From bc469bb898fd42c92d9b8b70660b4c94a93b3118 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 25 Sep 2013 16:36:24 +0100
Subject: [PATCH] JAL-1365 test that RNAAliFold service settings are stored
 and recovered from Jalview projects

---
 test/jalview/ws/jabaws/RNAStructExportImport.java |   40 ++++++++++-----------
 1 file changed, 18 insertions(+), 22 deletions(-)

diff --git a/test/jalview/ws/jabaws/RNAStructExportImport.java b/test/jalview/ws/jabaws/RNAStructExportImport.java
index a2c361b..2753e64 100644
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -48,30 +48,30 @@ public class RNAStructExportImport
   @BeforeClass
   public static void setUpBeforeClass() throws Exception
   {
-  	
-  	
+
     jalview.bin.Cache.initLogger();
     disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
-    
+
     for (Jws2Instance svc : disc.getServices())
     {
-    	
+
       if (svc.getServiceTypeURI().toLowerCase().contains("rnaalifoldws"))
       {
         rnaalifoldws = svc;
       }
     }
-    
+
     System.out.println("State of rnaalifoldws: " + rnaalifoldws);
-    
-    if (rnaalifoldws == null) System.exit(0);
-    
+
+    if (rnaalifoldws == null)
+      System.exit(0);
+
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
-    
+
     af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.FormatAdapter.FILE);
-    
+
     assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
-    
+
   }
 
   @AfterClass
@@ -87,13 +87,11 @@ public class RNAStructExportImport
   @Test
   public void testRNAStructExport()
   {
-  	
-  	
+
     alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, null);
-    
+
     af.getViewport().getCalcManager().startWorker(alifoldClient);
-    
-    
+
     do
     {
       try
@@ -104,10 +102,9 @@ public class RNAStructExportImport
       }
       ;
     } while (af.getViewport().getCalcManager().isWorking());
-    
-    
+
     AlignmentI orig_alig = af.getViewport().getAlignment();
-    
+
     testAnnotationFileIO("Testing RNAalifold Annotation IO", orig_alig);
 
   }
@@ -116,11 +113,10 @@ public class RNAStructExportImport
   {
     try
     {
-    	// what format would be appropriate for RNAalifold annotations?
+      // what format would be appropriate for RNAalifold annotations?
       String aligfileout = new FormatAdapter().formatSequences("PFAM",
               al.getSequencesArray());
-      
-      
+
       String anfileout = new AnnotationFile().printAnnotations(
               al.getAlignmentAnnotation(), al.getGroups(),
               al.getProperties());
-- 
1.7.10.2