Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

[jalview.git] / test / jalview / hmmer / HMMERTest.java

diff --git a/test/jalview/hmmer/HMMERTest.java b/test/jalview/hmmer/HMMERTest.java
new file mode 100644 (file)
index 0000000..e3b7067
--- /dev/null
+++ b/test/jalview/hmmer/HMMERTest.java
@@ -0,0 +1,134 @@
+package jalview.hmmer;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.io.HMMFile;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.simple.Option;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class HMMERTest {
+
+  AlignFrame frame;
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpBeforeClass() throws Exception
+  {
+    /*
+     * NB: check HMMER_PATH in testProps.jvprops is valid for
+     * the machine on which this runs
+     */
+    Jalview.main(
+            new String[]
+    { "-noquestionnaire", "-nonews", "-props",
+                "test/jalview/hmmer/testProps.jvprops", "-open",
+                "examples/uniref50.fa" });
+    frame = Desktop.getAlignFrames()[0];
+  }
+
+  @AfterClass(alwaysRun = true)
+  public static void tearDownAfterClass() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  /**
+   * Test with a dependency on locally installed hmmbuild binaries
+   * 
+   * @throws MalformedURLException
+   * @throws IOException
+   */
+  @Test(groups = "External")
+  public void testHMMBuildThenHMMAlign()
+          throws MalformedURLException, IOException
+  {
+    /*
+     * run hmmbuild
+     */
+    testHMMBuild();
+    List<SequenceI> hmms = frame.getViewport().getAlignment()
+            .getHmmSequences();
+    assertFalse(hmms.isEmpty());
+
+    /*
+     * now run hmmalign - by default with respect to the added HMM profile
+     */
+    testHMMAlign();
+  }
+
+  public void testHMMBuild()
+  {
+    /*
+     * set up argument to run hmmbuild for the alignment
+     */
+    ArrayList<ArgumentI> params = new ArrayList<>();
+    String argName = MessageManager.getString("label.hmmbuild_for");
+    String argValue = MessageManager.getString("label.alignment");
+    params.add(
+            new Option(argName, null, false, null, argValue, null, null));
+
+    HMMBuild builder = new HMMBuild(frame, params);
+    builder.run();
+
+    SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
+    HiddenMarkovModel hmm = seq.getHMM();
+    assertNotNull(hmm);
+
+    assertEquals(hmm.getLength(), 148);
+    assertEquals(hmm.getAlphabetType(), "amino");
+    assertEquals(hmm.getName(), "Alignment_HMM");
+    assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
+            "0.648193");
+  }
+
+  public void testHMMAlign()
+  {
+    HmmerCommand thread = new HMMAlign(frame,
+            new ArrayList<ArgumentI>());
+    thread.run();
+
+    AlignFrame[] alignFrames = Desktop.getAlignFrames();
+    if (alignFrames == null)
+    {
+      fail("No align frame loaded");
+    }
+
+    /*
+     * now have the original align frame, and another for realigned sequences
+     */
+    assertEquals(alignFrames.length, 2);
+    AlignmentI original = alignFrames[0].getViewport().getAlignment();
+    assertNotNull(original);
+    AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
+    assertNotNull(realigned);
+    assertFalse(original.getHmmSequences().isEmpty());
+    assertFalse(realigned.getHmmSequences().isEmpty());
+
+    SequenceI ferCapan = original.findName("FER_CAPAN");
+    assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));
+
+    SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
+    assertTrue(ferCapanRealigned.getSequenceAsString()
+            .startsWith("-------m-A----SVSAT"));
+  }
+}
+