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.io.HMMFile;
  15 import jalview.ws.params.ArgumentI;
  16
  17 import java.io.IOException;
  18 import java.net.MalformedURLException;
  19 import java.util.ArrayList;
  20
  21 import org.testng.annotations.AfterClass;
  22 import org.testng.annotations.BeforeClass;
  23 import org.testng.annotations.Test;
  24
  25 public class HMMERTest {
  26
  27   AlignFrame frame;
  28
  29   @BeforeClass(alwaysRun = true)
  30   public void setUpBeforeClass() throws Exception
  31   {
  32     Jalview.main(
  33             new String[]
  34     { "-noquestionnaire", "-nonews", "-props",
  35                 "test/jalview/hmmer/testProps.jvprops", "-open",
  36                 "examples/uniref50.fa" });
  37     // FastaFile file = null;
  38     // file = new FastaFile(
  39     // new FileParse("examples/uniref50.fa", DataSourceType.FILE));
  40     // SequenceI[] seqs = file.getSeqsAsArray();
  41     // AlignmentI al = new Alignment(seqs);
  42     // frame = new AlignFrame(al, 150, 20);
  43     frame = Desktop.getAlignFrames()[0];
  44   }
  45
  46   @AfterClass(alwaysRun = true)
  47   public static void tearDownAfterClass() throws Exception
  48   {
  49     Desktop.instance.closeAll_actionPerformed(null);
  50   }
  51
  52   /**
  53    * Test with a dependency on locally installed hmmbuild binaries
  54    *
  55    * @throws MalformedURLException
  56    * @throws IOException
  57    */
  58   @Test(groups = "External")
  59   public void testHMMBuildThenHMMAlign()
  60           throws MalformedURLException, IOException
  61   {
  62     /*
  63      * run hmmbuild - not the side-effect of selecting the HMM
  64      * sequence that gets added to the alignment
  65      */
  66     testHMMBuild();
  67     HiddenMarkovModel hmm = frame.getSelectedHMM();
  68
  69     /*
  70      * now run hmmalign - with respect to the select HMM profile
  71      */
  72     testHMMAlign();
  73   }
  74
  75   public void testHMMBuild()
  76   {
  77     HMMBuildThread thread = new HMMBuildThread(frame,
  78             new ArrayList<ArgumentI>());
  79     thread.hmmbuildWaitTillComplete();
  80
  81     SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
  82     HiddenMarkovModel hmm = seq.getHMM();
  83     assertNotNull(hmm);
  84
  85     assertEquals(hmm.getLength(), 148);
  86     assertEquals(hmm.getAlphabetType(), "amino");
  87     assertEquals(hmm.getName(), "Alignment");
  88     assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
  89             "0.648193");
  90     assertEquals(hmm.getConsensusAtAlignColumn(15), 's');
  91   }
  92
  93   public void testHMMAlign()
  94   {
  95     HMMAlignThread thread = new HMMAlignThread(frame,
  96             new ArrayList<ArgumentI>());
  97     thread.hmmalignWaitTillComplete();
  98
  99     AlignFrame[] alignFrames = Desktop.getAlignFrames();
 100     if (alignFrames == null)
 101     {
 102       fail("No align frame loaded");
 103     }
 104
 105     /*
 106      * now have the original align frame, and another for realigned sequences
 107      */
 108     assertEquals(alignFrames.length, 2);
 109     AlignmentI original = alignFrames[0].getViewport().getAlignment();
 110     assertNotNull(original);
 111     AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
 112     assertNotNull(realigned);
 113     assertNotNull(original.getHMMConsensusSequences());
 114     assertNotNull(realigned.getHMMConsensusSequences());
 115
 116     SequenceI ferCapan = original.findName("FER_CAPAN");
 117     assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));
 118
 119     SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
 120     assertTrue(ferCapanRealigned.getSequenceAsString()
 121             .startsWith("-------m-A----SVSAT"));
 122   }
 123 }
 124