Merge branch 'Jalview-JS/develop' into merge_js_develop

[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 3c83b71..292a48a 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -33,9 +33,10 @@ import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
 import jalview.project.Jalview2XML;
+import jalview.ws.api.ServiceWithParameters;
 import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.RNAalifoldClient;
+import jalview.ws.jws2.SeqAnnotationServiceCalcWorker;
 import jalview.ws.jws2.SequenceAnnotationWSClient;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.AutoCalcSetting;
@@ -79,7 +80,7 @@ public class RNAStructExportImport
 
   public static Jws2Instance rnaalifoldws;
 
-  jalview.ws.jws2.RNAalifoldClient alifoldClient;
+  SeqAnnotationServiceCalcWorker alifoldClient;
 
   public static jalview.gui.AlignFrame af = null;
 
@@ -96,12 +97,12 @@ public class RNAStructExportImport
       Thread.sleep(100);
     }
 
-    for (Jws2Instance svc : disc.getServices())
+    for (ServiceWithParameters svc : disc.getServices())
     {
 
       if (svc.getNameURI().toLowerCase().contains("rnaalifoldws"))
       {
-        rnaalifoldws = svc;
+        rnaalifoldws = (Jws2Instance) svc;
       }
     }
 
@@ -155,7 +156,8 @@ public class RNAStructExportImport
   public void testRNAAliFoldValidStructure()
   {
 
-    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+    alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
+            null);
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);
 
@@ -188,7 +190,8 @@ public class RNAStructExportImport
   public void testRNAStructExport()
   {
 
-    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+    alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
+            null);
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);
 
@@ -205,7 +208,7 @@ public class RNAStructExportImport
     AlignmentI orig_alig = af.getViewport().getAlignment();
     // 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.
+    // as an annotation file. bug is JAL-3122
     verifyAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
 
   }
@@ -281,7 +284,7 @@ public class RNAStructExportImport
         opts.add(rg);
       }
     }
-    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null,
+    alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
             JabaParamStore.getJwsArgsfromJaba(opts));
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);