JAL-3666 SequenceI.*HMM methods look to dataset sequence for HMM profile. Initial...

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 25e9611..d1f13c1 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1609,6 +1609,8 @@ public class Sequence extends ASequence implements SequenceI
           datasetSequence.addAlignmentAnnotation(_aa);
         }
       }
+      datasetSequence.setHMM(hmm);
+      hmm=null;
     }
     return datasetSequence;
   }
@@ -1888,13 +1890,23 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public HiddenMarkovModel getHMM()
   {
+    if (datasetSequence!=null)
+    {
+      return datasetSequence.getHMM();
+    }
     return hmm;
   }
 
   @Override
   public void setHMM(HiddenMarkovModel hmm)
   {
-    this.hmm = hmm;
+    if (datasetSequence!=null)
+    {
+      datasetSequence.setHMM(hmm);
+    } else {
+      this.hmm=hmm;
+    }
+    
   }
 
   @Override
@@ -2081,6 +2093,6 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public boolean hasHMMProfile()
   {
-    return hmm != null;
+    return hmm != null || (datasetSequence!=null && datasetSequence.hasHMMProfile());
   }
 }