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
  }
}