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