package jalview.io.gff;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertTrue;

import jalview.datamodel.ontology.OntologyI;

import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;

public class SequenceOntologyLiteTest
{
  private OntologyI so;

  @BeforeClass(alwaysRun = true)
  public void setUp()
  {
    so = new SequenceOntologyLite();
  }

  @Test(groups = "Functional")
  public void testIsA_sequenceVariant()
  {
    assertFalse(so.isA("CDS", "sequence_variant"));
    assertTrue(so.isA("sequence_variant", "sequence_variant"));

    /*
     * these should all be sub-types of sequence_variant
     */
    assertTrue(so.isA("structural_variant", "sequence_variant"));
    assertTrue(so.isA("feature_variant", "sequence_variant"));
    assertTrue(so.isA("gene_variant", "sequence_variant"));
    assertTrue(so.isA("transcript_variant", "sequence_variant"));
    assertTrue(so.isA("NMD_transcript_variant", "sequence_variant"));
    assertTrue(so.isA("missense_variant", "sequence_variant"));
    assertTrue(so.isA("synonymous_variant", "sequence_variant"));
    assertTrue(so.isA("frameshift_variant", "sequence_variant"));
    assertTrue(so.isA("5_prime_UTR_variant", "sequence_variant"));
    assertTrue(so.isA("3_prime_UTR_variant", "sequence_variant"));
    assertTrue(so.isA("stop_gained", "sequence_variant"));
    assertTrue(so.isA("stop_lost", "sequence_variant"));
    assertTrue(so.isA("inframe_deletion", "sequence_variant"));
    assertTrue(so.isA("inframe_insertion", "sequence_variant"));
    assertTrue(so.isA("splice_region_variant", "sequence_variant"));
  }

  @Test(groups = "Functional")
  public void testGetParentTerms()
  {
    Set<String> terms = new HashSet<>();
    terms.add("sequence_variant");
    terms.add("NMD_transcript_variant");
    terms.add("stop_lost");
    terms.add("chain"); // not an SO term
  
    Set<String> parents = so.getParentTerms(terms);
    assertEquals(parents.size(), 2);
    assertTrue(parents.contains("sequence_variant"));
    assertTrue(parents.contains("chain"));
  }

  @Test(groups = "Functional")
  public void testGetChildTerms()
  {
    List<String> terms = Collections.<String> emptyList();
    List<String> children = so.getChildTerms("exon", terms);
    assertTrue(children.isEmpty());

    terms = Arrays.asList("gene", "transcript", "snRNA", "junk", "mRNA");
    children = so.getChildTerms("exon", terms);
    assertTrue(children.isEmpty());
    children = so.getChildTerms("transcript", terms);
    assertEquals(children.size(), 2);
    assertTrue(children.contains("snRNA"));
    assertTrue(children.contains("mRNA"));

    terms = Arrays.asList("gene", "transcript", "synonymous_variant",
            "stop_lost", "chain");
    children = so.getChildTerms("sequence_variant", terms);
    assertEquals(children.size(), 2);
    assertTrue(children.contains("synonymous_variant"));
    assertTrue(children.contains("stop_lost"));
  }
}