test/jalview/io/gff/SequenceOntologyLiteTest.java

   1 package jalview.io.gff;
   2
   3 import static org.testng.Assert.assertEquals;
   4 import static org.testng.Assert.assertFalse;
   5 import static org.testng.Assert.assertTrue;
   6
   7 import jalview.datamodel.ontology.OntologyI;
   8
   9 import java.util.Arrays;
  10 import java.util.Collections;
  11 import java.util.HashSet;
  12 import java.util.List;
  13 import java.util.Set;
  14
  15 import org.testng.annotations.BeforeClass;
  16 import org.testng.annotations.Test;
  17
  18 public class SequenceOntologyLiteTest
  19 {
  20   private OntologyI so;
  21
  22   @BeforeClass(alwaysRun = true)
  23   public void setUp()
  24   {
  25     so = new SequenceOntologyLite();
  26   }
  27
  28   @Test(groups = "Functional")
  29   public void testIsA_sequenceVariant()
  30   {
  31     assertFalse(so.isA("CDS", "sequence_variant"));
  32     assertTrue(so.isA("sequence_variant", "sequence_variant"));
  33
  34     /*
  35      * these should all be sub-types of sequence_variant
  36      */
  37     assertTrue(so.isA("structural_variant", "sequence_variant"));
  38     assertTrue(so.isA("feature_variant", "sequence_variant"));
  39     assertTrue(so.isA("gene_variant", "sequence_variant"));
  40     assertTrue(so.isA("transcript_variant", "sequence_variant"));
  41     assertTrue(so.isA("NMD_transcript_variant", "sequence_variant"));
  42     assertTrue(so.isA("missense_variant", "sequence_variant"));
  43     assertTrue(so.isA("synonymous_variant", "sequence_variant"));
  44     assertTrue(so.isA("frameshift_variant", "sequence_variant"));
  45     assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant"));
  46     assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant"));
  47     assertTrue(so.isA("stop_gained", "sequence_variant"));
  48     assertTrue(so.isA("stop_lost", "sequence_variant"));
  49     assertTrue(so.isA("inframe_deletion", "sequence_variant"));
  50     assertTrue(so.isA("inframe_insertion", "sequence_variant"));
  51     assertTrue(so.isA("splice_region_variant", "sequence_variant"));
  52   }
  53
  54   @Test(groups = "Functional")
  55   public void testGetParentTerms()
  56   {
  57     Set<String> terms = new HashSet<>();
  58     terms.add("sequence_variant");
  59     terms.add("NMD_transcript_variant");
  60     terms.add("stop_lost");
  61     terms.add("chain"); // not an SO term
  62
  63     Set<String> parents = so.getParentTerms(terms);
  64     assertEquals(parents.size(), 2);
  65     assertTrue(parents.contains("sequence_variant"));
  66     assertTrue(parents.contains("chain"));
  67   }
  68
  69   @Test(groups = "Functional")
  70   public void testGetChildTerms()
  71   {
  72     List<String> terms = Collections.<String> emptyList();
  73     List<String> children = so.getChildTerms("exon", terms);
  74     assertTrue(children.isEmpty());
  75
  76     terms = Arrays.asList("gene", "transcript", "snRNA", "junk", "mRNA");
  77     children = so.getChildTerms("exon", terms);
  78     assertTrue(children.isEmpty());
  79     children = so.getChildTerms("transcript", terms);
  80     assertEquals(children.size(), 2);
  81     assertTrue(children.contains("snRNA"));
  82     assertTrue(children.contains("mRNA"));
  83
  84     terms = Arrays.asList("gene", "transcript", "synonymous_variant",
  85             "stop_lost", "chain");
  86     children = so.getChildTerms("sequence_variant", terms);
  87     assertEquals(children.size(), 2);
  88     assertTrue(children.contains("synonymous_variant"));
  89     assertTrue(children.contains("stop_lost"));
  90   }
  91 }