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     long now = System.currentTimeMillis();
  16     so = SequenceOntology.getInstance();
  17     long elapsed = System.currentTimeMillis() - now;
  18     System.out.println("Load and cache of Sequence Ontology took "
  19             + elapsed + "ms");
  20   }
  21
  22   @Test(groups = "Functional")
  23   public void testIsA()
  24   {
  25     assertFalse(so.isA(null, null));
  26     assertFalse(so.isA(null, "SO:0000087"));
  27     assertFalse(so.isA("SO:0000087", null));
  28     assertFalse(so.isA("complete", "garbage"));
  29
  30     assertTrue(so.isA("SO:0000087", "SO:0000704"));
  31     assertFalse(so.isA("SO:0000704", "SO:0000087"));
  32     assertTrue(so.isA("SO:0000736", "SO:0000735"));
  33
  34     // same thing:
  35     assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
  36     // direct parent:
  37     assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
  38     // grandparent:
  39     assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
  40     // great-grandparent:
  41     assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
  42
  43     // same thing by name / description:
  44     assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
  45     assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
  46     assertTrue(so.isA("SO:0000084", "SO:0000084"));
  47
  48     // SO name to description:
  49     assertTrue(so.isA("SO:0000084", "organelle_sequence"));
  50     assertTrue(so.isA("SO:0000084", "sequence_location"));
  51     assertTrue(so.isA("SO:0000084", "sequence_attribute"));
  52
  53     // description to SO name:
  54     assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
  55     assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
  56     assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
  57   }
  58
  59   @Test(groups = "Functional")
  60   public void testIsProteinMatch()
  61   {
  62     assertTrue(so.isProteinMatch("protein_match"));
  63     assertTrue(so.isProteinMatch("protein_hmm_match"));
  64     assertFalse(so.isProteinMatch("Protein_match")); // case-sensitive
  65   }
  66
  67   @Test(groups = "Functional")
  68   public void testIsNucleotideMatch()
  69   {
  70     assertTrue(so.isNucleotideMatch("nucleotide_match"));
  71     assertTrue(so.isNucleotideMatch("primer_match"));
  72     assertTrue(so.isNucleotideMatch("cross_genome_match"));
  73     assertTrue(so.isNucleotideMatch("expressed_sequence_match"));
  74     assertTrue(so.isNucleotideMatch("translated_nucleotide_match"));
  75     assertTrue(so.isNucleotideMatch("UST_match"));
  76     assertTrue(so.isNucleotideMatch("RST_match"));
  77     assertTrue(so.isNucleotideMatch("cDNA_match"));
  78     assertTrue(so.isNucleotideMatch("EST_match"));
  79     assertFalse(so.isNucleotideMatch("match")); // parent
  80   }
  81
  82   @Test(groups = "Functional")
  83   public void testIsCDS()
  84   {
  85     assertTrue(so.isA("CDS", "CDS"));
  86     assertTrue(so.isA("CDS_predicted", "CDS"));
  87     assertTrue(so.isA("transposable_element_CDS", "CDS"));
  88     assertTrue(so.isA("edited_CDS", "CDS"));
  89     assertTrue(so.isA("CDS_independently_known", "CDS"));
  90     assertTrue(so.isA("CDS_fragment", "CDS"));
  91     assertFalse(so.isA("CDS_region", "CDS"));// part_of
  92     assertFalse(so.isA("polypeptide", "CDS")); // derives_from
  93   }
  94 }