*
* @see java.lang.Object#finalize()
*/
+ @Override
protected void finalize() throws Throwable
{
sequenceRef = null;
}
/**
- * 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
* @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)
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)
{