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   {
  18     long now = System.currentTimeMillis();
  19     try
  20     {
  21       so = new SequenceOntology();
  22     } catch (Throwable t)
  23     {
  24       System.out.println("SOTest error ");
  25       t.printStackTrace(System.err);
  26     }
  27     long elapsed = System.currentTimeMillis() - now;
  28     System.out.println("Load and cache of Sequence Ontology took "
  29             + elapsed + "ms");
  30   }
  31
  32   @Test(groups = "Functional")
  33   public void testIsA()
  34   {
  35     assertFalse(so.isA(null, null));
  36     assertFalse(so.isA(null, "SO:0000087"));
  37     assertFalse(so.isA("SO:0000087", null));
  38     assertFalse(so.isA("complete", "garbage"));
  39
  40     assertTrue(so.isA("SO:0000087", "SO:0000704"));
  41     assertFalse(so.isA("SO:0000704", "SO:0000087"));
  42     assertTrue(so.isA("SO:0000736", "SO:0000735"));
  43
  44     // same thing:
  45     assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
  46     // direct parent:
  47     assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
  48     // grandparent:
  49     assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
  50     // great-grandparent:
  51     assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
  52
  53     // same thing by name / description:
  54     assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
  55     assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
  56     assertTrue(so.isA("SO:0000084", "SO:0000084"));
  57
  58     // SO name to description:
  59     assertTrue(so.isA("SO:0000084", "organelle_sequence"));
  60     assertTrue(so.isA("SO:0000084", "sequence_location"));
  61     assertTrue(so.isA("SO:0000084", "sequence_attribute"));
  62
  63     // description to SO name:
  64     assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
  65     assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
  66     assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
  67   }
  68
  69   @Test(groups = "Functional")
  70   public void testIsCDS()
  71   {
  72     assertTrue(so.isA("CDS", "CDS"));
  73     assertTrue(so.isA("CDS_predicted", "CDS"));
  74     assertTrue(so.isA("transposable_element_CDS", "CDS"));
  75     assertTrue(so.isA("edited_CDS", "CDS"));
  76     assertTrue(so.isA("CDS_independently_known", "CDS"));
  77     assertTrue(so.isA("CDS_fragment", "CDS"));
  78     assertFalse(so.isA("CDS_region", "CDS"));// part_of
  79     assertFalse(so.isA("polypeptide", "CDS")); // derives_from
  80   }
  81 }