test/jalview/io/gff/SequenceOntologyLiteTest.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.Test;
   7
   8 public class SequenceOntologyLiteTest
   9 {
  10   @Test(groups = "Functional")
  11   public void testIsA_sequenceVariant()
  12   {
  13     SequenceOntologyI so = new SequenceOntologyLite();
  14
  15     assertFalse(so.isA("CDS", "sequence_variant"));
  16     assertTrue(so.isA("sequence_variant", "sequence_variant"));
  17
  18     /*
  19      * these should all be sub-types of sequence_variant
  20      */
  21     assertTrue(so.isA("structural_variant", "sequence_variant"));
  22     assertTrue(so.isA("feature_variant", "sequence_variant"));
  23     assertTrue(so.isA("gene_variant", "sequence_variant"));
  24     assertTrue(so.isA("transcript_variant", "sequence_variant"));
  25     assertTrue(so.isA("NMD_transcript_variant", "sequence_variant"));
  26     assertTrue(so.isA("missense_variant", "sequence_variant"));
  27     assertTrue(so.isA("synonymous_variant", "sequence_variant"));
  28     assertTrue(so.isA("frameshift_variant", "sequence_variant"));
  29     assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant"));
  30     assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant"));
  31     assertTrue(so.isA("stop_gained", "sequence_variant"));
  32     assertTrue(so.isA("stop_lost", "sequence_variant"));
  33     assertTrue(so.isA("inframe_deletion", "sequence_variant"));
  34     assertTrue(so.isA("inframe_insertion", "sequence_variant"));
  35     assertTrue(so.isA("splice_region_variant", "sequence_variant"));
  36   }
  37 }