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.createInstance(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 }