Merge branch 'Release_2_8_2b1_Branch'

[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 519a946..57cbd50 100644 (file)
--- a/test/jalview/ws/jabaws/RNAStructExportImport.java
+++ b/test/jalview/ws/jabaws/RNAStructExportImport.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -70,7 +70,7 @@ public class RNAStructExportImport
   {
 
     jalview.bin.Cache.initLogger();
-    disc = JalviewJabawsTestUtils.getJabawsDiscoverer();
+    disc = JalviewJabawsTestUtils.getJabawsDiscoverer(false);
 
     for (Jws2Instance svc : disc.getServices())
     {
@@ -201,9 +201,9 @@ public class RNAStructExportImport
       }
     }
     alifoldClient = new RNAalifoldClient(rnaalifoldws, af, null, opts);
-    
+
     af.getViewport().getCalcManager().startWorker(alifoldClient);
-    
+
     do
     {
       try
@@ -214,39 +214,58 @@ public class RNAStructExportImport
       }
       ;
     } while (af.getViewport().getCalcManager().isWorking());
-    AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId());
+    AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(
+            alifoldClient.getCalcId());
     String oldsettings = oldacs.getWsParamFile();
     // write out parameters
-    jalview.gui.AlignFrame nalf=null;
-    assertTrue("Couldn't write out the Jar file",new Jalview2XML(false).SaveAlignment(af, "testRnalifold_param.jar","trial parameter writeout"));
-    assertTrue("Couldn't read back the Jar file",(nalf = new Jalview2XML(false).LoadJalviewAlign("testRnalifold_param.jar"))!=null);
-    if (nalf!=null)
+    jalview.gui.AlignFrame nalf = null;
+    assertTrue("Couldn't write out the Jar file",
+            new Jalview2XML(false).SaveAlignment(af,
+                    "testRnalifold_param.jar", "trial parameter writeout"));
+    assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
+            false).LoadJalviewAlign("testRnalifold_param.jar")) != null);
+    if (nalf != null)
     {
-      AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId());
-      assertTrue("Calc ID settings not recovered from viewport stash", acs.equals(oldacs));
-      assertTrue("Serialised Calc ID settings not identical to those recovered from viewport stash", acs.getWsParamFile().equals(oldsettings));
-      JMenu nmenu=new JMenu();
-      new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu, rnaalifoldws, af);
-      assertTrue("Couldn't get menu entry for service",nmenu.getItemCount()>0);
-      for (Component itm: nmenu.getMenuComponents())
+      AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(
+              alifoldClient.getCalcId());
+      assertTrue("Calc ID settings not recovered from viewport stash",
+              acs.equals(oldacs));
+      assertTrue(
+              "Serialised Calc ID settings not identical to those recovered from viewport stash",
+              acs.getWsParamFile().equals(oldsettings));
+      JMenu nmenu = new JMenu();
+      new SequenceAnnotationWSClient().attachWSMenuEntry(nmenu,
+              rnaalifoldws, af);
+      assertTrue("Couldn't get menu entry for service",
+              nmenu.getItemCount() > 0);
+      for (Component itm : nmenu.getMenuComponents())
       {
         if (itm instanceof JMenuItem)
         {
           JMenuItem i = (JMenuItem) itm;
-          if (i.getText().equals(rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
-                  {
+          if (i.getText().equals(
+                  rnaalifoldws.getAlignAnalysisUI().getAAconToggle()))
+          {
             i.doClick();
             break;
-                  }
+          }
         }
       }
       while (af.getViewport().isCalcInProgress())
       {
-        try { Thread.sleep(200);
-        } catch (Exception x) {};
+        try
+        {
+          Thread.sleep(200);
+        } catch (Exception x)
+        {
+        }
+        ;
       }
-      AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(alifoldClient.getCalcId());
-      assertTrue("Calc ID settings after recalculation has not been recovered.", acs2.getWsParamFile().equals(oldsettings));
+      AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(
+              alifoldClient.getCalcId());
+      assertTrue(
+              "Calc ID settings after recalculation has not been recovered.",
+              acs2.getWsParamFile().equals(oldsettings));
     }
   }
 }