* @author JimP
*
*/
-public class Alignment implements AlignmentI
+public class Alignment implements AlignmentI, AutoCloseable
{
private Alignment dataset;
{
synchronized (sequences)
{
-
+
if (i > -1 && i < sequences.size())
{
return sequences.get(i);
}
@Override
- public void finalize() throws Throwable
+ public void close()
{
if (getDataset() != null)
{
- getDataset().removeAlignmentRef();
+ try
+ {
+ getDataset().removeAlignmentRef();
+ } catch (Throwable e)
+ {
+ e.printStackTrace();
+ }
}
nullReferences();
- super.finalize();
}
/**
public int getWidth()
{
int maxLength = -1;
-
+
for (int i = 0; i < sequences.size(); i++)
{
maxLength = Math.max(maxLength, getSequenceAt(i).getLength());