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
  21 public class AptxJalviewTreeTest extends TreeViewTest
  22 {
  23   TreeBuilder jalviewTree;
  24
  25   TreePanel treePanel;
  26
  27   Phylogeny tree;
  28
  29   MainFrame aptx;
  30
  31   Jalview jalview;
  32
  33   @Override
  34   @BeforeClass(alwaysRun = true)
  35   public void setUpTree()
  36   {
  37     SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
  38     SequenceI seq2 = new Sequence("Seq2", "ABCDEFTHIJ");
  39     SequenceI seq3 = new Sequence("Seq3", "BCFWDHIJ");
  40     SequenceI seq4 = new Sequence("Seq4", "WTHISTHIS");
  41
  42     AlignmentI al = new Alignment(
  43             new SequenceI[]
  44             { seq1, seq2, seq3, seq4 });
  45     AlignViewport alignViewport = new AlignViewport(al);
  46
  47     ScoreModelI scoreModel = ScoreModels.getInstance().getBlosum62();
  48     SimilarityParamsI similarityParams = new SimilarityParams(true, true,
  49             true, false);
  50
  51     jalviewTree = new NJTree(alignViewport, scoreModel,
  52             similarityParams);
  53   }
  54
  55   @BeforeClass(dependsOnMethods = { "setUpTree" })
  56   public void createTreeView()
  57   {
  58     treeView = ArchaeopteryxInit.createInstance(jalviewTree);
  59     aptx = (MainFrame) treeView; // still pretty ugly
  60
  61     treePanel = aptx.getMainPanel().getCurrentTreePanel();
  62     tree = treePanel.getPhylogeny();
  63   }
  64
  65   @Override
  66   public void testChildNodesCount()
  67   {
  68     // TODO Auto-generated method stub
  69
  70   }
  71
  72   @Override
  73   public void testChildToParentBranchLength()
  74   {
  75     // TODO Auto-generated method stub
  76
  77   }
  78
  79   @Override
  80   public void testNodeToRootBranchLength()
  81   {
  82     // TODO Auto-generated method stub
  83
  84   }
  85
  86   @Override
  87   public void testDistantNodeToRootBranchLength()
  88   {
  89     // TODO Auto-generated method stub
  90
  91   }
  92
  93   @Override
  94   public void testTreeLoaded()
  95   {
  96     // TODO Auto-generated method stub
  97
  98   }
  99 }