JAL-2629 update spikes/mungo to latest

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 6b100ea..e3b4c64 100755 (executable)
--- 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 = '-';
@@ -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;
+  }
 }