X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=10ea1542cd7bae2cbe582fe61eeb036dfe1f92f1;hb=9807ea8cc4e867378c52d51b832168d4bc611d29;hp=69a5ac62b098c51d2cb45750d554bd587c523284;hpb=7e4c4ad887a30dc26496087b0150f4ac2fe355ec;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 69a5ac6..10ea154 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -219,28 +219,6 @@ public interface AlignmentI
      */
     public void deleteAllGroups();
 
-    /**
-     * Adds a super group. A SuperGroup is a group of groups.
-     *
-     * @param sg Adds a new SuperGroup to alignment
-     */
-    public void addSuperGroup(SuperGroup sg);
-
-    /**
-     * Removes SuperGroup from alignment.
-     *
-     * @param sg This SuperGroup will be deleted from alignment.
-     */
-    public void removeSuperGroup(SuperGroup sg);
-
-    /**
-     * Finds any SuperGroup that a given SequenceGroup may be part of.
-     *
-     * @param sg SequenceGroup to search for.
-     *
-     * @return SuperGroup that contains the given SequenceGroup.
-     */
-    public SuperGroup getSuperGroup(SequenceGroup sg);
 
     /**
      * Adds a new AlignmentAnnotation to this alignment
@@ -251,7 +229,9 @@ public interface AlignmentI
      * Adds a new AlignmentAnnotation to this alignment,
      *  associated to Sequence starting at sequence index
      */
-    public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index);
+    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);
+
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index);
 
     /**
      * Deletes a specific AlignmentAnnotation from the alignment.
@@ -312,5 +292,7 @@ public interface AlignmentI
      */
     public boolean padGaps();
 
+     public void adjustSequenceAnnotations();
+
 
 }