JAL-2629 choice of hmm profile now a parameter not a selection, apis simplified

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

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 2cf673c..b558f40 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -88,11 +88,6 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   private SequenceI seqrep;
 
-  /*
-   * HMM consensus sequence for group (if any)
-   */
-  private SequenceI hmmConsensus;
-
   private int width = -1;
 
   /*
@@ -1599,18 +1594,6 @@ public class SequenceGroup implements AnnotatedCollectionI
     hmmNormaliseSequenceLogo = state;
   }
 
-  @Override
-  public SequenceI getHmmConsensus()
-  {
-    return hmmConsensus;
-  }
-
-  @Override
-  public void setHmmConsensus(SequenceI hmmSeq)
-  {
-    this.hmmConsensus = hmmSeq;
-  }
-
   public ProfilesI getConsensusData()
   {
     return consensusProfiles;
@@ -1626,4 +1609,19 @@ public class SequenceGroup implements AnnotatedCollectionI
     this.hmmProfiles = hmmProfiles;
   }
 
+  @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;
+  }
+
 }