X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=7fe4627294d84d8674dadf08c25a4f4cb7b5bc86;hb=cb8ec179c020265666678572815ab056a024da22;hp=2a398472fa37aa4ef647c1d04e47ba395ece1acb;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2a39847..7fe4627 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -219,33 +219,19 @@ 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.
+     * Adds a new AlignmentAnnotation to this alignment
      */
-    public void removeSuperGroup(SuperGroup sg);
+    public void addAnnotation(AlignmentAnnotation aa);
 
     /**
-     * Finds any SuperGroup that a given SequenceGroup may be part of.
-     *
-     * @param sg SequenceGroup to search for.
-     *
-     * @return SuperGroup that contains the given SequenceGroup.
+     * Adds a new AlignmentAnnotation to this alignment,
+     *  associated to Sequence starting at sequence index
      */
-    public SuperGroup getSuperGroup(SequenceGroup sg);
+    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);
 
-    /**
-     * Adds a new AlignmentAnnotation to this alignment
-     */
-    public void addAnnotation(AlignmentAnnotation aa);
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index);
 
     /**
      * Deletes a specific AlignmentAnnotation from the alignment.
@@ -300,6 +286,14 @@ public interface AlignmentI
     public Alignment getDataset();
 
     public void setDataset(Alignment dataset);
+    /**
+     * pads sequences with gaps (to ensure the set looks like an alignment)
+     * @return boolean true if alignment was modified
+     */
+    public boolean padGaps();
+
+    public void adjustSequenceAnnotations();
 
+    public HiddenSequences getHiddenSequences();
 
 }