1 package jalview.schemes;
3 import static org.testng.Assert.assertEquals;
5 import jalview.io.DataSourceType;
6 import jalview.io.FileParse;
7 import jalview.io.HMMFile;
10 import java.io.IOException;
11 import java.net.MalformedURLException;
13 import org.testng.annotations.Test;
15 public class HMMERColourSchemeTest {
16 HMMERColourScheme scheme = new HMMERColourScheme();
19 public void testFindColour() throws MalformedURLException, IOException
22 HMMFile file = new HMMFile(new FileParse(
23 "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
25 scheme.hmm = file.getHMM();
27 Color actual = scheme.findColour('A', 1);
28 Color expected = new Color(1f, 1f - 0.06253430455f, 0f);
29 assertEquals(actual, expected);
31 actual = scheme.findColour('Y', 3);
32 expected = new Color(1f, 1f - 0.02082023351f, 0f);
33 assertEquals(actual, expected);
35 actual = scheme.findColour('M', 109);
36 expected = new Color(1f, 1f, 0);
37 assertEquals(actual, expected);
39 actual = scheme.findColour('I', 128);
40 expected = new Color(1f, 1f - 0.15097062462f, 0);
41 assertEquals(actual, expected);
43 actual = scheme.findColour('D', 181);
44 expected = new Color(1f, 1f - 0.08686935114f, 0);
45 assertEquals(actual, expected);
47 actual = scheme.findColour('Z', 1);
48 expected = new Color(1f, 1f, 0);
49 assertEquals(actual, expected);
51 actual = scheme.findColour('A', 4000);
52 expected = new Color(1f, 1f, 0);
53 assertEquals(actual, expected);