X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FNewickFileTests.java;h=4de36f2b33e36a293ff932449fcdab37a7675525;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=a016134be3e8d596eef552dbd4c8f22489f59345;hpb=c93b9ad2ebfab4cad4608a8890132918589576be;p=jalview.git

diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java
index a016134..4de36f2 100644
--- a/test/jalview/io/NewickFileTests.java
+++ b/test/jalview/io/NewickFileTests.java
@@ -56,19 +56,15 @@ public class NewickFileTests
   public static Collection data()
   {
     return Arrays
-            .asList(new Object[][]
-            {
+            .asList(new Object[][] {
 
-                new String[]
-                {
+                new String[] {
                     "Simple uniref50 newick",
                     "(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);" },
-                new String[]
-                {
+                new String[] {
                     "Tree with quotes",
                     "('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)|CK_Syn_MINOS11_750':1.063831);" },
-                new String[]
-                {
+                new String[] {
                     "Tree with double escaped comma in node",
                     "('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)''|CK_Syn_MINOS11_750':1.063831);" } });
   };
@@ -84,12 +80,12 @@ public class NewickFileTests
   /**
    * @throws java.lang.Exception
    */
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testTreeIO() throws Exception
   {
     String stage = "Init", treename = " '" + name + "' :";
@@ -99,15 +95,16 @@ public class NewickFileTests
       System.out.println(treename + "\n" + testTree);
       NewickFile nf = new NewickFile(testTree, FormatAdapter.PASTE);
       nf.parse();
-      AssertJUnit.assertTrue(stage + "Invalid Tree '" + nf.getWarningMessage() + "'",
+      AssertJUnit.assertTrue(
+              stage + "Invalid Tree '" + nf.getWarningMessage() + "'",
               nf.isValid());
       SequenceNode tree = nf.getTree();
       AssertJUnit.assertTrue(stage + "Null Tree", tree != null);
       stage = "Creating newick file from testTree " + treename;
       String gentree = new NewickFile(tree).print(nf.HasBootstrap(),
               nf.HasDistances());
-      AssertJUnit.assertTrue(stage + "Empty string generated", gentree != null
-              && gentree.trim().length() > 0);
+      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();
@@ -119,25 +116,27 @@ public class NewickFileTests
       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());
-      AssertJUnit.assertTrue(stage + "No nodes in original tree.", oseqs.size() > 0);
+      Vector<SequenceNode> oseqs, nseqs;
+      oseqs = new NJTree(new SequenceI[0], nf).findLeaves(nf.getTree());
+      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();
+        olsqs[i] = (SequenceI) oseqs.get(i).element();
       }
-      nseqs = new NJTree(new SequenceI[0], nf_regen).findLeaves(
-              nf_regen.getTree(), new Vector());
-      AssertJUnit.assertTrue(stage + "No nodes in regerated tree.", nseqs.size() > 0);
+      nseqs = new NJTree(new SequenceI[0], nf_regen).findLeaves(nf_regen
+              .getTree());
+      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();
+        nsqs[i] = (SequenceI) nseqs.get(i).element();
       }
-      AssertJUnit.assertTrue(stage + " Different number of leaves (original "
-              + olsqs.length + " and regen " + nsqs.length + ")",
+      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(
               nsqs);
@@ -172,7 +171,7 @@ public class NewickFileTests
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }