add HMMER colour scheme

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 463b909..a1a655e 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -51,6 +51,8 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   boolean colourText = false;
 
+  HiddenMarkovModel hmm;
+
   /**
    * True if the group is defined as a group on the alignment, false if it is
    * just a selection.
@@ -1457,4 +1459,18 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
   }
+
+  @Override
+  public HiddenMarkovModel getHMM()
+  {
+    // TODO Auto-generated method stub
+    return hmm;
+  }
+
+  @Override
+  public void setHMM(HiddenMarkovModel markov)
+  {
+    hmm = markov;
+
+  }
 }