X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentAnnotation.java;h=7990a5cfb6afb30796bdb60f1e1ca6945d1f0611;hb=ddcce112558a130196ca384c4683b4f9b7d7d133;hp=830dbc72a4645024a1baa4710396d9c51cd02171;hpb=837b34ffd916e7aa1cefd068b952652bad8482b5;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 830dbc7..7990a5c 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -245,6 +245,7 @@ public class AlignmentAnnotation
    * 
    * @see java.lang.Object#finalize()
    */
+  @Override
   protected void finalize() throws Throwable
   {
     sequenceRef = null;
@@ -1036,11 +1037,11 @@ public class AlignmentAnnotation
   }
 
   /**
-   * Associate this annotion with the aligned residues of a particular sequence.
-   * sequenceMapping will be updated in the following way: null sequenceI -
-   * existing mapping will be discarded but annotations left in mapped
-   * positions. valid sequenceI not equal to current sequenceRef: mapping is
-   * discarded and rebuilt assuming 1:1 correspondence TODO: overload with
+   * Associate this annotation with the aligned residues of a particular
+   * sequence. sequenceMapping will be updated in the following way: null
+   * sequenceI - existing mapping will be discarded but annotations left in
+   * mapped positions. valid sequenceI not equal to current sequenceRef: mapping
+   * is discarded and rebuilt assuming 1:1 correspondence TODO: overload with
    * parameter to specify correspondence between current and new sequenceRef
    * 
    * @param sequenceI
@@ -1304,7 +1305,8 @@ public class AlignmentAnnotation
    * @note caller should add the remapped annotation to newref if they have not
    *       already
    */
-  public void remap(SequenceI newref, int[][] mapping, int from, int to,
+  public void remap(SequenceI newref, HashMap<Integer, int[]> mapping,
+          int from, int to,
           int idxoffset)
   {
     if (mapping != null)
@@ -1312,7 +1314,7 @@ public class AlignmentAnnotation
       Map<Integer, Annotation> old = sequenceMapping;
       Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
       int index = -1;
-      for (int mp[] : mapping)
+      for (int mp[] : mapping.values())
       {
         if (index++ < 0)
         {