X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FNewickFileTests.java;h=d198f0f90db99a27a15c3c655baa76f880dba7e7;hb=f831ddf7f52d6c4a1918e87d94877b22bd322648;hp=f89f58bc8df125c007394f28a84f9dee4c18333b;hpb=cbc07eab0291f023f89b2554c488ae9e4587ae2a;p=jalview.git

diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java
index f89f58b..d198f0f 100644
--- a/test/jalview/io/NewickFileTests.java
+++ b/test/jalview/io/NewickFileTests.java
@@ -26,6 +26,7 @@ import jalview.analysis.NJTree;
 import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
+import jalview.gui.JvOptionPane;
 
 import java.util.Arrays;
 import java.util.Collection;
@@ -46,6 +47,13 @@ import org.testng.annotations.Test;
 public class NewickFileTests
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Factory
   public static Object[] factoryData()
   {
@@ -93,7 +101,7 @@ public class NewickFileTests
     {
       stage = "Parsing testTree " + treename;
       System.out.println(treename + "\n" + testTree);
-      NewickFile nf = new NewickFile(testTree, FormatAdapter.PASTE);
+      NewickFile nf = new NewickFile(testTree, DataSourceType.PASTE);
       nf.parse();
       AssertJUnit.assertTrue(
               stage + "Invalid Tree '" + nf.getWarningMessage() + "'",
@@ -106,7 +114,7 @@ public class NewickFileTests
       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);
+      NewickFile nf_regen = new NewickFile(gentree, DataSourceType.PASTE);
       nf_regen.parse();
       AssertJUnit.assertTrue(
               stage + "Newick file is invalid ('"
@@ -116,24 +124,23 @@ 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());
+      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());
+      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