Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

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

diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java
index 4de36f2..a92f5fb 100644 (file)
--- a/test/jalview/io/NewickFileTests.java
+++ b/test/jalview/io/NewickFileTests.java
@@ -22,10 +22,11 @@ package jalview.io;
 
 import static org.testng.ConversionUtils.wrapDataProvider;
 
-import jalview.analysis.NJTree;
 import jalview.analysis.SequenceIdMatcher;
+import jalview.analysis.TreeModel;
 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 ('"
@@ -117,7 +125,8 @@ public class NewickFileTests
       stage = "Compare original and generated tree" + treename;
 
       Vector<SequenceNode> oseqs, nseqs;
-      oseqs = new NJTree(new SequenceI[0], nf).findLeaves(nf.getTree());
+      oseqs = new TreeModel(new SequenceI[0], null, nf).findLeaves(nf
+              .getTree());
       AssertJUnit.assertTrue(stage + "No nodes in original tree.",
               oseqs.size() > 0);
       SequenceI[] olsqs = new SequenceI[oseqs.size()];
@@ -125,7 +134,8 @@ public class NewickFileTests
       {
         olsqs[i] = (SequenceI) oseqs.get(i).element();
       }
-      nseqs = new NJTree(new SequenceI[0], nf_regen).findLeaves(nf_regen
+      nseqs = new TreeModel(new SequenceI[0], null, nf_regen)
+              .findLeaves(nf_regen
               .getTree());
       AssertJUnit.assertTrue(stage + "No nodes in regerated tree.",
               nseqs.size() > 0);