package jalview.analysis;

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

import java.util.Arrays;

import org.testng.annotations.Test;

public class CodingUtilsTest
{

  @Test(groups ={ "Functional" })
  public void testDecodeCodon()
  {
    assertTrue(Arrays.equals(new char[]
    { 'A', 'A', 'A' }, CodingUtils.decodeCodon(0)));
    assertTrue(Arrays.equals(new char[]
    { 'A', 'A', 'C' }, CodingUtils.decodeCodon(1)));
    assertTrue(Arrays.equals(new char[]
    { 'A', 'A', 'G' }, CodingUtils.decodeCodon(2)));
    assertTrue(Arrays.equals(new char[]
    { 'A', 'A', 'T' }, CodingUtils.decodeCodon(3)));
    assertTrue(Arrays.equals(new char[]
    { 'A', 'C', 'A' }, CodingUtils.decodeCodon(4)));
    assertTrue(Arrays.equals(new char[]
    { 'C', 'A', 'A' }, CodingUtils.decodeCodon(16)));
    assertTrue(Arrays.equals(new char[]
    { 'G', 'G', 'G' }, CodingUtils.decodeCodon(42)));
    assertTrue(Arrays.equals(new char[]
    { 'T', 'T', 'T' }, CodingUtils.decodeCodon(63)));
  }

  @Test(groups ={ "Functional" })
  public void testDecodeNucleotide()
  {
    assertEquals('A', CodingUtils.decodeNucleotide(0));
    assertEquals('C', CodingUtils.decodeNucleotide(1));
    assertEquals('G', CodingUtils.decodeNucleotide(2));
    assertEquals('T', CodingUtils.decodeNucleotide(3));
    assertEquals('0', CodingUtils.decodeNucleotide(4));
  }

  @Test(groups ={ "Functional" })
  public void testEncodeCodon()
  {
    assertTrue(CodingUtils.encodeCodon('Z') < 0);
    assertEquals(0, CodingUtils.encodeCodon('a'));
    assertEquals(0, CodingUtils.encodeCodon('A'));
    assertEquals(1, CodingUtils.encodeCodon('c'));
    assertEquals(1, CodingUtils.encodeCodon('C'));
    assertEquals(2, CodingUtils.encodeCodon('g'));
    assertEquals(2, CodingUtils.encodeCodon('G'));
    assertEquals(3, CodingUtils.encodeCodon('t'));
    assertEquals(3, CodingUtils.encodeCodon('T'));
    assertEquals(3, CodingUtils.encodeCodon('u'));
    assertEquals(3, CodingUtils.encodeCodon('U'));
    
    assertEquals(-1, CodingUtils.encodeCodon(null));
    assertEquals(0, CodingUtils.encodeCodon(new char[]
    { 'A', 'A', 'A' }));
    assertEquals(1, CodingUtils.encodeCodon(new char[]
    { 'A', 'A', 'C' }));
    assertEquals(2, CodingUtils.encodeCodon(new char[]
    { 'A', 'A', 'G' }));
    assertEquals(3, CodingUtils.encodeCodon(new char[]
    { 'A', 'A', 'T' }));
    assertEquals(4, CodingUtils.encodeCodon(new char[]
    { 'A', 'C', 'A' }));
    assertEquals(16, CodingUtils.encodeCodon(new char[]
    { 'C', 'A', 'A' }));
    assertEquals(42, CodingUtils.encodeCodon(new char[]
    { 'G', 'G', 'G' }));
    assertEquals(63, CodingUtils.encodeCodon(new char[]
    { 'T', 'T', 'T' }));
  }

}