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