test/jalview/io/gff/SequenceOntologyTest.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.BeforeMethod;
   7 import org.testng.annotations.Test;
   8
   9 public class SequenceOntologyTest
  10 {
  11   private SequenceOntology so;
  12
  13   @BeforeMethod
  14   public void setUp() {
  15     so = SequenceOntology.getInstance();
  16   }
  17
  18   @Test(groups = "Functional")
  19   public void testTermIsA()
  20   {
  21     assertTrue(so.isA("SO:0000087", "SO:0000704"));
  22     assertFalse(so.isA("SO:0000704", "SO:0000087"));
  23     assertTrue(so.isA("SO:0000736", "SO:0000735"));
  24
  25     // direct parent:
  26     assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
  27     // grandparent:
  28     assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
  29     // great-grandparent:
  30     assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
  31
  32     // same thing:
  33     assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
  34   }
  35
  36   @Test(groups = "Functional")
  37   public void testIsProteinMatch()
  38   {
  39     assertTrue(so.isProteinMatch("protein_match"));
  40     assertTrue(so.isProteinMatch("protein_hmm_match"));
  41     assertFalse(so.isProteinMatch("Protein_match")); // case-sensitive
  42   }
  43
  44   @Test(groups = "Functional")
  45   public void testIsNucleotideMatch()
  46   {
  47     assertTrue(so.isNucleotideMatch("nucleotide_match"));
  48     assertTrue(so.isNucleotideMatch("primer_match"));
  49     assertTrue(so.isNucleotideMatch("cross_genome_match"));
  50     assertTrue(so.isNucleotideMatch("expressed_sequence_match"));
  51     assertTrue(so.isNucleotideMatch("translated_nucleotide_match"));
  52     assertTrue(so.isNucleotideMatch("UST_match"));
  53     assertTrue(so.isNucleotideMatch("RST_match"));
  54     assertTrue(so.isNucleotideMatch("cDNA_match"));
  55     assertTrue(so.isNucleotideMatch("EST_match"));
  56     assertFalse(so.isNucleotideMatch("match")); // parent
  57   }
  58
  59   @Test(groups = "Functional")
  60   public void testIsCDS()
  61   {
  62     assertTrue(so.isA("CDS", "CDS"));
  63     assertTrue(so.isA("CDS_predicted", "CDS"));
  64     assertTrue(so.isA("transposable_element_CDS", "CDS"));
  65     assertTrue(so.isA("edited_CDS", "CDS"));
  66     assertTrue(so.isA("CDS_independently_known", "CDS"));
  67     assertTrue(so.isA("CDS_fragment", "CDS"));
  68     assertFalse(so.isA("CDS_region", "CDS"));// part_of
  69     assertFalse(so.isA("polypeptide", "CDS")); // derives_from
  70   }
  71 }