test/jalview/datamodel/HMMNodeTest.java

   1 package jalview.datamodel;
   2
   3 import static org.testng.Assert.assertEquals;
   4
   5 import jalview.io.DataSourceType;
   6 import jalview.io.FileParse;
   7 import jalview.io.HMMFile;
   8
   9 import java.io.IOException;
  10 import java.net.MalformedURLException;
  11
  12 import org.testng.annotations.BeforeClass;
  13 import org.testng.annotations.Test;
  14
  15 public class HMMNodeTest
  16 {
  17   private HiddenMarkovModel hmm;
  18
  19   @BeforeClass(alwaysRun = true)
  20   public void setUp() throws MalformedURLException, IOException
  21   {
  22     /*
  23      * load hmm model of a Kinase domain to a HiddenMarkovModel
  24      */
  25     HMMFile file = new HMMFile(new FileParse(
  26             "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
  27     hmm = file.getHMM();
  28   }
  29
  30   @Test(groups="Functional")
  31   public void testGetMaxMatchEmissionIdex()
  32   {
  33     assertEquals(hmm.getAlphabetType(), "amino");
  34     String symbols = hmm.getSymbols();
  35
  36     assertEquals(hmm.getNode(1).getMaxMatchEmissionIndex(),
  37             symbols.indexOf('Y'));
  38
  39     assertEquals(hmm.getNode(17).getMaxMatchEmissionIndex(),
  40             symbols.indexOf('K'));
  41   }
  42 }