JAL-2629 storage and lifecycle of alignment/group HMM annotations revised

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

diff --git a/test/jalview/hmmer/HMMERTest.java b/test/jalview/hmmer/HMMERTest.java
index 4720dc2..7c8d637 100644 (file)
--- a/test/jalview/hmmer/HMMERTest.java
+++ b/test/jalview/hmmer/HMMERTest.java
@@ -60,11 +60,12 @@ public class HMMERTest {
           throws MalformedURLException, IOException
   {
     /*
-     * run hmmbuild - not the side-effect of selecting the HMM
+     * run hmmbuild - note the side-effect of selecting the HMM
      * sequence that gets added to the alignment
      */
     testHMMBuild();
     HiddenMarkovModel hmm = frame.getSelectedHMM();
+    assertNotNull(hmm);
 
     /*
      * now run hmmalign - with respect to the select HMM profile
@@ -74,9 +75,9 @@ public class HMMERTest {
 
   public void testHMMBuild()
   {
-    HMMBuildThread thread = new HMMBuildThread(frame,
+    HMMBuild builder = new HMMBuild(frame,
             new ArrayList<ArgumentI>());
-    thread.hmmbuildWaitTillComplete();
+    builder.run();
 
     SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
     HiddenMarkovModel hmm = seq.getHMM();
@@ -84,7 +85,7 @@ public class HMMERTest {
 
     assertEquals(hmm.getLength(), 148);
     assertEquals(hmm.getAlphabetType(), "amino");
-    assertEquals(hmm.getName(), "Alignment");
+    assertEquals(hmm.getName(), "Alignment_HMM");
     assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
             "0.648193");
     assertEquals(hmm.getConsensusAtAlignColumn(15), 's');
@@ -92,9 +93,9 @@ public class HMMERTest {
 
   public void testHMMAlign()
   {
-    HMMAlignThread thread = new HMMAlignThread(frame,
+    HMMAlign thread = new HMMAlign(frame,
             new ArrayList<ArgumentI>());
-    thread.hmmalignWaitTillComplete();
+    thread.run();
 
     AlignFrame[] alignFrames = Desktop.getAlignFrames();
     if (alignFrames == null)
@@ -110,8 +111,8 @@ public class HMMERTest {
     assertNotNull(original);
     AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
     assertNotNull(realigned);
-    assertNotNull(original.getHMMConsensusSequences());
-    assertNotNull(realigned.getHMMConsensusSequences());
+    assertNotNull(original.getHmmConsensus());
+    assertNotNull(realigned.getHmmConsensus());
 
     SequenceI ferCapan = original.findName("FER_CAPAN");
     assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));