X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=3b0ca46f83e01ac83aae1e3c7116fc5b1a09f71a;hb=f1698a3cc3dbeb218b63b157ff46bd092882537d;hp=93ad332d24f13d9babd3c7d253a151c745d971d1;hpb=ad8b755b7d5daaa914a61fc4ca476196551b2f0a;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 93ad332..3b0ca46 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;
 
@@ -302,15 +302,20 @@ 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();
   }
 
   /**
@@ -717,6 +722,17 @@ public class Alignment implements AlignmentI
     return maxLength;
   }
 
+  @Override
+  public int getVisibleWidth()
+  {
+    int w = getWidth();
+    if (hiddenCols != null)
+    {
+      w -= hiddenCols.getSize();
+    }
+    return w;
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -1893,9 +1909,12 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setHiddenColumns(HiddenColumns cols)
+  public boolean setHiddenColumns(HiddenColumns cols)
   {
+    boolean changed = cols == null ? hiddenCols != null
+            : !cols.equals(hiddenCols);
     hiddenCols = cols;
+    return changed;
   }
 
   @Override