test/jalview/hmmer/HMMERTest.java

   1 package jalview.hmmer;
   2
   3 import static org.testng.Assert.assertEquals;
   4 import static org.testng.Assert.assertNotNull;
   5 import static org.testng.Assert.assertTrue;
   6 import static org.testng.Assert.fail;
   7
   8 import jalview.bin.Jalview;
   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.ws.params.ArgumentI;
  15
  16 import java.io.IOException;
  17 import java.net.MalformedURLException;
  18 import java.util.ArrayList;
  19
  20 import org.testng.annotations.AfterClass;
  21 import org.testng.annotations.BeforeClass;
  22 import org.testng.annotations.Test;
  23
  24 public class HMMERTest {
  25
  26   AlignFrame frame;
  27
  28   @BeforeClass(alwaysRun = true)
  29   public void setUpBeforeClass() throws Exception
  30   {
  31     Jalview.main(
  32             new String[]
  33     { "-noquestionnaire", "-nonews", "-props",
  34                 "test/jalview/hmmer/testProps.jvprops", "-open",
  35                 "examples/uniref50.fa" });
  36     // FastaFile file = null;
  37     // file = new FastaFile(
  38     // new FileParse("examples/uniref50.fa", DataSourceType.FILE));
  39     // SequenceI[] seqs = file.getSeqsAsArray();
  40     // AlignmentI al = new Alignment(seqs);
  41     // frame = new AlignFrame(al, 150, 20);
  42     frame = Desktop.getAlignFrames()[0];
  43   }
  44
  45   @AfterClass(alwaysRun = true)
  46   public static void tearDownAfterClass() throws Exception
  47   {
  48     Desktop.instance.closeAll_actionPerformed(null);
  49   }
  50
  51   /**
  52    * Test with a dependency on locally installed hmmbuild binaries
  53    *
  54    * @throws MalformedURLException
  55    * @throws IOException
  56    */
  57   @Test(groups = "External")
  58   public void testHMMBuildThenHMMAlign()
  59           throws MalformedURLException, IOException
  60   {
  61     /*
  62      * run hmmbuild - not the side-effect of selecting the HMM
  63      * sequence that gets added to the alignment
  64      */
  65     testHMMBuild();
  66     HiddenMarkovModel hmm = frame.getSelectedHMM();
  67
  68     /*
  69      * now run hmmalign - with respect to the select HMM profile
  70      */
  71     testHMMAlign();
  72   }
  73
  74   public void testHMMBuild()
  75   {
  76     HMMBuildThread thread = new HMMBuildThread(frame,
  77             new ArrayList<ArgumentI>());
  78     thread.hmmbuildWaitTillComplete();
  79
  80     SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
  81     HiddenMarkovModel hmm = seq.getHMM();
  82     assertNotNull(hmm);
  83
  84     assertEquals(hmm.getLength().intValue(), 148);
  85     assertEquals(hmm.getAlphabetType(), "amino");
  86     assertEquals(hmm.getName(), "Alignment");
  87     assertEquals(hmm.getEffectiveNumberOfSequences(), 0.648193, 0.0001);
  88     assertEquals(hmm.getConsensusAtAlignColumn(15), 's');
  89   }
  90
  91   public void testHMMAlign()
  92   {
  93     HMMAlignThread thread = new HMMAlignThread(frame,
  94             new ArrayList<ArgumentI>());
  95     thread.hmmalignWaitTillComplete();
  96
  97     AlignFrame[] alignFrames = Desktop.getAlignFrames();
  98     if (alignFrames == null)
  99     {
 100       fail("No align frame loaded");
 101     }
 102
 103     /*
 104      * now have the original align frame, and another for realigned sequences
 105      */
 106     assertEquals(alignFrames.length, 2);
 107     AlignmentI original = alignFrames[0].getViewport().getAlignment();
 108     assertNotNull(original);
 109     AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
 110     assertNotNull(realigned);
 111     assertNotNull(original.getHMMConsensusSequences());
 112     assertNotNull(realigned.getHMMConsensusSequences());
 113
 114     SequenceI ferCapan = original.findName("FER_CAPAN");
 115     assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));
 116
 117     SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
 118     assertTrue(ferCapanRealigned.getSequenceAsString()
 119             .startsWith("-------m-A----SVSAT"));
 120   }
 121 }
 122