X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=c4098e26594753f3caa175ca4ae6922e41e0856f;hb=0aa7f6fab658c9a203b410d4bead72217da5c9a0;hp=02c423910c1bc010459c8812e563f3af91bca7dc;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 02c4239..c4098e2 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -47,7 +47,7 @@ import java.util.Vector;
  * @author JimP
  * 
  */
-public class Alignment implements AlignmentI
+public class Alignment implements AlignmentI, AutoCloseable
 {
   private Alignment dataset;
 
@@ -303,15 +303,20 @@ public class Alignment implements AlignmentI
   }
 
   @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();
   }
 
   /**
@@ -1190,7 +1195,8 @@ public class Alignment implements AlignmentI
     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--)
@@ -1207,7 +1213,7 @@ public class Alignment implements AlignmentI
     maxLength++;
 
     int cLength;
-    for (int i = 0; i < sequences.size(); i++)
+    for (int i = 0; i < nseq; i++)
     {
       current = getSequenceAt(i);
       cLength = current.getLength();