JAL-1705 JAL-1191 SequenceOntologyLite added as hard-coded alternative

[jalview.git] / test / jalview / io / gff / SequenceOntologyTest.java

diff --git a/test/jalview/io/gff/SequenceOntologyTest.java b/test/jalview/io/gff/SequenceOntologyTest.java
index 6c9226f..f791a1e 100644 (file)
--- a/test/jalview/io/gff/SequenceOntologyTest.java
+++ b/test/jalview/io/gff/SequenceOntologyTest.java
@@ -8,12 +8,12 @@ import org.testng.annotations.Test;
 
 public class SequenceOntologyTest
 {
-  private SequenceOntology so;
+  private SequenceOntologyI so;
 
   @BeforeMethod
   public void setUp() {
     long now = System.currentTimeMillis();
-    so = SequenceOntology.getInstance();
+    so = SequenceOntologyFactory.getInstance();
     long elapsed = System.currentTimeMillis() - now;
     System.out.println("Load and cache of Sequence Ontology took "
             + elapsed + "ms");
@@ -57,29 +57,6 @@ public class SequenceOntologyTest
   }
 
   @Test(groups = "Functional")
-  public void testIsProteinMatch()
-  {
-    assertTrue(so.isProteinMatch("protein_match"));
-    assertTrue(so.isProteinMatch("protein_hmm_match"));
-    assertFalse(so.isProteinMatch("Protein_match")); // case-sensitive
-  }
-
-  @Test(groups = "Functional")
-  public void testIsNucleotideMatch()
-  {
-    assertTrue(so.isNucleotideMatch("nucleotide_match"));
-    assertTrue(so.isNucleotideMatch("primer_match"));
-    assertTrue(so.isNucleotideMatch("cross_genome_match"));
-    assertTrue(so.isNucleotideMatch("expressed_sequence_match"));
-    assertTrue(so.isNucleotideMatch("translated_nucleotide_match"));
-    assertTrue(so.isNucleotideMatch("UST_match"));
-    assertTrue(so.isNucleotideMatch("RST_match"));
-    assertTrue(so.isNucleotideMatch("cDNA_match"));
-    assertTrue(so.isNucleotideMatch("EST_match"));
-    assertFalse(so.isNucleotideMatch("match")); // parent
-  }
-
-  @Test(groups = "Functional")
   public void testIsCDS()
   {
     assertTrue(so.isA("CDS", "CDS"));