JAL-3725 restrict mapped virtual feature location to mapped region

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 11d28a0..3b0ca46 100755 (executable)
--- 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();
   }
 
   /**
@@ -712,12 +717,8 @@ public class Alignment implements AlignmentI
   
     for (int i = 0; i < sequences.size(); i++)
     {
-      if (getSequenceAt(i).getLength() > maxLength)
-      {
-        maxLength = getSequenceAt(i).getLength();
-      }
+      maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
     }
-  
     return maxLength;
   }
 
@@ -1908,9 +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