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     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", "micronuclear_sequence"));
  34     assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
  35     assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
  36     assertTrue(so.isA("SO:0000084", "SO:0000084"));
  37
  38     // SO name to description:
  39     assertTrue(so.isA("SO:0000084", "organelle_sequence"));
  40     assertTrue(so.isA("SO:0000084", "sequence_location"));
  41     assertTrue(so.isA("SO:0000084", "sequence_attribute"));
  42
  43     // description to SO name:
  44     assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
  45     assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
  46     assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
  47   }
  48
  49   @Test(groups = "Functional")
  50   public void testIsProteinMatch()
  51   {
  52     assertTrue(so.isProteinMatch("protein_match"));
  53     assertTrue(so.isProteinMatch("protein_hmm_match"));
  54     assertFalse(so.isProteinMatch("Protein_match")); // case-sensitive
  55   }
  56
  57   @Test(groups = "Functional")
  58   public void testIsNucleotideMatch()
  59   {
  60     assertTrue(so.isNucleotideMatch("nucleotide_match"));
  61     assertTrue(so.isNucleotideMatch("primer_match"));
  62     assertTrue(so.isNucleotideMatch("cross_genome_match"));
  63     assertTrue(so.isNucleotideMatch("expressed_sequence_match"));
  64     assertTrue(so.isNucleotideMatch("translated_nucleotide_match"));
  65     assertTrue(so.isNucleotideMatch("UST_match"));
  66     assertTrue(so.isNucleotideMatch("RST_match"));
  67     assertTrue(so.isNucleotideMatch("cDNA_match"));
  68     assertTrue(so.isNucleotideMatch("EST_match"));
  69     assertFalse(so.isNucleotideMatch("match")); // parent
  70   }
  71
  72   @Test(groups = "Functional")
  73   public void testIsCDS()
  74   {
  75     assertTrue(so.isA("CDS", "CDS"));
  76     assertTrue(so.isA("CDS_predicted", "CDS"));
  77     assertTrue(so.isA("transposable_element_CDS", "CDS"));
  78     assertTrue(so.isA("edited_CDS", "CDS"));
  79     assertTrue(so.isA("CDS_independently_known", "CDS"));
  80     assertTrue(so.isA("CDS_fragment", "CDS"));
  81     assertFalse(so.isA("CDS_region", "CDS"));// part_of
  82     assertFalse(so.isA("polypeptide", "CDS")); // derives_from
  83   }
  84 }