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JAL-2216 explicitly null AnnotationPanel and AnnotationRenderer fields
[jalview.git]
/
src
/
jalview
/
gui
/
AlignmentPanel.java
diff --git
a/src/jalview/gui/AlignmentPanel.java
b/src/jalview/gui/AlignmentPanel.java
index
4d49bc2
..
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 boolean dontScrollComplement;
+ private PropertyChangeListener propertyChangeListener;
+
/**
* Creates a new AlignmentPanel object.
*
/**
* Creates a new AlignmentPanel object.
*
@@
-135,8
+137,9
@@
public class AlignmentPanel extends GAlignmentPanel implements
vscroll.addAdjustmentListener(this);
final AlignmentPanel ap = this;
vscroll.addAdjustmentListener(this);
final AlignmentPanel ap = this;
- av.addPropertyChangeListener(new PropertyChangeListener()
+ propertyChangeListener = new PropertyChangeListener()
{
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals("alignment"))
public void propertyChange(PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals("alignment"))
@@
-145,7
+148,8
@@
public class AlignmentPanel extends GAlignmentPanel implements
alignmentChanged();
}
}
alignmentChanged();
}
}
- });
+ };
+ av.addPropertyChangeListener(propertyChangeListener);
fontChanged();
adjustAnnotationHeight();
updateLayout();
fontChanged();
adjustAnnotationHeight();
updateLayout();
@@
-509,6
+513,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
* automatically adjust annotation panel height for new annotation whilst
* ensuring the alignment is still visible.
*/
* automatically adjust annotation panel height for new annotation whilst
* ensuring the alignment is still visible.
*/
+ @Override
public void adjustAnnotationHeight()
{
// TODO: display vertical annotation scrollbar if necessary
public void adjustAnnotationHeight()
{
// TODO: display vertical annotation scrollbar if necessary
@@
-749,6
+754,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
* @param evt
* DOCUMENT ME!
*/
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
int oldX = av.getStartRes();
public void adjustmentValueChanged(AdjustmentEvent evt)
{
int oldX = av.getStartRes();
@@
-782,6
+788,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
// as preference setting
SwingUtilities.invokeLater(new Runnable()
{
// as preference setting
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
setScrollValues(av.getStartRes(), av.getStartSeq());
public void run()
{
setScrollValues(av.getStartRes(), av.getStartSeq());
@@
-852,6
+859,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
* Repaint the alignment including the annotations and overview panels (if
* shown).
*/
* Repaint the alignment including the annotations and overview panels (if
* shown).
*/
+ @Override
public void paintAlignment(boolean updateOverview)
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
public void paintAlignment(boolean updateOverview)
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
@@
-878,6
+886,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
* @param g
* DOCUMENT ME!
*/
* @param g
* DOCUMENT ME!
*/
+ @Override
public void paintComponent(Graphics g)
{
invalidate();
public void paintComponent(Graphics g)
{
invalidate();
@@
-936,6
+945,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
* @throws PrinterException
* DOCUMENT ME!
*/
* @throws PrinterException
* DOCUMENT ME!
*/
+ @Override
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
{
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
{
@@
-1262,14
+1272,18
@@
public class AlignmentPanel extends GAlignmentPanel implements
void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
{
void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
{
- long progress = System.currentTimeMillis();
+ int boarderBottomOffset = 5;
+ long pSessionId = System.currentTimeMillis();
headless = (System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true"));
if (alignFrame != null && !headless)
{
headless = (System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true"));
if (alignFrame != null && !headless)
{
- alignFrame.setProgressBar(MessageManager.formatMessage(
+ if (file != null)
+ {
+ alignFrame.setProgressBar(MessageManager.formatMessage(
"status.saving_file", new Object[] { type.getLabel() }),
"status.saving_file", new Object[] { type.getLabel() }),
- progress);
+ pSessionId);
+ }
}
try
{
}
try
{
@@
-1295,14
+1309,15
@@
public class AlignmentPanel extends GAlignmentPanel implements
}
im = new jalview.util.ImageMaker(this, type, imageAction,
}
im = new jalview.util.ImageMaker(this, type, imageAction,
- aDimension.getWidth(), aDimension.getHeight(), file,
- imageTitle);
+ aDimension.getWidth(), aDimension.getHeight()
+ + boarderBottomOffset, file,
+ imageTitle, alignFrame, pSessionId, headless);
if (av.getWrapAlignment())
{
if (im.getGraphics() != null)
{
printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
if (av.getWrapAlignment())
{
if (im.getGraphics() != null)
{
printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
- aDimension.getHeight(), 0);
+ aDimension.getHeight() + boarderBottomOffset, 0);
im.writeImage();
}
}
im.writeImage();
}
}
@@
-1315,6
+1330,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
im.writeImage();
}
}
im.writeImage();
}
}
+
} catch (OutOfMemoryError err)
{
// Be noisy here.
} catch (OutOfMemoryError err)
{
// Be noisy here.
@@
-1328,12
+1344,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
}
} finally
{
}
} finally
{
- if (alignFrame != null && !headless)
- {
- alignFrame.setProgressBar(
- MessageManager.getString("status.export_complete"),
- progress);
- }
+
}
}
}
}
@@
-1587,8
+1598,18
@@
public class AlignmentPanel extends GAlignmentPanel implements
PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
PaintRefresher.RemoveComponent(this);
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)
{
if (av != null)
{
+ av.removePropertyChangeListener(propertyChangeListener);
jalview.structure.StructureSelectionManager ssm = av
.getStructureSelectionManager();
ssm.removeStructureViewerListener(getSeqPanel(), null);
jalview.structure.StructureSelectionManager ssm = av
.getStructureSelectionManager();
ssm.removeStructureViewerListener(getSeqPanel(), null);
@@
-1596,7
+1617,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
ssm.removeCommandListener(av);
ssm.removeStructureViewerListener(getSeqPanel(), null);
ssm.removeSelectionListener(getSeqPanel());
ssm.removeCommandListener(av);
ssm.removeStructureViewerListener(getSeqPanel(), null);
ssm.removeSelectionListener(getSeqPanel());
- av.setAlignment(null);
+ av.dispose();
av = null;
}
else
av = null;
}
else