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.assertNull;
   6 import static org.testng.Assert.assertTrue;
   7
   8 import jalview.datamodel.ontology.OntologyI;
   9
  10 import java.util.Arrays;
  11 import java.util.Collections;
  12 import java.util.HashSet;
  13 import java.util.List;
  14 import java.util.Set;
  15
  16 import org.testng.annotations.BeforeClass;
  17 import org.testng.annotations.Test;
  18
  19 public class SequenceOntologyLiteTest
  20 {
  21   private OntologyI so;
  22
  23   @BeforeClass(alwaysRun = true)
  24   public void setUp()
  25   {
  26     so = new SequenceOntologyLite();
  27   }
  28
  29   @Test(groups = "Functional")
  30   public void testIsA_sequenceVariant()
  31   {
  32     assertFalse(so.isA("CDS", "sequence_variant"));
  33     assertTrue(so.isA("sequence_variant", "sequence_variant"));
  34
  35     /*
  36      * these should all be sub-types of sequence_variant
  37      */
  38     assertTrue(so.isA("structural_variant", "sequence_variant"));
  39     assertTrue(so.isA("feature_variant", "sequence_variant"));
  40     assertTrue(so.isA("gene_variant", "sequence_variant"));
  41     assertTrue(so.isA("transcript_variant", "sequence_variant"));
  42     assertTrue(so.isA("NMD_transcript_variant", "sequence_variant"));
  43     assertTrue(so.isA("missense_variant", "sequence_variant"));
  44     assertTrue(so.isA("synonymous_variant", "sequence_variant"));
  45     assertTrue(so.isA("frameshift_variant", "sequence_variant"));
  46     assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant"));
  47     assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant"));
  48     assertTrue(so.isA("stop_gained", "sequence_variant"));
  49     assertTrue(so.isA("stop_lost", "sequence_variant"));
  50     assertTrue(so.isA("inframe_deletion", "sequence_variant"));
  51     assertTrue(so.isA("inframe_insertion", "sequence_variant"));
  52     assertTrue(so.isA("splice_region_variant", "sequence_variant"));
  53   }
  54
  55   @Test(groups = "Functional")
  56   public void testGetParentTerms()
  57   {
  58     Set<String> terms = new HashSet<>();
  59     terms.add("sequence_variant");
  60     terms.add("NMD_transcript_variant");
  61     terms.add("stop_lost");
  62     terms.add("chain"); // not an SO term
  63
  64     Set<String> parents = so.getParentTerms(terms);
  65     assertEquals(parents.size(), 2);
  66     assertTrue(parents.contains("sequence_variant"));
  67     assertTrue(parents.contains("chain"));
  68   }
  69
  70   @Test(groups = "Functional")
  71   public void testGetChildTerms()
  72   {
  73     List<String> terms = Collections.<String> emptyList();
  74     List<String> children = so.getChildTerms("exon", terms);
  75     assertTrue(children.isEmpty());
  76
  77     terms = Arrays.asList("gene", "transcript", "snRNA", "junk", "mRNA");
  78     children = so.getChildTerms("exon", terms);
  79     assertTrue(children.isEmpty());
  80     children = so.getChildTerms("transcript", terms);
  81     assertEquals(children.size(), 2);
  82     assertTrue(children.contains("snRNA"));
  83     assertTrue(children.contains("mRNA"));
  84
  85     terms = Arrays.asList("gene", "transcript", "synonymous_variant",
  86             "stop_lost", "chain");
  87     children = so.getChildTerms("sequence_variant", terms);
  88     assertEquals(children.size(), 2);
  89     assertTrue(children.contains("synonymous_variant"));
  90     assertTrue(children.contains("stop_lost"));
  91   }
  92
  93   @Test(groups = "Functional")
  94   public void testGetRootParents()
  95   {
  96     List<String> roots = so.getRootParents("xyz");
  97     assertNull(roots);
  98     roots = so.getRootParents(null);
  99     assertNull(roots);
 100
 101     roots = so.getRootParents("stop_gained");
 102     assertEquals(roots.size(), 1);
 103     assertEquals(roots.get(0), "sequence_variant");
 104   }
 105 }