test/jalview/ext/so/SequenceOntologyTest.java

   1 package jalview.ext.so;
   2
   3 import static org.testng.AssertJUnit.assertFalse;
   4 import static org.testng.AssertJUnit.assertTrue;
   5
   6 import jalview.ext.so.SequenceOntology;
   7 import jalview.io.gff.SequenceOntologyFactory;
   8 import jalview.io.gff.SequenceOntologyI;
   9
  10 import org.testng.annotations.AfterClass;
  11 import org.testng.annotations.BeforeClass;
  12 import org.testng.annotations.Test;
  13
  14 public class SequenceOntologyTest
  15 {
  16   private SequenceOntologyI so;
  17
  18   @BeforeClass
  19   public void setUp() {
  20     long now = System.currentTimeMillis();
  21     SequenceOntologyFactory.setInstance(new SequenceOntology());
  22     long elapsed = System.currentTimeMillis() - now;
  23     System.out.println("Load and cache of Sequence Ontology took "
  24             + elapsed + "ms");
  25     so = SequenceOntologyFactory.getInstance();
  26   }
  27
  28   @AfterClass
  29   public void tearDown()
  30   {
  31     SequenceOntologyFactory.setInstance(null);
  32   }
  33
  34   @Test(groups = "Functional")
  35   public void testIsA()
  36   {
  37     assertFalse(so.isA(null, null));
  38     assertFalse(so.isA(null, "SO:0000087"));
  39     assertFalse(so.isA("SO:0000087", null));
  40     assertFalse(so.isA("complete", "garbage"));
  41
  42     assertTrue(so.isA("SO:0000087", "SO:0000704"));
  43     assertFalse(so.isA("SO:0000704", "SO:0000087"));
  44     assertTrue(so.isA("SO:0000736", "SO:0000735"));
  45
  46     // same thing:
  47     assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
  48     // direct parent:
  49     assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
  50     // grandparent:
  51     assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
  52     // great-grandparent:
  53     assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
  54
  55     // same thing by name / description:
  56     assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
  57     assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
  58     assertTrue(so.isA("SO:0000084", "SO:0000084"));
  59
  60     // SO name to description:
  61     assertTrue(so.isA("SO:0000084", "organelle_sequence"));
  62     assertTrue(so.isA("SO:0000084", "sequence_location"));
  63     assertTrue(so.isA("SO:0000084", "sequence_attribute"));
  64
  65     // description to SO name:
  66     assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
  67     assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
  68     assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
  69   }
  70
  71   @Test(groups = "Functional")
  72   public void testIsCDS()
  73   {
  74     assertTrue(so.isA("CDS", "CDS"));
  75     assertTrue(so.isA("CDS_predicted", "CDS"));
  76     assertTrue(so.isA("transposable_element_CDS", "CDS"));
  77     assertTrue(so.isA("edited_CDS", "CDS"));
  78     assertTrue(so.isA("CDS_independently_known", "CDS"));
  79     assertTrue(so.isA("CDS_fragment", "CDS"));
  80     assertFalse(so.isA("CDS_region", "CDS"));// part_of
  81     assertFalse(so.isA("polypeptide", "CDS")); // derives_from
  82   }
  83 }