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.assertNotNull;
   6 import static org.testng.Assert.fail;
   7
   8 import jalview.bin.Jalview;
   9 import jalview.datamodel.Alignment;
  10 import jalview.datamodel.AlignmentI;
  11 import jalview.datamodel.HiddenMarkovModel;
  12 import jalview.datamodel.SequenceI;
  13 import jalview.gui.AlignFrame;
  14 import jalview.gui.Desktop;
  15 import jalview.io.DataSourceType;
  16 import jalview.io.FastaFile;
  17 import jalview.io.FileParse;
  18 import jalview.ws.params.ArgumentI;
  19
  20 import java.io.IOException;
  21 import java.net.MalformedURLException;
  22 import java.util.ArrayList;
  23 import java.util.List;
  24
  25 import org.testng.annotations.AfterClass;
  26 import org.testng.annotations.BeforeClass;
  27 import org.testng.annotations.Test;
  28
  29
  30 public class HMMERTest {
  31
  32   AlignFrame frame;
  33
  34   @BeforeClass(alwaysRun = true)
  35   public static void setUpBeforeClass() throws Exception
  36   {
  37     Jalview.main(
  38             new String[]
  39     { "-noquestionnaire", "-nonews", "-props",
  40         "test/jalview/hmmer/testProps.jvprops" });
  41   }
  42
  43   @AfterClass(alwaysRun = true)
  44   public static void tearDownAfterClass() throws Exception
  45   {
  46     Desktop.instance.closeAll_actionPerformed(null);
  47   }
  48
  49   @Test(priority = 0)
  50   public void testHMMBuild() throws MalformedURLException, IOException
  51   {
  52     FastaFile file = null;
  53     try
  54     {
  55       file = new FastaFile(
  56               new FileParse("examples/uniref50.fa", DataSourceType.FILE));
  57     } catch (IOException e)
  58     {
  59       e.printStackTrace();
  60       fail();
  61     }
  62     SequenceI[] seqs = file.getSeqsAsArray();
  63     AlignmentI al = new Alignment(seqs);
  64     frame = new AlignFrame(al, 150, 20);
  65
  66     HMMBuildThread thread = new HMMBuildThread(frame,
  67             new ArrayList<ArgumentI>());
  68     thread.hmmbuildWaitTillComplete();
  69
  70     SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
  71     HiddenMarkovModel hmm = seq.getHMM();
  72     if (hmm == null)
  73     {
  74       fail();
  75     }
  76
  77     assertEquals(hmm.getLength().intValue(), 148);
  78     assertEquals(hmm.getAlphabetType(), "amino");
  79     assertEquals(hmm.getName(), "Alignment");
  80     assertEquals(hmm.getEffectiveNumberOfSequences(), 0.648193, 0.0001);
  81     assertEquals(hmm.getConsensusAtAlignColumn(15), 's');
  82   }
  83
  84   @Test(priority = 1)
  85   public void testHMMAlign() throws MalformedURLException, IOException
  86   {
  87     HMMAlignThread thread = new HMMAlignThread(frame, true,
  88             new ArrayList<ArgumentI>());
  89     try
  90     {
  91       thread.hmmalignWaitTillComplete();
  92     } catch (Exception e)
  93     {
  94       e.printStackTrace();
  95       fail();
  96     }
  97
  98     if (Desktop.getAlignFrames() == null)
  99     {
 100       fail();
 101     }
 102
 103     AlignFrame fr = Desktop.getAlignFrames()[0];
 104     AlignmentI al = fr.getViewport().getAlignment();
 105     assertNotEquals(al, null);
 106     List<SequenceI> hmmSeqs = al.getHMMConsensusSequences();
 107     assertNotNull(hmmSeqs);
 108   }
 109 }
 110