add HMMER colour scheme

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 5d91b36..a88995d 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -68,6 +68,8 @@ public class Alignment implements AlignmentI
 
   private List<AlignedCodonFrame> codonFrameList;
 
+  HiddenMarkovModel hmm;
+
   private void initAlignment(SequenceI[] seqs)
   {
     groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
@@ -1959,4 +1961,19 @@ public class Alignment implements AlignmentI
   {
     hiddenCols = cols;
   }
+
+  @Override
+  public HiddenMarkovModel getHMM()
+  {
+
+    return hmm;
+  }
+
+  @Override
+  public void setHMM(HiddenMarkovModel markov)
+  {
+
+    hmm = markov;
+  }
+
 }