Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[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 bc11d2f..0a9cb19 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -21,7 +21,6 @@
 package jalview.ws.jabaws;
 
 import java.util.Locale;
-
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
@@ -36,8 +35,10 @@ 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;
@@ -81,7 +82,7 @@ public class RNAStructExportImport
 
   public static Jws2Instance rnaalifoldws;
 
-  jalview.ws.jws2.RNAalifoldClient alifoldClient;
+  SeqAnnotationServiceCalcWorker alifoldClient;
 
   public static jalview.gui.AlignFrame af = null;
 
@@ -98,13 +99,13 @@ public class RNAStructExportImport
       Thread.sleep(100);
     }
 
-    for (Jws2Instance svc : disc.getServices())
+    for (ServiceWithParameters svc : disc.getServices())
     {
 
       if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT)
               .contains("rnaalifoldws"))
       {
-        rnaalifoldws = svc;
+        rnaalifoldws = (Jws2Instance) svc;
       }
     }
 
@@ -159,7 +160,8 @@ 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);
 
@@ -192,7 +194,8 @@ 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);
 
@@ -209,7 +212,7 @@ 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);
 
   }
@@ -278,7 +281,8 @@ public class RNAStructExportImport
         opts.add(rg);
       }
     }
-    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
+    alifoldClient = new SeqAnnotationServiceCalcWorker(rnaalifoldws, af, null,
+            JabaParamStore.getJwsArgsfromJaba(opts));
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);