X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;fp=test%2Fjalview%2Fws%2Fjabaws%2FRNAStructExportImport.java;h=4e407afa775cde17fd46b368b8f14c3207760f77;hb=a4afd02409c7c45ee4042bf81b310a537d75c73d;hp=74a24aaa797d11c9d310e04a917d0931c3866286;hpb=f8164ef6f241c5eb111c413fb8594e67b49ce671;p=jalview.git

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index 74a24aa..4e407af 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -46,8 +46,6 @@ public class RNAStructExportImport
     for (Jws2Instance svc : disc.getServices())
     {
     	
-    	System.out.println("Service type: " + svc.serviceType);
-    	
       if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
       {
         rnaalifoldws = svc;
@@ -60,8 +58,6 @@ public class RNAStructExportImport
     
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
     
-    // Following this method a long way we find some (probably important!)
-    //  code that I have just commented out!
     af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
     
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
@@ -78,16 +74,13 @@ public class RNAStructExportImport
     }
   }
 
-  /**
-   * test for patches to JAL-1294
-   */
   @Test
   public void testRNAStructExport()
   {
+  	
+  	
     alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
     
-    
-    System.out.println("START FOLDING");
     af.getViewport().getCalcManager().startWorker(alifoldClient);
     
     
@@ -102,37 +95,9 @@ public class RNAStructExportImport
       ;
     } while (af.getViewport().getCalcManager().isWorking());
     
-    System.out.println("END FOLDING");
-    
-    // ALL FOR TESTING
-    AlignCalcManagerI test = af.getViewport().getCalcManager();
-    RNAalifoldClient testWorker = ((RNAalifoldClient)test.getRegisteredWorkersOfClass(RNAalifoldClient.class).get(0));
-    testWorker.updateResultAnnotation(true);
-    System.out.println("Annotation from RNAalifoldclient");
-    for (Annotation ann : testWorker.ourAnnots.get(0).annotations) {
-    	System.out.print(ann.toString()+"|");
-    }
-    System.out.println();
-    
     
-    // Why are the AlignViewport.alignment and the RNAalifoldClient alignment
-    //  Annotations different
     AlignmentI orig_alig = af.getViewport().getAlignment();
     
-    System.out.println("orig_alig has class: " + orig_alig.getClass());
-    
-    // some time before here but after the RNAalifoldClient Update method
-    //  the alignment annotation is replaced....
-    
-    System.out.println("orig_alig annotation:\n");
-    for (AlignmentAnnotation an : orig_alig.getAlignmentAnnotation()) {
-    	for (Annotation ann : an.annotations) {
-    		System.out.print(ann.toString()+"|");
-    	}
-    	System.out.println();
-    }
-    
-    
     testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
 
   }
@@ -141,11 +106,10 @@ public class RNAStructExportImport
   {
     try
     {
-      String aligfileout = new FormatAdapter().formatSequences("CLUSTAL",
+    	// what format would be appropriate for RNAalifold annotations?
+      String aligfileout = new FormatAdapter().formatSequences("PFAM",
               al.getSequencesArray());
       
-      // test
-//      System.out.println("aligfileout:\n" + aligfileout);
       
       String anfileout = new AnnotationFile().printAnnotations(
               al.getAlignmentAnnotation(), al.getGroups(),
@@ -164,8 +128,9 @@ public class RNAStructExportImport
       System.out.println("Output annotation file:\n" + anfileout
               + "\n<<EOF\n");
 
+      // again what format would be appropriate?
       AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
-              FormatAdapter.PASTE, "CLUSTAL");
+              FormatAdapter.PASTE, "PFAM");
       assertTrue(
               "Test "
                       + testname