test/jalview/ext/archaeopteryx/AptxJalviewTreeTest.java

   1 package jalview.ext.archaeopteryx;
   2
   3 import jalview.analysis.NJTree;
   4 import jalview.analysis.TreeBuilder;
   5 import jalview.analysis.scoremodels.ScoreModels;
   6 import jalview.analysis.scoremodels.SimilarityParams;
   7 import jalview.api.analysis.ScoreModelI;
   8 import jalview.api.analysis.SimilarityParamsI;
   9 import jalview.bin.Jalview;
  10 import jalview.datamodel.Alignment;
  11 import jalview.datamodel.AlignmentI;
  12 import jalview.datamodel.Sequence;
  13 import jalview.datamodel.SequenceI;
  14 import jalview.gui.AlignViewport;
  15
  16 import org.forester.archaeopteryx.MainFrame;
  17 import org.forester.archaeopteryx.TreePanel;
  18 import org.forester.phylogeny.Phylogeny;
  19 import org.testng.annotations.BeforeClass;
  20 import org.testng.annotations.Test;
  21
  22 public class AptxJalviewTreeTest extends TreeViewTest
  23 {
  24   TreeBuilder jalviewTree;
  25
  26   TreePanel treePanel;
  27
  28   Phylogeny tree;
  29
  30   MainFrame aptx;
  31
  32   Jalview jalview;
  33
  34   @Override
  35   @BeforeClass(alwaysRun = true)
  36   public void setUpTree()
  37   {
  38     SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
  39     SequenceI seq2 = new Sequence("Seq2", "ABCDEFTHIJ");
  40     SequenceI seq3 = new Sequence("Seq3", "BCFWDHIJ");
  41     SequenceI seq4 = new Sequence("Seq4", "WTHISTHIS");
  42
  43     AlignmentI al = new Alignment(
  44             new SequenceI[]
  45             { seq1, seq2, seq3, seq4 });
  46     AlignViewport alignViewport = new AlignViewport(al);
  47
  48     ScoreModelI scoreModel = ScoreModels.getInstance().getBlosum62();
  49     SimilarityParamsI similarityParams = new SimilarityParams(true, true,
  50             true, false);
  51
  52     jalviewTree = new NJTree(alignViewport, scoreModel,
  53             similarityParams);
  54   }
  55
  56   @Override
  57   @BeforeClass(dependsOnMethods = { "setUpTree" })
  58   public void createTreeView()
  59   {
  60     treeView = ArchaeopteryxInit.createInstance(jalviewTree);
  61     aptx = (MainFrame) treeView; // still pretty ugly
  62
  63     treePanel = aptx.getMainPanel().getCurrentTreePanel();
  64     tree = treePanel.getPhylogeny();
  65   }
  66
  67   @Override
  68   public void testChildNodesCount()
  69   {
  70     // TODO Auto-generated method stub
  71
  72   }
  73
  74   @Override
  75   public void testChildToParentBranchLength()
  76   {
  77     // TODO Auto-generated method stub
  78
  79   }
  80
  81   @Override
  82   public void testNodeToRootBranchLength()
  83   {
  84     // TODO Auto-generated method stub
  85
  86   }
  87
  88   @Override
  89   public void testDistantNodeToRootBranchLength()
  90   {
  91     // TODO Auto-generated method stub
  92
  93   }
  94
  95   @Override
  96   public void testTreeLoaded()
  97   {
  98     // TODO Auto-generated method stub
  99
 100   }
 101
 102
 103   @Test(
 104     groups = "Functional",
 105     expectedExceptions = IllegalArgumentException.class)
 106   public void testInvalidBranchName()
 107   {
 108     // TODO Auto-generated method stub
 109
 110   }
 111
 112   @Override
 113   public void testExistingBranchName()
 114   {
 115     // TODO Auto-generated method stub
 116
 117   }
 118 }