package jalview.util;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.fail;

import java.util.List;

import org.testng.annotations.Test;

public class DnaUtilsTest
{
  /**
   * Tests for parsing an ENA/GenBank location specifier
   * 
   * @see http://www.insdc.org/files/feature_table.html#3.4
   */
  @Test(groups = { "Functional" })
  public void testParseLocation()
  {
    /*
     * simple range
     */
    List<int[]> ranges = DnaUtils.parseLocation("12..78");
    assertEquals(1, ranges.size());
    assertEquals(12, ranges.get(0)[0]);
    assertEquals(78, ranges.get(0)[1]);

    /*
     * join of simple ranges
     */
    ranges = DnaUtils.parseLocation("join(12..78,134..202,322..345)");
    assertEquals(3, ranges.size());
    assertEquals(12, ranges.get(0)[0]);
    assertEquals(78, ranges.get(0)[1]);
    assertEquals(134, ranges.get(1)[0]);
    assertEquals(202, ranges.get(1)[1]);
    assertEquals(322, ranges.get(2)[0]);
    assertEquals(345, ranges.get(2)[1]);

    /*
     * complement of a simple range
     */
    ranges = DnaUtils.parseLocation("complement(34..126)");
    assertEquals(1, ranges.size());
    assertEquals(126, ranges.get(0)[0]);
    assertEquals(34, ranges.get(0)[1]);

    /*
     * complement of a join
     */
    ranges = DnaUtils
            .parseLocation("complement(join(2691..4571,4918..5163))");
    assertEquals(2, ranges.size());
    assertEquals(5163, ranges.get(0)[0]);
    assertEquals(4918, ranges.get(0)[1]);
    assertEquals(4571, ranges.get(1)[0]);
    assertEquals(2691, ranges.get(1)[1]);

    /*
     * join of two complements
     */
    ranges = DnaUtils
            .parseLocation("join(complement(4918..5163),complement(2691..4571))");
    assertEquals(2, ranges.size());
    assertEquals(5163, ranges.get(0)[0]);
    assertEquals(4918, ranges.get(0)[1]);
    assertEquals(4571, ranges.get(1)[0]);
    assertEquals(2691, ranges.get(1)[1]);

    /*
     * join complement to non-complement
     * @see http://www.ncbi.nlm.nih.gov/genbank/genomesubmit_annotation/ Transpliced Genes
     */
    ranges = DnaUtils
            .parseLocation("join(complement(36618..36700),86988..87064)");
    assertEquals(2, ranges.size());
    assertEquals(36700, ranges.get(0)[0]);
    assertEquals(36618, ranges.get(0)[1]);
    assertEquals(86988, ranges.get(1)[0]);
    assertEquals(87064, ranges.get(1)[1]);

    /*
     * valid things we don't yet handle
     */
    assertNull(DnaUtils.parseLocation("<34..126"));
    assertNull(DnaUtils.parseLocation("34..>126"));
    assertNull(DnaUtils.parseLocation("34.126"));
    assertNull(DnaUtils.parseLocation("34^126"));

    /*
     * invalid things
     */
    assertNull(DnaUtils.parseLocation(""));
    assertNull(DnaUtils.parseLocation("JOIN(1..2)"));
    assertNull(DnaUtils.parseLocation("join(1..2"));
    try
    {
      assertNull(DnaUtils.parseLocation(null));
      fail("Expected exception");
    } catch (NullPointerException e)
    {
      // expected
    }
  }

}