Merge branch 'develop' into developtomchmmer

[jalview.git] / src / jalview / analysis / SeqsetUtils.java

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 2c077b6..b50a2ce 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -46,14 +46,14 @@ public class SeqsetUtils
   {
     Hashtable sqinfo = new Hashtable();
     sqinfo.put("Name", seq.getName());
-    sqinfo.put("Start", new Integer(seq.getStart()));
-    sqinfo.put("End", new Integer(seq.getEnd()));
+    sqinfo.put("Start", Integer.valueOf(seq.getStart()));
+    sqinfo.put("End", Integer.valueOf(seq.getEnd()));
     if (seq.getDescription() != null)
     {
       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;
   }