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JAL-2488 remove finalize methods
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 1 Sep 2017 09:13:19 +0000
(10:13 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 1 Sep 2017 09:13:19 +0000
(10:13 +0100)
13 files changed:
src/jalview/appletgui/AlignViewport.java
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src/jalview/appletgui/AlignmentPanel.java
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src/jalview/controller/AlignViewController.java
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src/jalview/datamodel/AlignmentAnnotation.java
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src/jalview/datamodel/Mapping.java
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src/jalview/gui/AlignFrame.java
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src/jalview/gui/Jalview2XML.java
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src/jalview/gui/ViewSelectionMenu.java
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src/jalview/io/FileLoader.java
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src/jalview/io/InputStreamParser.java
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src/jalview/javascript/JSFunctionExec.java
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src/jalview/javascript/MouseOverStructureListener.java
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src/jalview/ws/jws2/jabaws2/Jws2Instance.java
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diff --git
a/src/jalview/appletgui/AlignViewport.java
b/src/jalview/appletgui/AlignViewport.java
index
b07666e
..
36cb185
100644
(file)
--- a/
src/jalview/appletgui/AlignViewport.java
+++ b/
src/jalview/appletgui/AlignViewport.java
@@
-62,15
+62,6
@@
public class AlignViewport extends AlignmentViewport
private AnnotationColumnChooser annotationColumnSelectionState;
private AnnotationColumnChooser annotationColumnSelectionState;
- @Override
- public void finalize()
- {
- applet = null;
- quality = null;
- alignment = null;
- colSel = null;
- }
-
public AlignViewport(AlignmentI al, JalviewLite applet)
{
super(al);
public AlignViewport(AlignmentI al, JalviewLite applet)
{
super(al);
diff --git
a/src/jalview/appletgui/AlignmentPanel.java
b/src/jalview/appletgui/AlignmentPanel.java
index
8e333ba
..
bb26caa
100644
(file)
--- a/
src/jalview/appletgui/AlignmentPanel.java
+++ b/
src/jalview/appletgui/AlignmentPanel.java
@@
-73,23
+73,6
@@
public class AlignmentPanel extends Panel
// this value is set false when selection area being dragged
boolean fastPaint = true;
// this value is set false when selection area being dragged
boolean fastPaint = true;
- @Override
- public void finalize() throws Throwable
- {
- alignFrame = null;
- av = null;
- vpRanges = null;
- seqPanel = null;
- seqPanelHolder = null;
- sequenceHolderPanel = null;
- scalePanel = null;
- scalePanelHolder = null;
- annotationPanel = null;
- annotationPanelHolder = null;
- annotationSpaceFillerHolder = null;
- super.finalize();
- }
-
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
try
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
try
diff --git
a/src/jalview/controller/AlignViewController.java
b/src/jalview/controller/AlignViewController.java
index
dd05843
..
e44c32d
100644
(file)
--- a/
src/jalview/controller/AlignViewController.java
+++ b/
src/jalview/controller/AlignViewController.java
@@
-52,14
+52,6
@@
public class AlignViewController implements AlignViewControllerI
*/
private AlignViewControllerGuiI avcg;
*/
private AlignViewControllerGuiI avcg;
- @Override
- protected void finalize() throws Throwable
- {
- viewport = null;
- alignPanel = null;
- avcg = null;
- };
-
public AlignViewController(AlignViewControllerGuiI alignFrame,
AlignViewportI viewport, AlignmentViewPanel alignPanel)
{
public AlignViewController(AlignViewControllerGuiI alignFrame,
AlignViewportI viewport, AlignmentViewPanel alignPanel)
{
diff --git
a/src/jalview/datamodel/AlignmentAnnotation.java
b/src/jalview/datamodel/AlignmentAnnotation.java
index
c464af2
..
09facbf
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentAnnotation.java
+++ b/
src/jalview/datamodel/AlignmentAnnotation.java
@@
-241,19
+241,6
@@
public class AlignmentAnnotation
private boolean isrna;
private boolean isrna;
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#finalize()
- */
- @Override
- protected void finalize() throws Throwable
- {
- sequenceRef = null;
- groupRef = null;
- super.finalize();
- }
-
public static int getGraphValueFromString(String string)
{
if (string.equalsIgnoreCase("BAR_GRAPH"))
public static int getGraphValueFromString(String string)
{
if (string.equalsIgnoreCase("BAR_GRAPH"))
diff --git
a/src/jalview/datamodel/Mapping.java
b/src/jalview/datamodel/Mapping.java
index
328b96a
..
b5184fb
100644
(file)
--- a/
src/jalview/datamodel/Mapping.java
+++ b/
src/jalview/datamodel/Mapping.java
@@
-693,19
+693,6
@@
public class Mapping
to = tto;
}
to = tto;
}
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#finalize()
- */
- @Override
- protected void finalize() throws Throwable
- {
- map = null;
- to = null;
- super.finalize();
- }
-
/**
* Returns an iterator which can serve up the aligned codon column positions
* and their corresponding peptide products
/**
* Returns an iterator which can serve up the aligned codon column positions
* and their corresponding peptide products
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
13b715e
..
fd640cf
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-2713,8
+2713,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
- true);
+ AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
if (!copyAnnotation)
{
/*
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
1658f0f
..
a64a475
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-216,34
+216,6
@@
public class Jalview2XML
}
}
}
}
- void clearSeqRefs()
- {
- if (_cleartables)
- {
- if (seqRefIds != null)
- {
- seqRefIds.clear();
- }
- if (seqsToIds != null)
- {
- seqsToIds.clear();
- }
- if (incompleteSeqs != null)
- {
- incompleteSeqs.clear();
- }
- // seqRefIds = null;
- // seqsToIds = null;
- }
- else
- {
- // do nothing
- warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
- // seqRefIds = new Hashtable();
- // seqsToIds = new IdentityHashMap();
- }
- }
-
void initSeqRefs()
{
if (seqsToIds == null)
void initSeqRefs()
{
if (seqsToIds == null)
@@
-5341,28
+5313,25
@@
public class Jalview2XML
}
}
- public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
- boolean keepSeqRefs)
+ /**
+ * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
+ * view as XML (but not to file), and then reloading it
+ *
+ * @param ap
+ * @return
+ */
+ public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
{
initSeqRefs();
JalviewModel jm = saveState(ap, null, null, null);
{
initSeqRefs();
JalviewModel jm = saveState(ap, null, null, null);
- if (!keepSeqRefs)
- {
- clearSeqRefs();
- jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
- }
- else
- {
- uniqueSetSuffix = "";
- jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
- // overwrite the
- // view we just
- // copied
- }
+ uniqueSetSuffix = "";
+ jm.getJalviewModelSequence().getViewport(0).setId(null);
+ // we don't overwrite the view we just copied
+
if (this.frefedSequence == null)
{
if (this.frefedSequence == null)
{
- frefedSequence = new Vector();
+ frefedSequence = new Vector<SeqFref>();
}
viewportsAdded.clear();
}
viewportsAdded.clear();
@@
-5382,32
+5351,8
@@
public class Jalview2XML
return af.alignPanel;
}
return af.alignPanel;
}
- /**
- * flag indicating if hashtables should be cleared on finalization TODO this
- * flag may not be necessary
- */
- private final boolean _cleartables = true;
-
private Hashtable jvids2vobj;
private Hashtable jvids2vobj;
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#finalize()
- */
- @Override
- protected void finalize() throws Throwable
- {
- // really make sure we have no buried refs left.
- if (_cleartables)
- {
- clearSeqRefs();
- }
- this.seqRefIds = null;
- this.seqsToIds = null;
- super.finalize();
- }
-
private void warn(String msg)
{
warn(msg, null);
private void warn(String msg)
{
warn(msg, null);
diff --git
a/src/jalview/gui/ViewSelectionMenu.java
b/src/jalview/gui/ViewSelectionMenu.java
index
cdbb4fa
..
2a7743a
100644
(file)
--- a/
src/jalview/gui/ViewSelectionMenu.java
+++ b/
src/jalview/gui/ViewSelectionMenu.java
@@
-60,15
+60,6
@@
public class ViewSelectionMenu extends JMenu
private ItemListener _handler;
private ItemListener _handler;
- @Override
- protected void finalize() throws Throwable
- {
- _selectedviews = null;
- _handler = null;
- _allviews = null;
- super.finalize();
- }
-
/**
* create a new view selection menu. This menu has some standard entries
* (select all, invert selection), and a checkbox for every view. Mousing over
/**
* create a new view selection menu. This menu has some standard entries
* (select all, invert selection), and a checkbox for every view. Mousing over
diff --git
a/src/jalview/io/FileLoader.java
b/src/jalview/io/FileLoader.java
index
26641b1
..
f26d6da
100755
(executable)
--- a/
src/jalview/io/FileLoader.java
+++ b/
src/jalview/io/FileLoader.java
@@
-606,18
+606,4
@@
public class FileLoader implements Runnable
return tempStructFile.toString();
}
return tempStructFile.toString();
}
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#finalize()
- */
- @Override
- protected void finalize() throws Throwable
- {
- source = null;
- alignFrame = null;
- viewport = null;
- super.finalize();
- }
-
}
}
diff --git
a/src/jalview/io/InputStreamParser.java
b/src/jalview/io/InputStreamParser.java
index
d269e97
..
65ba74a
100644
(file)
--- a/
src/jalview/io/InputStreamParser.java
+++ b/
src/jalview/io/InputStreamParser.java
@@
-47,11
+47,4
@@
public class InputStreamParser extends FileParse
error = false;
}
error = false;
}
- @Override
- protected void finalize() throws Throwable
- {
- dataIn = null;
- super.finalize();
- }
-
}
}
diff --git
a/src/jalview/javascript/JSFunctionExec.java
b/src/jalview/javascript/JSFunctionExec.java
index
083cd26
..
29f3fa9
100644
(file)
--- a/
src/jalview/javascript/JSFunctionExec.java
+++ b/
src/jalview/javascript/JSFunctionExec.java
@@
-39,19
+39,6
@@
public class JSFunctionExec implements Runnable
jvlite.setExecutor(this);
}
jvlite.setExecutor(this);
}
- @Override
- protected void finalize() throws Throwable
- {
- jvlite = null;
- executor = null;
- if (jsExecQueue != null)
- {
- jsExecQueue.clear();
- }
- jsExecQueue = null;
- super.finalize();
- }
-
private Vector jsExecQueue;
private Thread executor = null;
private Vector jsExecQueue;
private Thread executor = null;
diff --git
a/src/jalview/javascript/MouseOverStructureListener.java
b/src/jalview/javascript/MouseOverStructureListener.java
index
874bfd3
..
6071933
100644
(file)
--- a/
src/jalview/javascript/MouseOverStructureListener.java
+++ b/
src/jalview/javascript/MouseOverStructureListener.java
@@
-299,13
+299,6
@@
public class MouseOverStructureListener extends JSFunctionExec
}
@Override
}
@Override
- public void finalize() throws Throwable
- {
- jvlite = null;
- super.finalize();
- }
-
- @Override
public void releaseReferences(Object svl)
{
public void releaseReferences(Object svl)
{
diff --git
a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
index
cb8f75a
..
2f3c298
100644
(file)
--- a/
src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/
src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@
-170,13
+170,11
@@
public class Jws2Instance
{
try
{
{
try
{
- Closeable svc = (Closeable) service;
- service = null;
- svc.close();
- } catch (Exception e)
+ ((Closeable) service).close();
+ } catch (Throwable t)
{
{
+ // ignore
}
}
- ;
}
super.finalize();
}
}
super.finalize();
}