JAL-3291 issue fixed, passing tests added

[jalview.git] / test / jalview / datamodel / HiddenMarkovModelTest.java

diff --git a/test/jalview/datamodel/HiddenMarkovModelTest.java b/test/jalview/datamodel/HiddenMarkovModelTest.java
index 7978da2..65241b4 100644 (file)
--- a/test/jalview/datamodel/HiddenMarkovModelTest.java
+++ b/test/jalview/datamodel/HiddenMarkovModelTest.java
@@ -18,6 +18,8 @@ public class HiddenMarkovModelTest {
 
   HiddenMarkovModel hmm;
 
+  HiddenMarkovModel alignmentHmm;
+
   @BeforeClass(alwaysRun = true)
   public void setUp() throws MalformedURLException, IOException
   {
@@ -27,6 +29,12 @@ public class HiddenMarkovModelTest {
     HMMFile file = new HMMFile(new FileParse(
             "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
     hmm = file.getHMM();
+
+    // used to check if consensus sequence is automatically aligned with alignment
+    HMMFile alignmentTest = new HMMFile(
+            new FileParse("test/jalview/io/HMMAlignmentTestHMM.hmm",
+                    DataSourceType.FILE));
+    alignmentHmm = alignmentTest.getHMM();
   }
 
   @Test(groups = "Functional")
@@ -115,6 +123,14 @@ public class HiddenMarkovModelTest {
     assertEquals(subStr, "yelleklGsG");
     subStr = seq.getSequenceAsString().substring(150, 161);
     assertEquals(subStr, "-dllk------");
+
+    // test to see if consensus sequence maps to alignment correctly
+    // see HMMAlignmentTest.sto for corresponding alignment file
+    SequenceI seq2 = alignmentHmm.getConsensusSequence();
+    assertEquals(seq2.getCharAt(0), '-');
+    assertEquals(seq2.getCharAt(7), '-');
+    assertEquals(seq2.getCharAt(8), 's');
+
   }
 
   /**