1 package jalview.datamodel;
3 import static org.testng.Assert.assertEquals;
5 import jalview.io.DataSourceType;
6 import jalview.io.FileParse;
7 import jalview.io.HMMFile;
9 import java.io.IOException;
10 import java.net.MalformedURLException;
12 import org.testng.annotations.BeforeClass;
13 import org.testng.annotations.Test;
15 public class HMMNodeTest
17 private HiddenMarkovModel hmm;
19 @BeforeClass(alwaysRun = true)
20 public void setUp() throws MalformedURLException, IOException
23 * load hmm model of a Kinase domain to a HiddenMarkovModel
25 HMMFile file = new HMMFile(new FileParse(
26 "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
30 @Test(groups="Functional")
31 public void testGetMaxMatchEmissionIdex()
33 assertEquals(hmm.getAlphabetType(), "amino");
34 String symbols = hmm.getSymbols();
36 assertEquals(hmm.getNode(1).getMaxMatchEmissionIndex(),
37 symbols.indexOf('Y'));
39 assertEquals(hmm.getNode(17).getMaxMatchEmissionIndex(),
40 symbols.indexOf('K'));