JAL-3285 code changes to HMMER colour schemes not included in merge

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

diff --git a/test/jalview/datamodel/HiddenMarkovModelTest.java b/test/jalview/datamodel/HiddenMarkovModelTest.java
index b283809..7978da2 100644 (file)
--- a/test/jalview/datamodel/HiddenMarkovModelTest.java
+++ b/test/jalview/datamodel/HiddenMarkovModelTest.java
@@ -59,6 +59,8 @@ public class HiddenMarkovModelTest {
   {
     double iep = hmm.getInsertEmissionProbability(2, 'A');
     assertEquals(iep, Math.pow(Math.E, -2.68618), 0.0001d);
+    // symbol is not case-sensitive
+    assertEquals(iep, hmm.getInsertEmissionProbability(2, 'a'));
 
     iep = hmm.getInsertEmissionProbability(5, 'T');
     assertEquals(iep, Math.pow(Math.E, -2.77519), 0.0001d);
@@ -106,23 +108,13 @@ public class HiddenMarkovModelTest {
   }
   
   @Test(groups = "Functional")
-  public void testGetConsensusAtAlignColumn()
-  {
-    assertEquals(hmm.getConsensusAtAlignColumn(10), 's');
-    assertEquals(hmm.getConsensusAtAlignColumn(50), 'k');
-    hmm.setConsensusResidueStatus(false);
-    assertEquals(hmm.getConsensusAtAlignColumn(100), 'l');
-    assertEquals(hmm.getConsensusAtAlignColumn(400), 'k');
-  }
-
-  @Test(groups = "Functional")
   public void testGetConsensusSequence()
   {
     SequenceI seq = hmm.getConsensusSequence();
     String subStr = seq.getSequenceAsString().substring(0, 10);
-    assertEquals(subStr, "YELLEKLGSG");
+    assertEquals(subStr, "yelleklGsG");
     subStr = seq.getSequenceAsString().substring(150, 161);
-    assertEquals(subStr, "-DLLK------");
+    assertEquals(subStr, "-dllk------");
   }
 
   /**
@@ -140,7 +132,7 @@ public class HiddenMarkovModelTest {
             .get("amino");
     int col = 4;
     float expected = 0f;
-    for (char aa : hmm.getSymbols())
+    for (char aa : hmm.getSymbols().toCharArray())
     {
       double mep = hmm.getMatchEmissionProbability(col, aa);
       float background = uniprotFreqs.get(aa);