X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=9464c7430ea9b6f002391bb92eda14c3efd3a363;hb=37f0332f53a8564ba7a9d55b993f8bfd2f368c80;hp=755abbb18e74ad3a976c435bbcb90c1d1c17f0ba;hpb=499fbdac5e7260dcfd51456e0b7eb1dd7ff613b5;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 755abbb..9464c74 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -343,13 +343,9 @@ public class Sequence extends ASequence implements SequenceI
         this.addPDBId(new PDBEntry(pdb));
       }
     }
-    if (seq.isHMMConsensusSequence())
-    {
-      this.isHMMConsensusSequence = true;
-    }
     if (seq.getHMM() != null)
     {
-      this.hmm = new HiddenMarkovModel(seq.getHMM());
+      this.hmm = new HiddenMarkovModel(seq.getHMM(), this);
     }
 
   }
@@ -1916,18 +1912,6 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public boolean isHMMConsensusSequence()
-  {
-    return isHMMConsensusSequence;
-  }
-
-  @Override
-  public void setIsHMMConsensusSequence(boolean value)
-  {
-    this.isHMMConsensusSequence = value;
-  }
-
-  @Override
   public boolean hasHMMAnnotation()
   {
     if (this.annotation == null) {
@@ -2107,4 +2091,10 @@ public class Sequence extends ASequence implements SequenceI
     // otherwise, sequence was completely hidden
     return 0;
   }
+
+  @Override
+  public boolean hasHMMProfile()
+  {
+    return hmm != null;
+  }
 }