNAStructExportImport
   @Test(groups = { "Network" })
   public void testRnaalifoldSettingsRecovery()
   {
-    List<Argument> opts = new ArrayList<Argument>();
+    List<Argument> opts = new ArrayList<>();
     for (Argument rg : (List<Argument>) rnaalifoldws.getRunnerConfig()
             .getArguments())
     {