package jalview.schemes;

import static org.testng.Assert.assertEquals;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.HMMFile;

import java.awt.Color;
import java.io.IOException;
import java.net.MalformedURLException;

import org.testng.annotations.Test;

public class HmmerGlobalBackgroundTest {

  @Test(groups = "Functional")
  public void testFindColour() throws MalformedURLException, IOException
  {
    HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
            DataSourceType.FILE);

    SequenceI hmmSeq = file.getSeqsAsArray()[0];
    AlignmentI al = new Alignment(new SequenceI[] { hmmSeq });
    ColourSchemeI scheme = new HmmerGlobalBackground(al);

    /*
     * 'A' in column 1, node 2, match emission 2.77204
     * e-2.77204 = 0.0625 
     * background frequency is 0.0826
     * ratio is 0.757, log is negative, colour is Orange
     */
    Color actual = scheme.findColour('A', 1, null, null, 0);
    assertEquals(actual, Color.ORANGE);

    // gap is white
    actual = scheme.findColour('-', 2, null, null, 0);
    assertEquals(actual, Color.WHITE);
    actual = scheme.findColour(' ', 2, null, null, 0);
    assertEquals(actual, Color.WHITE);
    actual = scheme.findColour('.', 2, null, null, 0);
    assertEquals(actual, Color.WHITE);

    /*
     * 'Y' in column 4, node 5, match emission 4.41426
     * e-4.41426 = 0.0121 
     * background frequency is 0.0292
     * ratio is 0.414, log is negative, colour is Orange
     */
    actual = scheme.findColour('Y', 4, null, null, 0);
    assertEquals(actual, Color.ORANGE);

    /*
     * 'M' in column 109, no matching node, colour is reddish
     */
    actual = scheme.findColour('M', 109, null, null, 0);
    assertEquals(actual, new Color(230, 0, 0));

    /*
     * 'I' in column 6, node 7, match emission 1.33015
     * e-1.33015 = 0.2644
     * background frequency is 0.0593
     * ratio is 4.459, log is 1.495
     * colour is graduated 1.495/4.52 or 84/255 of the way from
     * white(255, 255, 255) to blue(0, 0, 255)
     */
    actual = scheme.findColour('I', 6, null, null, 0);
    assertEquals(actual, new Color(171, 171, 255));

    /*
     * 'V' in column 14, node 15, match emission 0.44769
     * e-0.44769 = 0.6391
     * background frequency is 0.0686
     * ratio is 9.316, log is 2.232
     * colour is graduated 2.232/4.52 or 126/255 of the way from
     * white(255, 255, 255) to blue(0, 0, 255)
     */
    actual = scheme.findColour('V', 14, null, null, 0);
    assertEquals(actual, new Color(129, 129, 255));

    /*
     * invalid symbol is White
     */
    actual = scheme.findColour('X', 2, null, null, 0);
    assertEquals(actual, Color.WHITE);
  }

}