1 package jalview.schemes;
3 import static org.testng.Assert.assertEquals;
5 import jalview.datamodel.Alignment;
6 import jalview.datamodel.AnnotatedCollectionI;
7 import jalview.datamodel.Sequence;
8 import jalview.datamodel.SequenceI;
9 import jalview.io.DataSourceType;
10 import jalview.io.HMMFile;
12 import java.awt.Color;
13 import java.io.IOException;
14 import java.net.MalformedURLException;
16 import org.testng.annotations.Test;
18 public class HMMERAlignmentColourSchemeTest {
20 @Test(groups = "Functional")
21 public void testFindColour() throws MalformedURLException, IOException
23 HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
27 * alignment with 20 residues and background frequencies:
32 * log(totalCount) = log(20) = 2.996
34 SequenceI seq1 = new Sequence("seq1", "AAMMMKKKVV");
35 SequenceI seq2 = new Sequence("seq2", "aAM-QKRSSSL");
36 AnnotatedCollectionI ac = new Alignment(new SequenceI[] { seq1, seq2 });
37 ColourSchemeI scheme = new HMMERAlignmentColourScheme(ac,
41 * 'A' in column 1, node 2, match emission 2.77204
43 * background frequency is 0.15
44 * ratio is < 1, log is negative, colour is Orange
46 Color actual = scheme.findColour('A', 1, null, null, 0);
47 assertEquals(actual, Color.ORANGE);
50 actual = scheme.findColour('-', 2, null, null, 0);
51 assertEquals(actual, Color.WHITE);
52 actual = scheme.findColour(' ', 2, null, null, 0);
53 assertEquals(actual, Color.WHITE);
54 actual = scheme.findColour('.', 2, null, null, 0);
55 assertEquals(actual, Color.WHITE);
58 * 'L' in column 3, node 4, match emission 1.98342
60 * background frequency is 0.05
61 * ratio is 2.752, log is 1.012
62 * colour is graduated 1.012/2.996 or 86/255 of the way from
63 * white(255, 255, 255) to blue(0, 0, 255)
65 actual = scheme.findColour('L', 3, null, null, 0);
66 assertEquals(actual, new Color(169, 169, 255));
69 * invalid symbol is White
71 actual = scheme.findColour('X', 2, null, null, 0);
72 assertEquals(actual, Color.WHITE);