JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSequence

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 755abbb..9464c74 100755 (executable)
--- 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;
+  }
 }