JAL-3070 rough-and-ready refactor of JABA SequenceAnnotation style services - needs...

[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 089c29f..4af8086 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -26,15 +26,16 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
-import jalview.gui.Jalview2XML;
 import jalview.gui.JvOptionPane;
 import jalview.io.AnnotationFile;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.StockholmFileTest;
+import jalview.project.Jalview2XML;
+import jalview.ws.jws2.AbstractJabaCalcWorker;
+import jalview.ws.jws2.JabaParamStore;
 import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.RNAalifoldClient;
 import jalview.ws.jws2.SequenceAnnotationWSClient;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.AutoCalcSetting;
@@ -78,7 +79,7 @@ public class RNAStructExportImport
 
   public static Jws2Instance rnaalifoldws;
 
-  jalview.ws.jws2.RNAalifoldClient alifoldClient;
+  AbstractJabaCalcWorker alifoldClient;
 
   public static jalview.gui.AlignFrame af = null;
 
@@ -98,7 +99,7 @@ public class RNAStructExportImport
     for (Jws2Instance svc : disc.getServices())
     {
 
-      if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
+      if (svc.getNameURI().toLowerCase().contains("rnaalifoldws"))
       {
         rnaalifoldws = svc;
       }
@@ -118,7 +119,7 @@ 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())
     {
@@ -154,7 +155,8 @@ public class RNAStructExportImport
   public void testRNAAliFoldValidStructure()
   {
 
-    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+    alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+            null);
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);
 
@@ -187,7 +189,8 @@ public class RNAStructExportImport
   public void testRNAStructExport()
   {
 
-    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
+    alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+            null);
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);
 
@@ -204,7 +207,7 @@ 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);
 
   }
@@ -259,7 +262,7 @@ 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())
     {
@@ -280,7 +283,8 @@ public class RNAStructExportImport
         opts.add(rg);
       }
     }
-    alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
+    alifoldClient = new AbstractJabaCalcWorker(rnaalifoldws, af, null,
+            JabaParamStore.getJwsArgsfromJaba(opts));
 
     af.getViewport().getCalcManager().startWorker(alifoldClient);