Add annotation with sequence ref updated

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 69a5ac6..ebd95d9 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -251,7 +251,9 @@ 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 +314,7 @@ public interface AlignmentI
      */\r
     public boolean padGaps();\r
 \r
+     public void adjustSequenceAnnotations();\r
+\r
 \r
 }\r