JAL-1805 test envirionment separation

[jalview.git] / test / jalview / io / NewickFileTests.java

diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java
index 07672c8..a783b1e 100644 (file)
--- a/test/jalview/io/NewickFileTests.java
+++ b/test/jalview/io/NewickFileTests.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.
  * 
@@ -20,34 +20,38 @@
  */
 package jalview.io;
 
-import static org.junit.Assert.*;
-
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.Vector;
+import static org.testng.ConversionUtils.wrapDataProvider;
 
 import jalview.analysis.NJTree;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 
-import org.jmol.util.ArrayUtil;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.junit.runners.Parameterized;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Vector;
+
 import org.junit.runners.Parameterized.Parameters;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Factory;
+import org.testng.annotations.Test;
 
 /**
  * @author jimp
  * 
  */
-@RunWith(Parameterized.class)
 public class NewickFileTests
 {
 
+  @Factory
+  public static Object[] factoryData()
+  {
+    return wrapDataProvider(NewickFileTests.class, data());
+  }
+
   @Parameters
   public static Collection data()
   {
@@ -85,7 +89,7 @@ public class NewickFileTests
   {
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testTreeIO() throws Exception
   {
     String stage = "Init", treename = " '" + name + "' :";
@@ -95,44 +99,44 @@ public class NewickFileTests
       System.out.println(treename + "\n" + testTree);
       NewickFile nf = new NewickFile(testTree, FormatAdapter.PASTE);
       nf.parse();
-      assertTrue(stage + "Invalid Tree '" + nf.getWarningMessage() + "'",
+      AssertJUnit.assertTrue(stage + "Invalid Tree '" + nf.getWarningMessage() + "'",
               nf.isValid());
       SequenceNode tree = nf.getTree();
-      assertTrue(stage + "Null Tree", tree != null);
+      AssertJUnit.assertTrue(stage + "Null Tree", tree != null);
       stage = "Creating newick file from testTree " + treename;
       String gentree = new NewickFile(tree).print(nf.HasBootstrap(),
               nf.HasDistances());
-      assertTrue(stage + "Empty string generated", gentree != null
+      AssertJUnit.assertTrue(stage + "Empty string generated", gentree != null
               && gentree.trim().length() > 0);
       stage = "Parsing regenerated testTree " + treename;
       NewickFile nf_regen = new NewickFile(gentree, FormatAdapter.PASTE);
       nf_regen.parse();
-      assertTrue(
+      AssertJUnit.assertTrue(
               stage + "Newick file is invalid ('"
                       + nf_regen.getWarningMessage() + "')",
               nf_regen.isValid());
       SequenceNode tree_regen = nf.getTree();
-      assertTrue(stage + "Null Tree", tree_regen != null);
+      AssertJUnit.assertTrue(stage + "Null Tree", tree_regen != null);
       stage = "Compare original and generated tree" + treename;
 
       Vector oseqs, nseqs;
       oseqs = new NJTree(new SequenceI[0], nf).findLeaves(nf.getTree(),
               new Vector());
-      assertTrue(stage + "No nodes in original tree.", oseqs.size() > 0);
+      AssertJUnit.assertTrue(stage + "No nodes in original tree.", oseqs.size() > 0);
       SequenceI[] olsqs = new SequenceI[oseqs.size()];
       for (int i = 0, iSize = oseqs.size(); i < iSize; i++)
       {
         olsqs[i] = (SequenceI) ((SequenceNode) oseqs.get(i)).element();
       }
-      nseqs = (Vector) new NJTree(new SequenceI[0], nf_regen).findLeaves(
+      nseqs = new NJTree(new SequenceI[0], nf_regen).findLeaves(
               nf_regen.getTree(), new Vector());
-      assertTrue(stage + "No nodes in regerated tree.", nseqs.size() > 0);
+      AssertJUnit.assertTrue(stage + "No nodes in regerated tree.", nseqs.size() > 0);
       SequenceI[] nsqs = new SequenceI[nseqs.size()];
       for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
       {
         nsqs[i] = (SequenceI) ((SequenceNode) nseqs.get(i)).element();
       }
-      assertTrue(stage + " Different number of leaves (original "
+      AssertJUnit.assertTrue(stage + " Different number of leaves (original "
               + olsqs.length + " and regen " + nsqs.length + ")",
               olsqs.length == nsqs.length);
       SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs), nmatcher = new SequenceIdMatcher(
@@ -157,7 +161,7 @@ public class NewickFileTests
 
       if (warns.length() > 0)
       {
-        fail(stage + warns);
+        Assert.fail(stage + warns);
       }
     } catch (Exception x)
     {