From 37e1fa33b20cd2fb68cb7f72c15784897cb8a6b1 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 22 Sep 2016 14:19:44 +0100
Subject: [PATCH 1/1] JAL-2216 new dispose() method to null references

---
 src/jalview/api/AlignViewportI.java          |    5 ++++
 src/jalview/gui/AlignViewport.java           |    3 ++-
 src/jalview/viewmodel/AlignmentViewport.java |   35 +++++++++++++++++++++++---
 3 files changed, 39 insertions(+), 4 deletions(-)

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index c08527c..0840520 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -122,6 +122,11 @@ public interface AlignViewportI extends ViewStyleI
   boolean isClosed();
 
   /**
+   * Dispose of all references or resources held by the viewport
+   */
+  void dispose();
+
+  /**
    * get the associated calculation thread manager for the view
    * 
    * @return
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 62e05d0..f755b25 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -419,10 +419,11 @@ public class AlignViewport extends AlignmentViewport implements
    * @param align
    *          DOCUMENT ME!
    */
+  @Override
   public void setAlignment(AlignmentI align)
   {
     replaceMappings(align);
-    this.alignment = align;
+    super.setAlignment(align);
   }
 
   /**
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a746e1f..cb43d90 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -58,6 +58,7 @@ import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
 import java.awt.Color;
+import java.beans.PropertyChangeSupport;
 import java.util.ArrayDeque;
 import java.util.ArrayList;
 import java.util.BitSet;
@@ -914,6 +915,35 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return false;
   }
 
+  public void setAlignment(AlignmentI align)
+  {
+    this.alignment = align;
+  }
+
+  /**
+   * Clean up references when this viewport is closed
+   */
+  @Override
+  public void dispose()
+  {
+    /*
+     * defensively null out references to large objects in case
+     * this object is not garbage collected (as if!)
+     */
+    consensus = null;
+    complementConsensus = null;
+    strucConsensus = null;
+    conservation = null;
+    quality = null;
+    groupConsensus = null;
+    groupConservation = null;
+    hconsensus = null;
+    hcomplementConsensus = null;
+    // TODO removed listeners from changeSupport?
+    changeSupport = null;
+    setAlignment(null);
+  }
+
   @Override
   public boolean isClosed()
   {
@@ -1241,10 +1271,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return ignoreGapsInConsensusCalculation;
   }
 
-  // / property change stuff
-
+  // property change stuff
   // JBPNote Prolly only need this in the applet version.
-  private final java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+  private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
           this);
 
   protected boolean showConservation = true;
-- 
1.7.10.2