package jalview.datamodel.xdb.embl;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertSame;

import jalview.util.MappingUtils;

import java.util.Arrays;
import java.util.Vector;

import org.testng.annotations.Test;

public class EmblEntryTest
{
  @Test(groups = "Functional")
  public void testGetCdsRanges()
  {
    EmblEntry testee = new EmblEntry();

    /*
     * Make a (CDS) Feature with 4 locations
     */
    EmblFeature cds = new EmblFeature();
    Vector<EmblFeatureLocations> locs = new Vector<EmblFeatureLocations>();
    cds.setLocations(locs);

    /*
     * single range [10-20]
     */
    EmblFeatureLocations loc = new EmblFeatureLocations();
    loc.setLocationType("single");
    loc.setLocationComplement(false);
    Vector<EmblFeatureLocElement> elements = new Vector<EmblFeatureLocElement>();
    EmblFeatureLocElement locElement = new EmblFeatureLocElement();
    BasePosition b1 = new BasePosition();
    b1.setPos("10");
    BasePosition b2 = new BasePosition();
    b2.setPos("20");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    loc.setLocElements(elements);
    locs.add(loc);

    /*
     * complement range [30-40]
     */
    loc = new EmblFeatureLocations();
    loc.setLocationType("single");
    loc.setLocationComplement(true);
    elements = new Vector<EmblFeatureLocElement>();
    locElement = new EmblFeatureLocElement();
    b1 = new BasePosition();
    b1.setPos("30");
    b2 = new BasePosition();
    b2.setPos("40");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    loc.setLocElements(elements);
    locs.add(loc);

    /*
     * join range [50-60], [70-80]
     */
    loc = new EmblFeatureLocations();
    loc.setLocationType("join");
    loc.setLocationComplement(false);
    elements = new Vector<EmblFeatureLocElement>();
    locElement = new EmblFeatureLocElement();
    b1 = new BasePosition();
    b1.setPos("50");
    b2 = new BasePosition();
    b2.setPos("60");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    locElement = new EmblFeatureLocElement();
    b1 = new BasePosition();
    b1.setPos("70");
    b2 = new BasePosition();
    b2.setPos("80");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    loc.setLocElements(elements);
    locs.add(loc);

    /*
     * complement range [90-100], [110-120]
     * this should be the same as complement(join(90..100,110.120))
     * which is "join 90-100 and 110-120, then complement"
     */
    loc = new EmblFeatureLocations();
    loc.setLocationType("join");
    loc.setLocationComplement(true);
    elements = new Vector<EmblFeatureLocElement>();
    locElement = new EmblFeatureLocElement();
    b1 = new BasePosition();
    b1.setPos("90");
    b2 = new BasePosition();
    b2.setPos("100");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    locElement = new EmblFeatureLocElement();
    b1 = new BasePosition();
    b1.setPos("110");
    b2 = new BasePosition();
    b2.setPos("120");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    loc.setLocElements(elements);
    locs.add(loc);

    int[] exons = testee.getCdsRanges(cds);
    assertEquals("[10, 20, 40, 30, 50, 60, 70, 80, 120, 110, 100, 90]",
            Arrays.toString(exons));
  }

  @Test(groups = "Functional")
  public void testGetCdsRanges_badData()
  {
    EmblEntry testee = new EmblEntry();

    /*
     * Make a (CDS) Feature with 4 locations
     */
    EmblFeature cds = new EmblFeature();
    Vector<EmblFeatureLocations> locs = new Vector<EmblFeatureLocations>();
    cds.setLocations(locs);

    /*
     * single range [10-20]
     */
    EmblFeatureLocations loc = new EmblFeatureLocations();
    loc.setLocationType("single");
    loc.setLocationComplement(false);
    Vector<EmblFeatureLocElement> elements = new Vector<EmblFeatureLocElement>();
    EmblFeatureLocElement locElement = new EmblFeatureLocElement();
    BasePosition b1 = new BasePosition();
    b1.setPos("10");
    BasePosition b2 = new BasePosition();
    b2.setPos("20");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    loc.setLocElements(elements);
    locs.add(loc);

    /*
     * single range with missing end position - should be skipped
     */
    loc = new EmblFeatureLocations();
    loc.setLocationType("single");
    loc.setLocationComplement(false);
    elements = new Vector<EmblFeatureLocElement>();
    locElement = new EmblFeatureLocElement();
    b1 = new BasePosition();
    b1.setPos("30");
    locElement.setBasePositions(new BasePosition[] { b1 });
    elements.add(locElement);
    loc.setLocElements(elements);
    locs.add(loc);

    /*
     * single range with extra base position - should be skipped
     */
    loc = new EmblFeatureLocations();
    loc.setLocationType("single");
    loc.setLocationComplement(false);
    elements = new Vector<EmblFeatureLocElement>();
    locElement = new EmblFeatureLocElement();
    b1 = new BasePosition();
    b1.setPos("30");
    locElement.setBasePositions(new BasePosition[] { b1, b1, b1 });
    elements.add(locElement);
    loc.setLocElements(elements);
    locs.add(loc);

    /*
     * single valid range [50-60] to finish
     */
    loc = new EmblFeatureLocations();
    loc.setLocationType("single");
    loc.setLocationComplement(false);
    elements = new Vector<EmblFeatureLocElement>();
    locElement = new EmblFeatureLocElement();
    b1 = new BasePosition();
    b1.setPos("50");
    b2 = new BasePosition();
    b2.setPos("60");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    loc.setLocElements(elements);
    locs.add(loc);

    int[] exons = testee.getCdsRanges(cds);
    assertEquals("[10, 20, 50, 60]", Arrays.toString(exons));
  }

  /**
   * Test retrieval of exon locations matching an accession id
   */
  @Test(groups = "Functional")
  public void testGetCdsRanges_forAccession()
  {
    EmblEntry testee = new EmblEntry();
    String accession = "A1234";
    testee.setAccession(accession);
    /*
     * Make a (CDS) Feature with 4 locations
     */
    EmblFeature cds = new EmblFeature();
    Vector<EmblFeatureLocations> locs = new Vector<EmblFeatureLocations>();
    cds.setLocations(locs);
  
    /*
     * single range [10-20] for 'this' accession
     */
    EmblFeatureLocations loc = new EmblFeatureLocations();
    loc.setLocationType("single");
    loc.setLocationComplement(false);
    Vector<EmblFeatureLocElement> elements = new Vector<EmblFeatureLocElement>();
    EmblFeatureLocElement locElement = new EmblFeatureLocElement();
    locElement.setAccession(accession);
    BasePosition b1 = new BasePosition();
    b1.setPos("10");
    BasePosition b2 = new BasePosition();
    b2.setPos("20");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    loc.setLocElements(elements);
    locs.add(loc);
  
    /*
     * complement range [30-40] - no accession
     */
    loc = new EmblFeatureLocations();
    loc.setLocationType("single");
    loc.setLocationComplement(true);
    elements = new Vector<EmblFeatureLocElement>();
    locElement = new EmblFeatureLocElement();
    b1 = new BasePosition();
    b1.setPos("30");
    b2 = new BasePosition();
    b2.setPos("40");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    loc.setLocElements(elements);
    locs.add(loc);
  
    /*
     * join range [50-60] this accession, [70-80] another
     */
    loc = new EmblFeatureLocations();
    loc.setLocationType("join");
    loc.setLocationComplement(false);
    elements = new Vector<EmblFeatureLocElement>();
    locElement = new EmblFeatureLocElement();
    locElement.setAccession(accession);
    b1 = new BasePosition();
    b1.setPos("50");
    b2 = new BasePosition();
    b2.setPos("60");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    locElement = new EmblFeatureLocElement();
    locElement.setAccession("notme");
    b1 = new BasePosition();
    b1.setPos("70");
    b2 = new BasePosition();
    b2.setPos("80");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    loc.setLocElements(elements);
    locs.add(loc);
  
    /*
     * complement range [90-100] wrong accession, [110-120] good 
     * this should be the same as complement(join(90..100,110.120))
     * which is "join 90-100 and 110-120, then complement"
     */
    loc = new EmblFeatureLocations();
    loc.setLocationType("join");
    loc.setLocationComplement(true);
    elements = new Vector<EmblFeatureLocElement>();
    locElement = new EmblFeatureLocElement();
    locElement.setAccession("wrong");
    b1 = new BasePosition();
    b1.setPos("90");
    b2 = new BasePosition();
    b2.setPos("100");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    locElement = new EmblFeatureLocElement();
    locElement.setAccession(accession);
    b1 = new BasePosition();
    b1.setPos("110");
    b2 = new BasePosition();
    b2.setPos("120");
    locElement.setBasePositions(new BasePosition[] { b1, b2 });
    elements.add(locElement);
    loc.setLocElements(elements);
    locs.add(loc);
  
    /*
     * verify we pick out only ranges for A1234
     */
    int[] exons = testee.getCdsRanges(cds);
    assertEquals("[10, 20, 50, 60, 120, 110]",
            Arrays.toString(exons));
  }
}