2.08, not 2.07

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 69a5ac6..7fe4627 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -219,28 +219,6 @@ public interface AlignmentI
      */\r
     public void deleteAllGroups();\r
 \r
-    /**\r
-     * Adds a super group. A SuperGroup is a group of groups.\r
-     *\r
-     * @param sg Adds a new SuperGroup to alignment\r
-     */\r
-    public void addSuperGroup(SuperGroup sg);\r
-\r
-    /**\r
-     * Removes SuperGroup from alignment.\r
-     *\r
-     * @param sg This SuperGroup will be deleted from alignment.\r
-     */\r
-    public void removeSuperGroup(SuperGroup sg);\r
-\r
-    /**\r
-     * Finds any SuperGroup that a given SequenceGroup may be part of.\r
-     *\r
-     * @param sg SequenceGroup to search for.\r
-     *\r
-     * @return SuperGroup that contains the given SequenceGroup.\r
-     */\r
-    public SuperGroup getSuperGroup(SequenceGroup sg);\r
 \r
     /**\r
      * Adds a new AlignmentAnnotation to this alignment\r
@@ -251,7 +229,9 @@ public interface AlignmentI
      * Adds a new AlignmentAnnotation to this alignment,\r
      *  associated to Sequence starting at sequence index\r
      */\r
-    public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index);\r
+    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);\r
+\r
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index);\r
 \r
     /**\r
      * Deletes a specific AlignmentAnnotation from the alignment.\r
@@ -312,5 +292,8 @@ public interface AlignmentI
      */\r
     public boolean padGaps();\r
 \r
+    public void adjustSequenceAnnotations();\r
+\r
+    public HiddenSequences getHiddenSequences();\r
 \r
 }\r