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 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"));
26 assertTrue(so.isA("SO:0000087", "SO:0000704"));
27 assertFalse(so.isA("SO:0000704", "SO:0000087"));
28 assertTrue(so.isA("SO:0000736", "SO:0000735"));
31 assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
33 assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
35 assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
37 assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
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"));
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"));
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"));
55 @Test(groups = "Functional")
56 public void testIsProteinMatch()
58 assertTrue(so.isProteinMatch("protein_match"));
59 assertTrue(so.isProteinMatch("protein_hmm_match"));
60 assertFalse(so.isProteinMatch("Protein_match")); // case-sensitive
63 @Test(groups = "Functional")
64 public void testIsNucleotideMatch()
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
78 @Test(groups = "Functional")
79 public void testIsCDS()
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