1 package jalview.io.gff;
3 import static org.testng.AssertJUnit.assertFalse;
4 import static org.testng.AssertJUnit.assertTrue;
6 import org.testng.annotations.BeforeMethod;
7 import org.testng.annotations.Test;
9 public class SequenceOntologyTest
11 private SequenceOntology so;
15 so = SequenceOntology.getInstance();
18 @Test(groups = "Functional")
21 assertTrue(so.isA("SO:0000087", "SO:0000704"));
22 assertFalse(so.isA("SO:0000704", "SO:0000087"));
23 assertTrue(so.isA("SO:0000736", "SO:0000735"));
26 assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
28 assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
30 assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
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"));
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"));
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"));
49 @Test(groups = "Functional")
50 public void testIsProteinMatch()
52 assertTrue(so.isProteinMatch("protein_match"));
53 assertTrue(so.isProteinMatch("protein_hmm_match"));
54 assertFalse(so.isProteinMatch("Protein_match")); // case-sensitive
57 @Test(groups = "Functional")
58 public void testIsNucleotideMatch()
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
72 @Test(groups = "Functional")
73 public void testIsCDS()
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