X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fhmmer%2FHMMERTest.java;h=e3b70679c05d5b900a828e885d071a9fd224c978;hb=61632514caf99d7897843f8bb3e4378aa715d040;hp=7c8d637967e0b8837bdfeb3dfaba767da9d81503;hpb=4389a166735bf1203894abdf3cf7dd57c4856dbc;p=jalview.git

diff --git a/test/jalview/hmmer/HMMERTest.java b/test/jalview/hmmer/HMMERTest.java
index 7c8d637..e3b7067 100644
--- a/test/jalview/hmmer/HMMERTest.java
+++ b/test/jalview/hmmer/HMMERTest.java
@@ -1,6 +1,7 @@
 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;
@@ -12,11 +13,14 @@ 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;
@@ -29,17 +33,15 @@ public class HMMERTest {
   @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" });
-    // FastaFile file = null;
-    // file = new FastaFile(
-    // new FileParse("examples/uniref50.fa", DataSourceType.FILE));
-    // SequenceI[] seqs = file.getSeqsAsArray();
-    // AlignmentI al = new Alignment(seqs);
-    // frame = new AlignFrame(al, 150, 20);
     frame = Desktop.getAlignFrames()[0];
   }
 
@@ -60,23 +62,31 @@ public class HMMERTest {
           throws MalformedURLException, IOException
   {
     /*
-     * run hmmbuild - note the side-effect of selecting the HMM
-     * sequence that gets added to the alignment
+     * run hmmbuild
      */
     testHMMBuild();
-    HiddenMarkovModel hmm = frame.getSelectedHMM();
-    assertNotNull(hmm);
+    List<SequenceI> hmms = frame.getViewport().getAlignment()
+            .getHmmSequences();
+    assertFalse(hmms.isEmpty());
 
     /*
-     * now run hmmalign - with respect to the select HMM profile
+     * now run hmmalign - by default with respect to the added HMM profile
      */
     testHMMAlign();
   }
 
   public void testHMMBuild()
   {
-    HMMBuild builder = new HMMBuild(frame,
-            new ArrayList<ArgumentI>());
+    /*
+     * 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);
@@ -88,12 +98,11 @@ public class HMMERTest {
     assertEquals(hmm.getName(), "Alignment_HMM");
     assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
             "0.648193");
-    assertEquals(hmm.getConsensusAtAlignColumn(15), 's');
   }
 
   public void testHMMAlign()
   {
-    HMMAlign thread = new HMMAlign(frame,
+    HmmerCommand thread = new HMMAlign(frame,
             new ArrayList<ArgumentI>());
     thread.run();
 
@@ -111,8 +120,8 @@ public class HMMERTest {
     assertNotNull(original);
     AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
     assertNotNull(realigned);
-    assertNotNull(original.getHmmConsensus());
-    assertNotNull(realigned.getHmmConsensus());
+    assertFalse(original.getHmmSequences().isEmpty());
+    assertFalse(realigned.getHmmSequences().isEmpty());
 
     SequenceI ferCapan = original.findName("FER_CAPAN");
     assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));