Added abstract class for tree viewer testing, rearranged existing tests

[jalview.git] / test / jalview / ext / archaeopteryx / AptxJalviewTreeTest.java

diff --git a/test/jalview/ext/archaeopteryx/AptxJalviewTreeTest.java b/test/jalview/ext/archaeopteryx/AptxJalviewTreeTest.java
index a5beee2..4fdc473 100644 (file)
--- a/test/jalview/ext/archaeopteryx/AptxJalviewTreeTest.java
+++ b/test/jalview/ext/archaeopteryx/AptxJalviewTreeTest.java
@@ -1,14 +1,24 @@
 package jalview.ext.archaeopteryx;
 
+import jalview.analysis.NJTree;
 import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Jalview;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
 
 import org.forester.archaeopteryx.MainFrame;
 import org.forester.archaeopteryx.TreePanel;
 import org.forester.phylogeny.Phylogeny;
 import org.testng.annotations.BeforeClass;
 
-public class AptxJalviewTreeTest
+public class AptxJalviewTreeTest extends TreeViewTest
 {
   TreeBuilder jalviewTree;
 
@@ -20,20 +30,70 @@ public class AptxJalviewTreeTest
 
   Jalview jalview;
   
+  @Override
   @BeforeClass(alwaysRun = true)
   public void setUpTree()
   {
+    SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
+    SequenceI seq2 = new Sequence("Seq2", "ABCDEFTHIJ");
+    SequenceI seq3 = new Sequence("Seq3", "BCFWDHIJ");
+    SequenceI seq4 = new Sequence("Seq4", "WTHISTHIS");
 
+    AlignmentI al = new Alignment(
+            new SequenceI[]
+            { seq1, seq2, seq3, seq4 });
+    AlignViewport alignViewport = new AlignViewport(al);
+
+    ScoreModelI scoreModel = ScoreModels.getInstance().getBlosum62();
+    SimilarityParamsI similarityParams = new SimilarityParams(true, true,
+            true, false);
+
+    jalviewTree = new NJTree(alignViewport, scoreModel,
+            similarityParams);
   }
 
   @BeforeClass(dependsOnMethods = { "setUpTree" })
-  public void setUpJalview()
+  public void createTreeView()
   {
-    String[] args = new String[0];
-    Jalview.main(args);
-    aptx = ArchaeopteryxInit.createInstance(jalviewTree);
+    treeView = ArchaeopteryxInit.createInstance(jalviewTree);
+    aptx = (MainFrame) treeView; // still pretty ugly
 
     treePanel = aptx.getMainPanel().getCurrentTreePanel();
     tree = treePanel.getPhylogeny();
   }
+
+  @Override
+  public void testChildNodesCount()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void testChildToParentBranchLength()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void testNodeToRootBranchLength()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void testDistantNodeToRootBranchLength()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void testTreeLoaded()
+  {
+    // TODO Auto-generated method stub
+
+  }
 }