JAL-2216 explicitly null AnnotationPanel and AnnotationRenderer fields

when closing AlignmentPanel

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 87d5933..424d52f 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -101,6 +101,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   private boolean dontScrollComplement;
 
+  private PropertyChangeListener propertyChangeListener;
+
   /**
    * Creates a new AlignmentPanel object.
    * 
@@ -135,7 +137,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     vscroll.addAdjustmentListener(this);
 
     final AlignmentPanel ap = this;
-    av.addPropertyChangeListener(new PropertyChangeListener()
+    propertyChangeListener = new PropertyChangeListener()
     {
       @Override
       public void propertyChange(PropertyChangeEvent evt)
@@ -146,7 +148,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
           alignmentChanged();
         }
       }
-    });
+    };
+    av.addPropertyChangeListener(propertyChangeListener);
     fontChanged();
     adjustAnnotationHeight();
     updateLayout();
@@ -1595,8 +1598,18 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
     PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
     PaintRefresher.RemoveComponent(this);
+
+    /*
+     * try to ensure references are nulled
+     */
+    if (annotationPanel != null)
+    {
+      annotationPanel.dispose();
+    }
+
     if (av != null)
     {
+      av.removePropertyChangeListener(propertyChangeListener);
       jalview.structure.StructureSelectionManager ssm = av
               .getStructureSelectionManager();
       ssm.removeStructureViewerListener(getSeqPanel(), null);
@@ -1604,7 +1617,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       ssm.removeCommandListener(av);
       ssm.removeStructureViewerListener(getSeqPanel(), null);
       ssm.removeSelectionListener(getSeqPanel());
-      av.setAlignment(null);
+      av.dispose();
       av = null;
     }
     else

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 7450555..0b2f6cc 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -123,8 +123,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
   boolean mouseDragging = false;
 
-  boolean MAC = false;
-
   // for editing cursor
   int cursorX = 0;
 
@@ -142,9 +140,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
    */
   public AnnotationPanel(AlignmentPanel ap)
   {
-
-    MAC = jalview.util.Platform.isAMac();
-
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
     ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -1139,4 +1134,25 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return null;
     }
   }
+
+  /**
+   * Try to ensure any references held are nulled
+   */
+  public void dispose()
+  {
+    av = null;
+    ap = null;
+    image = null;
+    fadedImage = null;
+    gg = null;
+    _mwl = null;
+
+    /*
+     * I created the renderer so I will dispose of it
+     */
+    if (renderer != null)
+    {
+      renderer.dispose();
+    }
+  }
 }

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 82f6ffb..e58ba02 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -30,6 +30,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
+import jalview.util.Platform;
 
 import java.awt.BasicStroke;
 import java.awt.Color;
@@ -57,6 +58,70 @@ public class AnnotationRenderer
    */
   private final boolean debugRedraw;
 
+  private int charWidth, endRes, charHeight;
+
+  private boolean validCharWidth, hasHiddenColumns;
+
+  private FontMetrics fm;
+
+  private final boolean MAC = Platform.isAMac();
+
+  boolean av_renderHistogram = true, av_renderProfile = true,
+          av_normaliseProfile = false;
+
+  ColourSchemeI profcolour = null;
+
+  private ColumnSelection columnSelection;
+
+  private Hashtable[] hconsensus;
+
+  private Hashtable[] complementConsensus;
+
+  private Hashtable[] hStrucConsensus;
+
+  private boolean av_ignoreGapsConsensus;
+
+  /**
+   * attributes set from AwtRenderPanelI
+   */
+  /**
+   * old image used when data is currently being calculated and cannot be
+   * rendered
+   */
+  private Image fadedImage;
+
+  /**
+   * panel being rendered into
+   */
+  private ImageObserver annotationPanel;
+
+  /**
+   * width of image to render in panel
+   */
+  private int imgWidth;
+
+  /**
+   * offset to beginning of visible area
+   */
+  private int sOffset;
+
+  /**
+   * offset to end of visible area
+   */
+  private int visHeight;
+
+  /**
+   * indicate if the renderer should only render the visible portion of the
+   * annotation given the current view settings
+   */
+  private boolean useClip = true;
+
+  /**
+   * master flag indicating if renderer should ever try to clip. not enabled for
+   * jalview 2.8.1
+   */
+  private boolean canClip = false;
+
   public AnnotationRenderer()
   {
     this(false);
@@ -74,6 +139,18 @@ public class AnnotationRenderer
     this.debugRedraw = debugRedraw;
   }
 
+  /**
+   * Remove any references and resources when this object is no longer required
+   */
+  public void dispose()
+  {
+    hconsensus = null;
+    complementConsensus = null;
+    hStrucConsensus = null;
+    fadedImage = null;
+    annotationPanel = null;
+  }
+
   void drawStemAnnot(Graphics g, Annotation[] row_annotations,
           int lastSSX, int x, int y, int iconOffset, int startRes,
           int column, boolean validRes, boolean validEnd)
@@ -134,70 +211,6 @@ public class AnnotationRenderer
     g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
   }
 
-  private int charWidth, endRes, charHeight;
-
-  private boolean validCharWidth, hasHiddenColumns;
-
-  private FontMetrics fm;
-
-  private final boolean MAC = jalview.util.Platform.isAMac();
-
-  boolean av_renderHistogram = true, av_renderProfile = true,
-          av_normaliseProfile = false;
-
-  ColourSchemeI profcolour = null;
-
-  private ColumnSelection columnSelection;
-
-  private Hashtable[] hconsensus;
-
-  private Hashtable[] complementConsensus;
-
-  private Hashtable[] hStrucConsensus;
-
-  private boolean av_ignoreGapsConsensus;
-
-  /**
-   * attributes set from AwtRenderPanelI
-   */
-  /**
-   * old image used when data is currently being calculated and cannot be
-   * rendered
-   */
-  private Image fadedImage;
-
-  /**
-   * panel being rendered into
-   */
-  private ImageObserver annotationPanel;
-
-  /**
-   * width of image to render in panel
-   */
-  private int imgWidth;
-
-  /**
-   * offset to beginning of visible area
-   */
-  private int sOffset;
-
-  /**
-   * offset to end of visible area
-   */
-  private int visHeight;
-
-  /**
-   * indicate if the renderer should only render the visible portion of the
-   * annotation given the current view settings
-   */
-  private boolean useClip = true;
-
-  /**
-   * master flag indicating if renderer should ever try to clip. not enabled for
-   * jalview 2.8.1
-   */
-  private boolean canClip = false;
-
   void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
           Annotation[] row_annotations, int lastSSX, int x, int y,
           int iconOffset, int startRes, int column, boolean validRes,