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