JAL-1358 Cleaned up RNAalifoldClient.java. RNA helices colouring bug and parameters...

[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 74a24aa..4e407af 100644 (file)
--- 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