package jalview.analysis.scoremodels;

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

import java.io.ByteArrayInputStream;

import org.testng.annotations.Test;

public class ScoreMatrixTest
{
  @Test(groups = "Functional")
  public void testBuildSymbolIndex()
  {
    short[] index = ScoreMatrix.buildSymbolIndex("AX-. yxYp".toCharArray());

    assertEquals(index.length, 128); // ASCII character set size

    assertEquals(index['A'], 0);
    assertEquals(index['a'], 0); // lower-case mapping added
    assertEquals(index['X'], 1);
    assertEquals(index['-'], 2);
    assertEquals(index['.'], 3);
    assertEquals(index[' '], 4);
    assertEquals(index['y'], 5); // lower-case override
    assertEquals(index['x'], 6); // lower-case override
    assertEquals(index['Y'], 7);
    assertEquals(index['p'], 8);
    assertEquals(index['P'], -1); // lower-case doesn't map upper-case

    /*
     * check all unmapped symbols have index for unmapped
     */
    for (int c = 0; c < index.length; c++)
    {
      if (!"AaXx-. Yyp".contains(String.valueOf((char) c)))
      {
        assertEquals(index[c], -1);
      }
    }
  }

  /**
   * check that characters not in the basic ASCII set are simply ignored
   */
  @Test(groups = "Functional")
  public void testBuildSymbolIndex_nonAscii()
  {
    char[] weird = new char[] { 128, 245, 'P' };
    short[] index = ScoreMatrix.buildSymbolIndex(weird);
    assertEquals(index.length, 128);
    assertEquals(index['P'], 2);
    assertEquals(index['p'], 2);
    for (int c = 0; c < index.length; c++)
    {
      if (c != 'P' && c != 'p')
      {
        assertEquals(index[c], -1);
      }
    }
  }

  /**
   * Test a successful parse of a (small) score matrix file
   */
  @Test(groups = "Functional")
  public void testParse()
  {
    /*
     * some messy but valid input data, with comma, space
     * or tab (or combinations) as score value delimiters
     */
    String data = "ScoreMatrix MyTest\n" + "ATU tx-\n"
            + "1.1,1.2,1.3,1.4, 1.5, 1.6, 1.7\n"
            + "2.1 2.2 2.3 2.4 2.5 2.6 2.7\n"
            + "3.1\t3.2\t3.3\t3.4\t3.5\t3.6\t3.7\n"
            + " 4.1 ,4.2,\t,4.3 ,\t4.4\t, \4.5,4.6 4.7\n"
            + ", 5.1,5.3,5.3,5.4,5.5, 5.6, 5.7\n"
            + "\t6.1, 6.2 6.3 6.4 6.5 6.6 6.7\n"
            + ", \t7.1\t7.2 7.3, 7.4, 7.5\t,7.6,7.7\n";
    ScoreMatrix sm = ScoreMatrix.parse(new ByteArrayInputStream(data
            .getBytes()));
    assertNotNull(sm);
    assertEquals(sm.getName(), "MyTest");
    assertTrue(sm.isDNA());
    assertFalse(sm.isProtein());
    assertEquals(sm.getPairwiseScore('A', 'A'), 1.1f);
    assertEquals(sm.getPairwiseScore('A', 'T'), 1.2f);
    assertEquals(sm.getPairwiseScore('a', 'T'), 1.2f); // A/a equivalent
    assertEquals(sm.getPairwiseScore('A', 't'), 1.5f); // T/t not equivalent
    assertEquals(sm.getPairwiseScore('a', 't'), 1.5f);
    assertEquals(sm.getPairwiseScore('T', ' '), 2.4f);
    assertEquals(sm.getPairwiseScore('U', 'x'), 3.6f);
    assertEquals(sm.getPairwiseScore('u', 'x'), 3.6f);
    assertEquals(sm.getPairwiseScore('U', 'X'), 0f); // X (upper) unmapped
    assertEquals(sm.getPairwiseScore('A', '.'), 0f); // . unmapped
    assertEquals(sm.getPairwiseScore('-', '-'), 7.7f);
    assertEquals(sm.getPairwiseScore('A', (char) 128), 0f); // out of range
  }

  @Test(groups = "Functional")
  public void testParse_invalidInput()
  {
    /*
     * valid first
     */
    String data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n";
    ScoreMatrix sm = ScoreMatrix.parse(new ByteArrayInputStream(data
            .getBytes()));
    assertNotNull(sm);

    /*
     * Name missing
     */
    data = "ScoreMatrix\nXY\n1 2\n3 4\n";
    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
    assertNull(sm);

    /*
     * ScoreMatrix header missing
     */
    data = "XY\n1 2\n3 4\n";
    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
    assertNull(sm);

    /*
     * Not enough rows
     */
    data = "ScoreMatrix MyTest\nXY\n1 2\n";
    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
    assertNull(sm);

    /*
     * Not enough columns
     */
    data = "ScoreMatrix MyTest\nXY\n1 2\n3\n";
    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
    assertNull(sm);

    /*
     * Too many columns
     */
    data = "ScoreMatrix MyTest\nXY\n1 2\n3 4 5\n";
    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
    assertNull(sm);

    /*
     * Too many rows
     */
    data = "ScoreMatrix MyTest\nXY\n1 2\n3 4\n6 7";
    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
    assertNull(sm);

    /*
     * unsupported delimiter |
     */
    data = "ScoreMatrix MyTest\nXY\n1|2\n3|4\n";
    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
    assertNull(sm);

    /*
     * Bad float value
     */
    data = "ScoreMatrix MyTest\nXY\n1 2\n3 four\n";
    sm = ScoreMatrix.parse(new ByteArrayInputStream(data.getBytes()));
    assertNull(sm);

  }
}