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.util.MessageManager;
  16 import jalview.ws.params.ArgumentI;
  17 import jalview.ws.params.simple.Option;
  18
  19 import java.io.IOException;
  20 import java.net.MalformedURLException;
  21 import java.util.ArrayList;
  22
  23 import org.testng.annotations.AfterClass;
  24 import org.testng.annotations.BeforeClass;
  25 import org.testng.annotations.Test;
  26
  27 public class HMMERTest {
  28
  29   AlignFrame frame;
  30
  31   @BeforeClass(alwaysRun = true)
  32   public void setUpBeforeClass() throws Exception
  33   {
  34     /*
  35      * NB: check HMMER_PATH in testProps.jvprops is valid for
  36      * the machine on which this runs
  37      */
  38     Jalview.main(
  39             new String[]
  40     { "-noquestionnaire", "-nonews", "-props",
  41                 "test/jalview/hmmer/testProps.jvprops", "-open",
  42                 "examples/uniref50.fa" });
  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 - note the side-effect of selecting the HMM
  64      * sequence that gets added to the alignment
  65      */
  66     testHMMBuild();
  67     HiddenMarkovModel hmm = frame.getSelectedHMM();
  68     assertNotNull(hmm);
  69
  70     /*
  71      * now run hmmalign - with respect to the select HMM profile
  72      */
  73     testHMMAlign();
  74   }
  75
  76   public void testHMMBuild()
  77   {
  78     /*
  79      * set up argument to run hmmbuild for the alignment
  80      */
  81     ArrayList<ArgumentI> params = new ArrayList<>();
  82     String argName = MessageManager.getString("label.hmmbuild_for");
  83     String argValue = MessageManager.getString("label.alignment");
  84     params.add(
  85             new Option(argName, null, false, null, argValue, null, null));
  86
  87     HMMBuild builder = new HMMBuild(frame, params);
  88     builder.run();
  89
  90     SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
  91     HiddenMarkovModel hmm = seq.getHMM();
  92     assertNotNull(hmm);
  93
  94     assertEquals(hmm.getLength(), 148);
  95     assertEquals(hmm.getAlphabetType(), "amino");
  96     assertEquals(hmm.getName(), "Alignment_HMM");
  97     assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
  98             "0.648193");
  99   }
 100
 101   public void testHMMAlign()
 102   {
 103     HmmerCommand thread = new HMMAlign(frame,
 104             new ArrayList<ArgumentI>());
 105     thread.run();
 106
 107     AlignFrame[] alignFrames = Desktop.getAlignFrames();
 108     if (alignFrames == null)
 109     {
 110       fail("No align frame loaded");
 111     }
 112
 113     /*
 114      * now have the original align frame, and another for realigned sequences
 115      */
 116     assertEquals(alignFrames.length, 2);
 117     AlignmentI original = alignFrames[0].getViewport().getAlignment();
 118     assertNotNull(original);
 119     AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
 120     assertNotNull(realigned);
 121     assertNotNull(original.getHmmConsensus());
 122     assertNotNull(realigned.getHmmConsensus());
 123
 124     SequenceI ferCapan = original.findName("FER_CAPAN");
 125     assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));
 126
 127     SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
 128     assertTrue(ferCapanRealigned.getSequenceAsString()
 129             .startsWith("-------m-A----SVSAT"));
 130   }
 131 }
 132