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 testIsA()
  20   {
  21     assertFalse(so.isA(null, null));
  22     assertFalse(so.isA(null, "SO:0000087"));
  23     assertFalse(so.isA("SO:0000087", null));
  24     assertFalse(so.isA("complete", "garbage"));
  25
  26     assertTrue(so.isA("SO:0000087", "SO:0000704"));
  27     assertFalse(so.isA("SO:0000704", "SO:0000087"));
  28     assertTrue(so.isA("SO:0000736", "SO:0000735"));
  29
  30     // same thing:
  31     assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
  32     // direct parent:
  33     assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
  34     // grandparent:
  35     assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
  36     // great-grandparent:
  37     assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
  38
  39     // same thing by name / description:
  40     assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
  41     assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
  42     assertTrue(so.isA("SO:0000084", "SO:0000084"));
  43
  44     // SO name to description:
  45     assertTrue(so.isA("SO:0000084", "organelle_sequence"));
  46     assertTrue(so.isA("SO:0000084", "sequence_location"));
  47     assertTrue(so.isA("SO:0000084", "sequence_attribute"));
  48
  49     // description to SO name:
  50     assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
  51     assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
  52     assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
  53   }
  54
  55   @Test(groups = "Functional")
  56   public void testIsProteinMatch()
  57   {
  58     assertTrue(so.isProteinMatch("protein_match"));
  59     assertTrue(so.isProteinMatch("protein_hmm_match"));
  60     assertFalse(so.isProteinMatch("Protein_match")); // case-sensitive
  61   }
  62
  63   @Test(groups = "Functional")
  64   public void testIsNucleotideMatch()
  65   {
  66     assertTrue(so.isNucleotideMatch("nucleotide_match"));
  67     assertTrue(so.isNucleotideMatch("primer_match"));
  68     assertTrue(so.isNucleotideMatch("cross_genome_match"));
  69     assertTrue(so.isNucleotideMatch("expressed_sequence_match"));
  70     assertTrue(so.isNucleotideMatch("translated_nucleotide_match"));
  71     assertTrue(so.isNucleotideMatch("UST_match"));
  72     assertTrue(so.isNucleotideMatch("RST_match"));
  73     assertTrue(so.isNucleotideMatch("cDNA_match"));
  74     assertTrue(so.isNucleotideMatch("EST_match"));
  75     assertFalse(so.isNucleotideMatch("match")); // parent
  76   }
  77
  78   @Test(groups = "Functional")
  79   public void testIsCDS()
  80   {
  81     assertTrue(so.isA("CDS", "CDS"));
  82     assertTrue(so.isA("CDS_predicted", "CDS"));
  83     assertTrue(so.isA("transposable_element_CDS", "CDS"));
  84     assertTrue(so.isA("edited_CDS", "CDS"));
  85     assertTrue(so.isA("CDS_independently_known", "CDS"));
  86     assertTrue(so.isA("CDS_fragment", "CDS"));
  87     assertFalse(so.isA("CDS_region", "CDS"));// part_of
  88     assertFalse(so.isA("polypeptide", "CDS")); // derives_from
  89   }
  90 }