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   @Override
  56   @BeforeClass(dependsOnMethods = { "setUpTree" })
  57   public void createTreeView()
  58   {
  59     treeView = ArchaeopteryxInit.createInstance(jalviewTree);
  60     aptx = (MainFrame) treeView; // still pretty ugly
  61
  62     treePanel = aptx.getMainPanel().getCurrentTreePanel();
  63     tree = treePanel.getPhylogeny();
  64   }
  65
  66   @Override
  67   public void testChildNodesCount()
  68   {
  69     // TODO Auto-generated method stub
  70
  71   }
  72
  73   @Override
  74   public void testChildToParentBranchLength()
  75   {
  76     // TODO Auto-generated method stub
  77
  78   }
  79
  80   @Override
  81   public void testNodeToRootBranchLength()
  82   {
  83     // TODO Auto-generated method stub
  84
  85   }
  86
  87   @Override
  88   public void testDistantNodeToRootBranchLength()
  89   {
  90     // TODO Auto-generated method stub
  91
  92   }
  93
  94   @Override
  95   public void testTreeLoaded()
  96   {
  97     // TODO Auto-generated method stub
  98
  99   }
 100
 101
 102   @Override
 103   public void testInvalidBranchName()
 104   {
 105     // TODO Auto-generated method stub
 106
 107   }
 108
 109   @Override
 110   public void testExistingBranchName()
 111   {
 112     // TODO Auto-generated method stub
 113
 114   }
 115 }