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