package jalview.analysis;

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

import jalview.analysis.ResidueCount.SymbolCounts;

import org.junit.Assert;
import org.testng.annotations.Test;

public class ResidueCountTest
{
  /**
   * Test a mix of add and put for nucleotide counting
   */
  @Test(groups = "Functional")
  public void test_countNucleotide()
  {
    ResidueCount rc = new ResidueCount(true);
    assertEquals(rc.getCount('A'), 0);
    assertEquals(rc.getGapCount(), 0);
    // add then add
    assertEquals(rc.add('A'), 1);
    assertEquals(rc.add('a'), 2);
    // put then add
    rc.put('g', 3);
    assertEquals(rc.add('G'), 4);
    // add then put
    assertEquals(rc.add('c'), 1);
    rc.put('C', 4);
    assertEquals(rc.add('N'), 1);

    assertEquals(rc.getCount('a'), 2);
    assertEquals(rc.getCount('A'), 2);
    assertEquals(rc.getCount('G'), 4);
    assertEquals(rc.getCount('c'), 4);
    assertEquals(rc.getCount('T'), 0); // never seen
    assertEquals(rc.getCount('N'), 1);
    assertEquals(rc.getCount('?'), 0);
    assertEquals(rc.getCount('-'), 0);

    assertFalse(rc.isCountingInts());
    assertFalse(rc.isUsingOtherData());
  }

  /**
   * Test adding to gap count (either using addGap or add)
   */
  @Test(groups = "Functional")
  public void testAddGap()
  {
    ResidueCount rc = new ResidueCount(true);
    rc.addGap();
    rc.add('-');
    rc.add('.');
    rc.add(' ');
    
    assertEquals(rc.getGapCount(), 4);
    assertEquals(rc.getCount(' '), 4);
    assertEquals(rc.getCount('-'), 4);
    assertEquals(rc.getCount('.'), 4);
    assertFalse(rc.isUsingOtherData());
    assertFalse(rc.isCountingInts());
  }

  @Test(groups = "Functional")
  public void testOverflow()
  {
    /*
     * overflow from add
     */
    ResidueCount rc = new ResidueCount(true);
    rc.put('A', Short.MAX_VALUE - 1);
    assertFalse(rc.isCountingInts());
    rc.add('A');
    assertFalse(rc.isCountingInts());
    rc.add('A');
    assertTrue(rc.isCountingInts());
    assertEquals(rc.getCount('a'), Short.MAX_VALUE + 1);

    /*
     * overflow from put
     */
    rc = new ResidueCount(true);
    rc.put('G', Short.MAX_VALUE + 1);
    assertTrue(rc.isCountingInts());
    assertEquals(rc.getCount('g'), Short.MAX_VALUE + 1);
  }

  /**
   * Test a mix of add and put for peptide counting
   */
  @Test(groups = "Functional")
  public void test_countPeptide()
  {
    ResidueCount rc = new ResidueCount(false);
    rc.put('q', 4);
    rc.add('Q');
    rc.add('X');
    rc.add('x');
    rc.add('W');
    rc.put('w', 7);
    rc.put('m', 12);
    rc.put('M', 13);

    assertEquals(rc.getCount('q'), 5);
    assertEquals(rc.getCount('X'), 2);
    assertEquals(rc.getCount('W'), 7);
    assertEquals(rc.getCount('m'), 13);
    assertEquals(rc.getCount('G'), 0);
    assertEquals(rc.getCount('-'), 0);

    assertFalse(rc.isCountingInts());
    assertFalse(rc.isUsingOtherData());
  }

  @Test(groups = "Functional")
  public void test_unexpectedPeptide()
  {
    ResidueCount rc = new ResidueCount(false);
    // expected characters (upper or lower case):
    String aas = "ACDEFGHIKLMNPQRSTVWXY";
    String lower = aas.toLowerCase();
    for (int i = 0; i < aas.length(); i++)
    {
      rc.put(aas.charAt(i), i);
      rc.add(lower.charAt(i));
    }
    for (int i = 0; i < aas.length(); i++)
    {
      assertEquals(rc.getCount(aas.charAt(i)), i + 1);
    }
    assertFalse(rc.isUsingOtherData());

    rc.put('J', 4);
    assertTrue(rc.isUsingOtherData());
  }

  @Test(groups = "Functional")
  public void test_unexpectedNucleotide()
  {
    ResidueCount rc = new ResidueCount(true);
    // expected characters (upper or lower case):
    String nucs = "ACGTUN";
    String lower = nucs.toLowerCase();
    for (int i = 0; i < nucs.length(); i++)
    {
      rc.put(nucs.charAt(i), i);
      rc.add(lower.charAt(i));
    }
    for (int i = 0; i < nucs.length(); i++)
    {
      assertEquals(rc.getCount(nucs.charAt(i)), i + 1);
    }
    assertFalse(rc.isUsingOtherData());

    rc.add('J');
    assertTrue(rc.isUsingOtherData());
  }

  @Test(groups = "Functional")
  public void testGetModalCount()
  {
    ResidueCount rc = new ResidueCount();
    rc.add('c');
    rc.add('g');
    rc.add('c');
    assertEquals(rc.getModalCount(), 2);

    // modal count is in the 'short overflow' counts
    rc = new ResidueCount();
    rc.add('c');
    rc.put('g', Short.MAX_VALUE);
    rc.add('G');
    assertEquals(rc.getModalCount(), Short.MAX_VALUE + 1);

    // modal count is in the 'other data' counts
    rc = new ResidueCount();
    rc.add('Q');
    rc.add('{');
    rc.add('{');
    assertEquals(rc.getModalCount(), 2);

    // verify modal count excludes gap
    rc = new ResidueCount();
    rc.add('Q');
    rc.add('P');
    rc.add('Q');
    rc.addGap();
    rc.addGap();
    rc.addGap();
    assertEquals(rc.getModalCount(), 2);
  }

  @Test(groups = "Functional")
  public void testGetResiduesForCount()
  {
    ResidueCount rc = new ResidueCount();
    rc.add('c');
    rc.add('g');
    rc.add('c');
    assertEquals(rc.getResiduesForCount(2), "C");
    assertEquals(rc.getResiduesForCount(1), "G");
    assertEquals(rc.getResiduesForCount(3), "");
    assertEquals(rc.getResiduesForCount(0), "");
    assertEquals(rc.getResiduesForCount(-1), "");

    // modal count is in the 'short overflow' counts
    rc = new ResidueCount();
    rc.add('c');
    rc.put('g', Short.MAX_VALUE);
    rc.add('G');
    assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "G");
    assertEquals(rc.getResiduesForCount(1), "C");
  
    // modal count is in the 'other data' counts
    rc = new ResidueCount();
    rc.add('Q');
    rc.add('{');
    rc.add('{');
    assertEquals(rc.getResiduesForCount(1), "Q");
    assertEquals(rc.getResiduesForCount(2), "{");

    // residues share modal count
    rc = new ResidueCount();
    rc.add('G');
    rc.add('G');
    rc.add('c');
    rc.add('C');
    rc.add('U');
    assertEquals(rc.getResiduesForCount(1), "U");
    assertEquals(rc.getResiduesForCount(2), "CG");

    // expected and unexpected symbols share modal count
    rc = new ResidueCount();
    rc.add('G');
    rc.add('t');
    rc.add('[');
    rc.add('[');
    rc.add('t');
    rc.add('G');
    rc.add('c');
    rc.add('C');
    rc.add('U');
    assertEquals(rc.getResiduesForCount(1), "U");
    assertEquals(rc.getResiduesForCount(2), "CGT[");
  }

  @Test(groups = "Functional")
  public void testGetSymbolCounts()
  {
    ResidueCount rc = new ResidueCount();
    rc.add('q');
    rc.add('c');
    rc.add('Q');
    rc.add('J'); // 'otherData'
    rc.add('q');
    rc.add('x');

    SymbolCounts sc = rc.getSymbolCounts();
    Assert.assertArrayEquals(new char[] { 'C', 'Q', 'X', 'J' }, sc.symbols);
    Assert.assertArrayEquals(new int[] { 1, 3, 1, 1 }, sc.values);

    // now with overflow to int counts
    rc.put('g', Short.MAX_VALUE);
    rc.add('g');
    sc = rc.getSymbolCounts();
    Assert.assertArrayEquals(new char[] { 'C', 'G', 'Q', 'X', 'J' },
            sc.symbols);
    Assert.assertArrayEquals(new int[] { 1, 32768, 3, 1, 1 }, sc.values);
  }

  @Test(groups = "Functional")
  public void testToString()
  {
    ResidueCount rc = new ResidueCount();
    rc.add('q');
    rc.add('c');
    rc.add('Q');
    assertEquals(rc.toString(), "[ C:1 Q:2 ]");

    // add 'other data'
    rc.add('{');
    assertEquals(rc.toString(), "[ C:1 Q:2 {:1 ]");

    // switch from short to int counting:
    rc.put('G', Short.MAX_VALUE);
    rc.add('g');
    assertEquals(rc.toString(), "[ C:1 G:32768 Q:2 {:1 ]");
  }
}