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 HmmerLocalBackgroundTest {
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 SequenceI hmmSeq = file.getSeqsAsArray()[0];
37 AnnotatedCollectionI ac = new Alignment(
39 { hmmSeq, seq1, seq2 });
40 ColourSchemeI scheme = new HmmerLocalBackground(ac);
43 * 'A' in column 1, node 2, match emission 2.77204
45 * background frequency is 0.15
46 * ratio is < 1, log is negative, colour is Orange
48 Color actual = scheme.findColour('A', 1, null, null, 0);
49 assertEquals(actual, Color.ORANGE);
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);
56 actual = scheme.findColour('.', 2, null, null, 0);
57 assertEquals(actual, Color.WHITE);
60 * 'L' in column 3, node 4, match emission 1.98342
62 * background frequency is 0.05
63 * ratio is 2.752, log is 1.012
64 * colour is graduated 1.012/2.996 or 86/255 of the way from
65 * white(255, 255, 255) to blue(0, 0, 255)
67 actual = scheme.findColour('L', 3, null, null, 0);
68 assertEquals(actual, new Color(169, 169, 255));
71 * invalid symbol is White
73 actual = scheme.findColour('X', 2, null, null, 0);
74 assertEquals(actual, Color.WHITE);