X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;fp=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=921ab2aea4a5be70b50b4a6107a53ebf564ad416;hb=9ce5bbd251a067e0c5b1969725121498bcfb28a0;hp=2c077b65196a652c214b21b0283c5bdc1cdfd40e;hpb=04a4d60a50394d846d0479c442facebe360b5b9c;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 2c077b6..921ab2a 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -53,7 +53,7 @@ public class SeqsetUtils
       sqinfo.put("Description", seq.getDescription());
     }
 
-    Vector<SequenceFeature> sfeat = new Vector<SequenceFeature>();
+    Vector<SequenceFeature> sfeat = new Vector<>();
     List<SequenceFeature> sfs = seq.getFeatures().getAllFeatures();
     sfeat.addAll(sfs);
 
@@ -70,7 +70,7 @@ public class SeqsetUtils
               (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
                       : new Sequence("THISISAPLACEHOLDER", ""));
     }
-    if (seq.isHMMConsensusSequence())
+    if (seq.hasHMMProfile())
     {
       sqinfo.put("HMM", seq.getHMM());
     }
@@ -143,8 +143,7 @@ public class SeqsetUtils
 
     if (hmm != null)
     {
-      sq.setHMM(new HiddenMarkovModel(hmm));
-      sq.setIsHMMConsensusSequence(true);
+      sq.setHMM(new HiddenMarkovModel(hmm, sq));
     }
     return namePresent;
   }