package jalview.io.gff;

import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;

import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;

public class SequenceOntologyTest
{
  private SequenceOntology so;

  @BeforeMethod
  public void setUp() {
    so = SequenceOntology.getInstance();
  }

  @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 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"));
    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
  }
}