test/jalview/io/gff/SequenceOntologyTest.java

   1 package jalview.io.gff;
   2
   3 import static org.testng.AssertJUnit.assertFalse;
   4 import static org.testng.AssertJUnit.assertTrue;
   5
   6 import org.testng.annotations.AfterClass;
   7 import org.testng.annotations.BeforeClass;
   8 import org.testng.annotations.Test;
   9
  10 public class SequenceOntologyTest
  11 {
  12   private SequenceOntologyI so;
  13
  14   @BeforeClass
  15   public void setUp() {
  16     long now = System.currentTimeMillis();
  17     SequenceOntologyFactory.setInstance(new SequenceOntology());
  18     long elapsed = System.currentTimeMillis() - now;
  19     System.out.println("Load and cache of Sequence Ontology took "
  20             + elapsed + "ms");
  21     so = SequenceOntologyFactory.getInstance();
  22   }
  23
  24   @AfterClass
  25   public void tearDown()
  26   {
  27     SequenceOntologyFactory.setInstance(null);
  28   }
  29
  30   @Test(groups = "Functional")
  31   public void testIsA()
  32   {
  33     assertFalse(so.isA(null, null));
  34     assertFalse(so.isA(null, "SO:0000087"));
  35     assertFalse(so.isA("SO:0000087", null));
  36     assertFalse(so.isA("complete", "garbage"));
  37
  38     assertTrue(so.isA("SO:0000087", "SO:0000704"));
  39     assertFalse(so.isA("SO:0000704", "SO:0000087"));
  40     assertTrue(so.isA("SO:0000736", "SO:0000735"));
  41
  42     // same thing:
  43     assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
  44     // direct parent:
  45     assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
  46     // grandparent:
  47     assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
  48     // great-grandparent:
  49     assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
  50
  51     // same thing by name / description:
  52     assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
  53     assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
  54     assertTrue(so.isA("SO:0000084", "SO:0000084"));
  55
  56     // SO name to description:
  57     assertTrue(so.isA("SO:0000084", "organelle_sequence"));
  58     assertTrue(so.isA("SO:0000084", "sequence_location"));
  59     assertTrue(so.isA("SO:0000084", "sequence_attribute"));
  60
  61     // description to SO name:
  62     assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
  63     assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
  64     assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
  65   }
  66
  67   @Test(groups = "Functional")
  68   public void testIsCDS()
  69   {
  70     assertTrue(so.isA("CDS", "CDS"));
  71     assertTrue(so.isA("CDS_predicted", "CDS"));
  72     assertTrue(so.isA("transposable_element_CDS", "CDS"));
  73     assertTrue(so.isA("edited_CDS", "CDS"));
  74     assertTrue(so.isA("CDS_independently_known", "CDS"));
  75     assertTrue(so.isA("CDS_fragment", "CDS"));
  76     assertFalse(so.isA("CDS_region", "CDS"));// part_of
  77     assertFalse(so.isA("polypeptide", "CDS")); // derives_from
  78   }
  79 }