test/jalview/hmmer/HMMERTest.java

   1 package jalview.hmmer;
   2
   3 import static org.testng.Assert.assertEquals;
   4 import static org.testng.Assert.assertFalse;
   5 import static org.testng.Assert.assertNotNull;
   6 import static org.testng.Assert.assertTrue;
   7 import static org.testng.Assert.fail;
   8
   9 import jalview.bin.Jalview;
  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.HMMFile;
  16 import jalview.util.MessageManager;
  17 import jalview.ws.params.ArgumentI;
  18 import jalview.ws.params.simple.Option;
  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 public class HMMERTest {
  30
  31   AlignFrame frame;
  32
  33   @BeforeClass(alwaysRun = true)
  34   public void setUpBeforeClass() throws Exception
  35   {
  36     /*
  37      * NB: check HMMER_PATH in testProps.jvprops is valid for
  38      * the machine on which this runs
  39      */
  40     Jalview.main(
  41             new String[]
  42     { "-noquestionnaire", "-nonews", "-props",
  43                 "test/jalview/hmmer/testProps.jvprops", "-open",
  44                 "examples/uniref50.fa" });
  45     frame = Desktop.getAlignFrames()[0];
  46   }
  47
  48   @AfterClass(alwaysRun = true)
  49   public static void tearDownAfterClass() throws Exception
  50   {
  51     Desktop.getInstance().closeAll_actionPerformed(null);
  52   }
  53
  54   /**
  55    * Test with a dependency on locally installed hmmbuild binaries
  56    *
  57    * @throws MalformedURLException
  58    * @throws IOException
  59    */
  60   @Test(groups = "External")
  61   public void testHMMBuildThenHMMAlign()
  62           throws MalformedURLException, IOException
  63   {
  64     /*
  65      * run hmmbuild
  66      */
  67     testHMMBuild();
  68     List<SequenceI> hmms = frame.getViewport().getAlignment()
  69             .getHmmSequences();
  70     assertFalse(hmms.isEmpty());
  71
  72     /*
  73      * now run hmmalign - by default with respect to the added HMM profile
  74      */
  75     testHMMAlign();
  76   }
  77
  78   public void testHMMBuild()
  79   {
  80     /*
  81      * set up argument to run hmmbuild for the alignment
  82      */
  83     ArrayList<ArgumentI> params = new ArrayList<>();
  84     String argName = MessageManager.getString("label.hmmbuild_for");
  85     String argValue = MessageManager.getString("label.alignment");
  86     params.add(
  87             new Option(argName, null, false, null, argValue, null, null));
  88
  89     HMMBuild builder = new HMMBuild(frame, params);
  90     builder.run();
  91
  92     SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
  93     HiddenMarkovModel hmm = seq.getHMM();
  94     assertNotNull(hmm);
  95
  96     assertEquals(hmm.getLength(), 148);
  97     assertEquals(hmm.getAlphabetType(), "amino");
  98     assertEquals(hmm.getName(), "Alignment_HMM");
  99     assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
 100             "0.648193");
 101   }
 102
 103   public void testHMMAlign()
 104   {
 105     HmmerCommand thread = new HMMAlign(frame,
 106             new ArrayList<ArgumentI>());
 107     thread.run();
 108
 109     AlignFrame[] alignFrames = Desktop.getAlignFrames();
 110     if (alignFrames == null)
 111     {
 112       fail("No align frame loaded");
 113     }
 114
 115     /*
 116      * now have the original align frame, and another for realigned sequences
 117      */
 118     assertEquals(alignFrames.length, 2);
 119     AlignmentI original = alignFrames[0].getViewport().getAlignment();
 120     assertNotNull(original);
 121     AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
 122     assertNotNull(realigned);
 123     assertFalse(original.getHmmSequences().isEmpty());
 124     assertFalse(realigned.getHmmSequences().isEmpty());
 125
 126     SequenceI ferCapan = original.findName("FER_CAPAN");
 127     assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));
 128
 129     SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
 130     assertTrue(ferCapanRealigned.getSequenceAsString()
 131             .startsWith("-------m-A----SVSAT"));
 132   }
 133 }
 134