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JAL-3930 Added a customizedId="JALVIEW" to launcher for use by file associations...
[jalview.git]
/
src
/
jalview
/
datamodel
/
Alignment.java
diff --git
a/src/jalview/datamodel/Alignment.java
b/src/jalview/datamodel/Alignment.java
index
02c4239
..
c4098e2
100755
(executable)
--- a/
src/jalview/datamodel/Alignment.java
+++ b/
src/jalview/datamodel/Alignment.java
@@
-47,7
+47,7
@@
import java.util.Vector;
* @author JimP
*
*/
* @author JimP
*
*/
-public class Alignment implements AlignmentI
+public class Alignment implements AlignmentI, AutoCloseable
{
private Alignment dataset;
{
private Alignment dataset;
@@
-303,15
+303,20
@@
public class Alignment implements AlignmentI
}
@Override
}
@Override
- public void finalize() throws Throwable
+ public void close()
{
if (getDataset() != null)
{
{
if (getDataset() != null)
{
- getDataset().removeAlignmentRef();
+ try
+ {
+ getDataset().removeAlignmentRef();
+ } catch (Throwable e)
+ {
+ e.printStackTrace();
+ }
}
nullReferences();
}
nullReferences();
- super.finalize();
}
/**
}
/**
@@
-1190,7
+1195,8
@@
public class Alignment implements AlignmentI
int maxLength = -1;
SequenceI current;
int maxLength = -1;
SequenceI current;
- for (int i = 0; i < sequences.size(); i++)
+ int nseq = sequences.size();
+ for (int i = 0; i < nseq; i++)
{
current = getSequenceAt(i);
for (int j = current.getLength(); j > maxLength; j--)
{
current = getSequenceAt(i);
for (int j = current.getLength(); j > maxLength; j--)
@@
-1207,7
+1213,7
@@
public class Alignment implements AlignmentI
maxLength++;
int cLength;
maxLength++;
int cLength;
- for (int i = 0; i < sequences.size(); i++)
+ for (int i = 0; i < nseq; i++)
{
current = getSequenceAt(i);
cLength = current.getLength();
{
current = getSequenceAt(i);
cLength = current.getLength();