X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=5adb70dc257b3b83711e814f8d7a3810ce77e5b9;hb=e4132370d9c650072833b53b93a4dc8dcbf92bda;hp=62b9ea9cbebb195aef8d97a76d336b021ffb0199;hpb=2a64503d035e47cf9a40e5de979fd22980e50106;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 62b9ea9..5adb70d 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -13,6 +13,7 @@ public class Alignment implements AlignmentI
   protected Vector      groups = new Vector();
   protected ArrayList   superGroup = new ArrayList();
   protected char        gapCharacter = '-';
+  public boolean featuresAdded = false;
 
   /** Make an alignment from an array of Sequences.
   *
@@ -40,14 +41,11 @@ public class Alignment implements AlignmentI
   }
 
   /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-   * Should put the new sequence in a sequence group!!!
    *
    * @param snew
    */
   public void addSequence(SequenceI snew) {
     sequences.addElement(snew);
-
-    ((SequenceGroup)groups.lastElement()).addSequence(snew);
   }
 
   public void addSequence(SequenceI[] seq) {
@@ -57,8 +55,7 @@ public class Alignment implements AlignmentI
   }
 
   /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-   * Should put the new sequence in a sequence group!!!
-   *
+    *
    * @param snew
    */
   public void setSequenceAt(int i,SequenceI snew) {
@@ -66,8 +63,6 @@ public class Alignment implements AlignmentI
     deleteSequence(oldseq);
 
     sequences.setElementAt(snew,i);
-
-    ((SequenceGroup)groups.lastElement()).addSequence(snew);
   }
 
   public Vector getGroups() {