X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=e3b4c64f3fec9679514b885fa55a72b281680d84;hb=536caaf2e1766309334134bb4efae5a2365de5fe;hp=3ae46b8ac4167b59a47edea353a067e2c9a187b8;hpb=4306800413a28da102c15fe7301bcac7816445fe;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3ae46b8..e3b4c64 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -53,8 +53,6 @@ public class Alignment implements AlignmentI
 
   private List<SequenceI> sequences;
 
-  private SequenceI hmmConsensus;
-
   protected List<SequenceGroup> groups;
 
   protected char gapCharacter = '-';
@@ -1661,7 +1659,7 @@ public class Alignment implements AlignmentI
     annot.hasText = false;
     if (calcId != null)
     {
-      annot.setCalcId(new String(calcId));
+      annot.setCalcId(calcId);
     }
     annot.autoCalculated = autoCalc;
     if (seqRef != null)
@@ -1956,18 +1954,6 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public SequenceI getHmmConsensus()
-  {
-    return hmmConsensus;
-  }
-
-  @Override
-  public void setHmmConsensus(SequenceI hmmConsensus)
-  {
-    this.hmmConsensus = hmmConsensus;
-  }
-
-  @Override
   public void setupJPredAlignment()
   {
     SequenceI repseq = getSequenceAt(0);
@@ -2078,4 +2064,19 @@ public class Alignment implements AlignmentI
       }
     }
   }
+
+  @Override
+  public List<SequenceI> getHmmSequences()
+  {
+    List<SequenceI> result = new ArrayList<>();
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      SequenceI seq = sequences.get(i);
+      if (seq.hasHMMProfile())
+      {
+        result.add(seq);
+      }
+    }
+    return result;
+  }
 }