test/jalview/ext/archaeopteryx/AptxJalviewSequenceTreeTest.java

   1 // package jalview.ext.archaeopteryx;
   2 //
   3 // import static org.testng.Assert.assertEquals;
   4 // import static org.testng.Assert.assertTrue;
   5 //
   6 // import jalview.analysis.NJTree;
   7 // import jalview.analysis.TreeBuilder;
   8 // import jalview.analysis.scoremodels.ScoreModels;
   9 // import jalview.analysis.scoremodels.SimilarityParams;
  10 // import jalview.api.analysis.ScoreModelI;
  11 // import jalview.api.analysis.SimilarityParamsI;
  12 // import jalview.bin.Jalview;
  13 // import jalview.datamodel.Alignment;
  14 // import jalview.datamodel.AlignmentI;
  15 // import jalview.datamodel.Sequence;
  16 // import jalview.datamodel.SequenceI;
  17 // import jalview.gui.AlignViewport;
  18 //
  19 // import org.forester.archaeopteryx.MainFrame;
  20 // import org.forester.archaeopteryx.TreePanel;
  21 // import org.forester.phylogeny.Phylogeny;
  22 // import org.testng.annotations.BeforeClass;
  23 // import org.testng.annotations.Test;
  24 //
  25 // public class AptxJalviewSequenceTreeTest extends TreeViewTest
  26 // {
  27 // TreeBuilder jalviewTree;
  28 //
  29 // TreePanel treePanel;
  30 //
  31 // Phylogeny tree;
  32 //
  33 // MainFrame aptx;
  34 //
  35 // Jalview jalview;
  36 //
  37 // @Override
  38 // @BeforeClass(alwaysRun = true)
  39 // public void setUpTree()
  40 // {
  41 // SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
  42 // SequenceI seq2 = new Sequence("Seq2", "ABCDEFTHIJ");
  43 // SequenceI seq3 = new Sequence("Seq3", "BCFWDHIJ");
  44 // SequenceI seq4 = new Sequence("Seq4", "WTHISTHIS");
  45 //
  46 // AlignmentI al = new Alignment(
  47 // new SequenceI[]
  48 // { seq1, seq2, seq3, seq4 });
  49 // AlignViewport alignViewport = new AlignViewport(al);
  50 //
  51 // ScoreModelI scoreModel = ScoreModels.getInstance().getBlosum62();
  52 // SimilarityParamsI similarityParams = new SimilarityParams(true, true,
  53 // true, false);
  54 //
  55 // jalviewTree = new NJTree(alignViewport, scoreModel,
  56 // similarityParams);
  57 // }
  58 //
  59 // @Override
  60 // @BeforeClass(dependsOnMethods = { "setUpTree" })
  61 // public void createTreeView()
  62 // {
  63 // treeView = AptxInit.createInstanceFromCalculation(jalviewTree);
  64 // aptx = (MainFrame) treeView; // still pretty ugly
  65 //
  66 // treePanel = aptx.getMainPanel().getCurrentTreePanel();
  67 // tree = treePanel.getPhylogeny();
  68 //
  69 // }
  70 //
  71 // @Override
  72 // public void testTreeLoaded()
  73 // {
  74 // assertTrue(tree != null);
  75 //
  76 // }
  77 //
  78 // @Override
  79 // public void testTreeTitle()
  80 // {
  81 // assertTrue(tree.getName().contains("Neighbour Joining Using BLOSUM62"));
  82 //
  83 // }
  84 //
  85 // @Override
  86 // public void testChildNodesCount()
  87 // {
  88 // assertEquals(
  89 // tree.getNode("Seq2").getParent().getNumberOfExternalNodes(), 2);
  90 //
  91 // }
  92 //
  93 // @Override
  94 // public void testExistingBranchName()
  95 // {
  96 // tree.getNode("Seq4");
  97 //
  98 // }
  99 //
 100 // @Override
 101 // public void testChildToParentBranchLength()
 102 // {
 103 // assertEquals(tree.getNode("Seq1").getDistanceToParent(), 5.25);
 104 //
 105 // }
 106 //
 107 // @Test(
 108 // groups = "Functional",
 109 // expectedExceptions = IllegalArgumentException.class)
 110 // public void testInvalidBranchName()
 111 // {
 112 // tree.getNode("I shouldn't exist");
 113 //
 114 // }
 115 //
 116 // @Override
 117 // public void testNodeToRootBranchLength()
 118 // {
 119 // assertEquals(tree.getNode("Seq3").calculateDistanceToRoot(), 19.13);
 120 //
 121 // }
 122 //
 123 // @Override
 124 // public void testDistantNodeToRootBranchLength()
 125 // {
 126 // assertEquals(tree.getNode("Seq2").calculateDistanceToRoot(),
 127 // 3.75 + 35.75 + 19.13);
 128 //
 129 // }
 130 //
 131 //
 132 //
 133 //
 134 // }