JAL-1191 isolated SequenceOntology (BioJava wrapper) to /ext/so folder

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

diff --git a/test/jalview/io/gff/SequenceOntologyTest.java b/test/jalview/io/gff/SequenceOntologyTest.java
deleted file mode 100644 (file)
index 0b72515..0000000
--- a/test/jalview/io/gff/SequenceOntologyTest.java
+++ /dev/null
@@ -1,79 +0,0 @@
-package jalview.io.gff;
-
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertTrue;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class SequenceOntologyTest
-{
-  private SequenceOntologyI so;
-
-  @BeforeClass
-  public void setUp() {
-    long now = System.currentTimeMillis();
-    SequenceOntologyFactory.setInstance(new SequenceOntology());
-    long elapsed = System.currentTimeMillis() - now;
-    System.out.println("Load and cache of Sequence Ontology took "
-            + elapsed + "ms");
-    so = SequenceOntologyFactory.getInstance();
-  }
-
-  @AfterClass
-  public void tearDown()
-  {
-    SequenceOntologyFactory.setInstance(null);
-  }
-
-  @Test(groups = "Functional")
-  public void testIsA()
-  {
-    assertFalse(so.isA(null, null));
-    assertFalse(so.isA(null, "SO:0000087"));
-    assertFalse(so.isA("SO:0000087", null));
-    assertFalse(so.isA("complete", "garbage"));
-
-    assertTrue(so.isA("SO:0000087", "SO:0000704"));
-    assertFalse(so.isA("SO:0000704", "SO:0000087"));
-    assertTrue(so.isA("SO:0000736", "SO:0000735"));
-
-    // same thing:
-    assertTrue(so.isA("micronuclear_sequence", "micronuclear_sequence"));
-    // direct parent:
-    assertTrue(so.isA("micronuclear_sequence", "organelle_sequence"));
-    // grandparent:
-    assertTrue(so.isA("micronuclear_sequence", "sequence_location"));
-    // great-grandparent:
-    assertTrue(so.isA("micronuclear_sequence", "sequence_attribute"));
-
-    // same thing by name / description:
-    assertTrue(so.isA("micronuclear_sequence", "SO:0000084"));
-    assertTrue(so.isA("SO:0000084", "micronuclear_sequence"));
-    assertTrue(so.isA("SO:0000084", "SO:0000084"));
-
-    // SO name to description:
-    assertTrue(so.isA("SO:0000084", "organelle_sequence"));
-    assertTrue(so.isA("SO:0000084", "sequence_location"));
-    assertTrue(so.isA("SO:0000084", "sequence_attribute"));
-
-    // description to SO name:
-    assertTrue(so.isA("micronuclear_sequence", "SO:0000736"));
-    assertTrue(so.isA("micronuclear_sequence", "SO:0000735"));
-    assertTrue(so.isA("micronuclear_sequence", "SO:0000400"));
-  }
-
-  @Test(groups = "Functional")
-  public void testIsCDS()
-  {
-    assertTrue(so.isA("CDS", "CDS"));
-    assertTrue(so.isA("CDS_predicted", "CDS"));
-    assertTrue(so.isA("transposable_element_CDS", "CDS"));
-    assertTrue(so.isA("edited_CDS", "CDS"));
-    assertTrue(so.isA("CDS_independently_known", "CDS"));
-    assertTrue(so.isA("CDS_fragment", "CDS"));
-    assertFalse(so.isA("CDS_region", "CDS"));// part_of
-    assertFalse(so.isA("polypeptide", "CDS")); // derives_from
-  }
-}