test/jalview/hmmer/HMMERTest.java

   1 package jalview.hmmer;
   2
   3 import static org.testng.Assert.assertEquals;
   4 import static org.testng.Assert.assertNotEquals;
   5 import static org.testng.Assert.fail;
   6
   7 import jalview.bin.Jalview;
   8 import jalview.datamodel.Alignment;
   9 import jalview.datamodel.AlignmentI;
  10 import jalview.datamodel.HiddenMarkovModel;
  11 import jalview.datamodel.SequenceI;
  12 import jalview.gui.AlignFrame;
  13 import jalview.gui.Desktop;
  14 import jalview.io.DataSourceType;
  15 import jalview.io.FastaFile;
  16 import jalview.io.FileParse;
  17
  18 import java.io.IOException;
  19 import java.net.MalformedURLException;
  20 import java.util.List;
  21
  22 import org.testng.annotations.AfterClass;
  23 import org.testng.annotations.BeforeClass;
  24 import org.testng.annotations.Test;
  25
  26
  27 public class HMMERTest {
  28
  29   AlignFrame frame;
  30
  31   @BeforeClass(alwaysRun = true)
  32   public static void setUpBeforeClass() throws Exception
  33   {
  34     Jalview.main(
  35             new String[]
  36     { "-noquestionnaire", "-nonews", "-props",
  37         "test/jalview/hmmer/testProps.jvprops" });
  38   }
  39
  40   @AfterClass(alwaysRun = true)
  41   public static void tearDownAfterClass() throws Exception
  42   {
  43     Desktop.instance.closeAll_actionPerformed(null);
  44   }
  45
  46   @Test(priority = 0)
  47   public void testHMMBuild() throws MalformedURLException, IOException
  48   {
  49     FastaFile file = null;
  50     try
  51     {
  52       file = new FastaFile(
  53               new FileParse("examples/uniref50.fa", DataSourceType.FILE));
  54     } catch (IOException e)
  55     {
  56       e.printStackTrace();
  57       fail();
  58     }
  59     SequenceI[] seqs = file.getSeqsAsArray();
  60     AlignmentI al = new Alignment(seqs);
  61     frame = new AlignFrame(al, 150, 20);
  62
  63     HMMBuildThread thread = new HMMBuildThread(frame);
  64     thread.hmmbuildWaitTillComplete();
  65
  66     SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
  67     HiddenMarkovModel hmm = seq.getHMM();
  68     if (hmm == null)
  69     {
  70       fail();
  71     }
  72
  73     assertEquals(hmm.getLength().intValue(), 148);
  74     assertEquals(hmm.getAlphabetType(), "amino");
  75     assertEquals(hmm.getName(), "Alignment");
  76     assertEquals(hmm.getEffectiveNumberOfSequences(), 0.648193, 0.0001);
  77     assertEquals(hmm.getConsensusAtAlignColumn(15), 's');
  78   }
  79
  80   @Test(priority = 1)
  81   public void testHMMAlign() throws MalformedURLException, IOException
  82   {
  83     HMMAlignThread thread = new HMMAlignThread(frame, true);
  84     try
  85     {
  86       thread.hmmalignWaitTillComplete();
  87     } catch (Exception e)
  88     {
  89       e.printStackTrace();
  90       fail();
  91     }
  92
  93     if (Desktop.getAlignFrames() == null)
  94     {
  95       fail();
  96     }
  97
  98     AlignFrame frame = Desktop.getAlignFrames()[0];
  99     AlignmentI al = frame.getViewport().getAlignment();
 100     assertNotEquals(al, null);
 101     List<SequenceI> hmmSeqs = al.getHMMConsensusSequences(false);
 102     assertNotEquals(hmmSeqs, null);
 103
 104   }
 105 }
 106