X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fjabaws%2FJpredJabaStructExportImport.java;h=0b1716921e2bed34de1be37a5ff40e3a0938cbb9;hb=3412b273e964fb1a9d22564b04a5f0c827ec2461;hp=1e920e0aa171d9f480624b6f3ddbd4e145fcd524;hpb=8d6b113f475c6b5916f7685cfd289e054d95a9ee;p=jalview.git

diff --git a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
index 1e920e0..0b17169 100644
--- a/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
+++ b/test/jalview/ws/jabaws/JpredJabaStructExportImport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,21 +20,8 @@
  */
 package jalview.ws.jabaws;
 
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import jalview.datamodel.AlignmentI;
-import jalview.gui.Jalview2XML;
-import jalview.io.AnnotationFile;
-import jalview.io.FormatAdapter;
-import jalview.io.StockholmFileTest;
-import jalview.ws.jws2.JPred301Client;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.SequenceAnnotationWSClient;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.AutoCalcSetting;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
 
 import java.awt.Component;
 import java.util.ArrayList;
@@ -43,13 +30,26 @@ import java.util.List;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 import compbio.metadata.Argument;
 import compbio.metadata.WrongParameterException;
 
+import jalview.datamodel.AlignmentI;
+import jalview.gui.Jalview2XML;
+import jalview.io.AnnotationFile;
+import jalview.io.FormatAdapter;
+import jalview.io.StockholmFileTest;
+import jalview.ws.jws2.JPred301Client;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.SequenceAnnotationWSClient;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.AutoCalcSetting;
+
 public class JpredJabaStructExportImport
 {
   public static String testseqs = "examples/uniref50.fa";
@@ -81,7 +81,9 @@ public class JpredJabaStructExportImport
     System.out.println("State of jpredws: " + jpredws);
 
     if (jpredws == null)
-      System.exit(0);
+    {
+      Assert.fail("jpredws is null");
+    }
 
     jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
 
@@ -142,7 +144,7 @@ public class JpredJabaStructExportImport
         if (!success)
         {
           jpredClient.cancelCurrentJob();
-          fail("Jpred Client didn't run with hardwired default parameters.");
+          Assert.fail("Jpred Client didn't run with hardwired default parameters.");
         }
 
       } catch (InterruptedException x)
@@ -213,21 +215,21 @@ public class JpredJabaStructExportImport
                       FormatAdapter.PASTE));
 
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
       return;
     } catch (Exception e)
     {
       e.printStackTrace();
     }
-    fail("Test "
+    Assert.fail("Test "
             + testname
             + "\nCouldn't complete Annotation file roundtrip input/output/input test.");
   }
 
-  // @Test
+  @Test
   public void testJpredwsSettingsRecovery()
   {
-    fail("not implemnented");
+    Assert.fail("not implemnented");
     List<compbio.metadata.Argument> opts = new ArrayList<compbio.metadata.Argument>();
     for (compbio.metadata.Argument rg : (List<compbio.metadata.Argument>) jpredws
             .getRunnerConfig().getArguments())
@@ -239,7 +241,7 @@ public class JpredJabaStructExportImport
           rg.setValue("292");
         } catch (WrongParameterException q)
         {
-          fail("Couldn't set the temperature parameter "
+          Assert.fail("Couldn't set the temperature parameter "
                   + q.getStackTrace());
         }
         opts.add(rg);
@@ -269,10 +271,10 @@ public class JpredJabaStructExportImport
     // write out parameters
     jalview.gui.AlignFrame nalf = null;
     assertTrue("Couldn't write out the Jar file",
-            new Jalview2XML(false).SaveAlignment(af,
+            new Jalview2XML(false).saveAlignment(af,
                     "testJPredWS_param.jar", "trial parameter writeout"));
     assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
-            false).LoadJalviewAlign("testJpredWS_param.jar")) != null);
+            false).loadJalviewAlign("testJpredWS_param.jar")) != null);
     if (nalf != null)
     {
       AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(