package jalview.schemes;

import static org.testng.Assert.assertEquals;

import jalview.datamodel.Alignment;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.Sequence;
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 HmmerLocalBackgroundTest {

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

    /*
     * alignment with 20 residues and background frequencies:
     * A/a, S 3/20 = 0.15
     * M, K 4/20 = 0.2
     * V 2/20 = 0.1
     * Q, R, L 1/20 = 0.05
     * log(totalCount) = log(20) = 2.996
     */
    SequenceI seq1 = new Sequence("seq1", "AAMMMKKKVV");
    SequenceI seq2 = new Sequence("seq2", "aAM-QKRSSSL");
    SequenceI hmmSeq = file.getSeqsAsArray()[0];
    AnnotatedCollectionI ac = new Alignment(
            new SequenceI[]
            { hmmSeq, seq1, seq2 });
    ColourSchemeI scheme = new HmmerLocalBackground(ac);

    /*
     * 'A' in column 1, node 2, match emission 2.77204
     * e-2.77204 = 0.0625 
     * background frequency is 0.15
     * ratio is < 1, 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);

    /*
     * 'L' in column 3, node 4, match emission 1.98342
     * e-1.98342 = 0.1376 
     * background frequency is 0.05
     * ratio is 2.752, log is 1.012
     * colour is graduated 1.012/2.996 or 86/255 of the way from
     * white(255, 255, 255) to blue(0, 0, 255)
     */
    actual = scheme.findColour('L', 3, null, null, 0);
    assertEquals(actual, new Color(169, 169, 255));

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

}