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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git]
/
src
/
jalview
/
gui
/
StructureViewerBase.java
diff --git
a/src/jalview/gui/StructureViewerBase.java
b/src/jalview/gui/StructureViewerBase.java
index
085be71
..
bd757e8
100644
(file)
--- a/
src/jalview/gui/StructureViewerBase.java
+++ b/
src/jalview/gui/StructureViewerBase.java
@@
-90,8
+90,9
@@
public abstract class StructureViewerBase extends GStructureViewer
}
/**
}
/**
- * Singleton list of all (open) instances of structureViewerBase
- * TODO: JAL-3362 - review and adopt the swingJS-safe singleton pattern so each structure viewer base instance is kept to its own JalviewJS parent
+ * Singleton list of all (open) instances of structureViewerBase TODO:
+ * JAL-3362 - review and adopt the swingJS-safe singleton pattern so each
+ * structure viewer base instance is kept to its own JalviewJS parent
*/
private static List<JalviewStructureDisplayI> svbs = new ArrayList<>();
*/
private static List<JalviewStructureDisplayI> svbs = new ArrayList<>();
@@
-607,7
+608,8
@@
public abstract class StructureViewerBase extends GStructureViewer
chainMenu.add(menuItem);
}
}
chainMenu.add(menuItem);
}
}
- void setHetatmMenuItems(Map<String,String> hetatmNames)
+
+ void setHetatmMenuItems(Map<String, String> hetatmNames)
{
hetatmMenu.removeAll();
if (hetatmNames == null || hetatmNames.isEmpty())
{
hetatmMenu.removeAll();
if (hetatmNames == null || hetatmNames.isEmpty())
@@
-616,7
+618,7
@@
public abstract class StructureViewerBase extends GStructureViewer
return;
}
hetatmMenu.setVisible(true);
return;
}
hetatmMenu.setVisible(true);
- allHetatmBeingSelected=false;
+ allHetatmBeingSelected = false;
JMenuItem allMenuItem = new JMenuItem(
MessageManager.getString("label.all"));
JMenuItem noneMenuItem = new JMenuItem(
JMenuItem allMenuItem = new JMenuItem(
MessageManager.getString("label.all"));
JMenuItem noneMenuItem = new JMenuItem(
@@
-624,46
+626,52
@@
public abstract class StructureViewerBase extends GStructureViewer
allMenuItem.addActionListener(new ActionListener()
{
@Override
allMenuItem.addActionListener(new ActionListener()
{
@Override
- public void actionPerformed(ActionEvent e) {
+ public void actionPerformed(ActionEvent e)
{
{
- allHetatmBeingSelected=true;
- // Toggle state of everything - on
- for (int i = 0; i < hetatmMenu.getItemCount(); i++)
{
{
- if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ allHetatmBeingSelected = true;
+ // Toggle state of everything - on
+ for (int i = 0; i < hetatmMenu.getItemCount(); i++)
{
{
- ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(true);
+ if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(true);
+ }
}
}
+ allHetatmBeingSelected = false;
+ showSelectedHetatms();
}
}
- allHetatmBeingSelected=false;
- showSelectedHetatms();
}
}
- }});
+ });
noneMenuItem.addActionListener(new ActionListener()
{
@Override
noneMenuItem.addActionListener(new ActionListener()
{
@Override
- public void actionPerformed(ActionEvent e) {
+ public void actionPerformed(ActionEvent e)
{
{
- allHetatmBeingSelected=true;
- // Toggle state of everything off
- for (int i = 0; i < hetatmMenu.getItemCount(); i++)
{
{
- if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ allHetatmBeingSelected = true;
+ // Toggle state of everything off
+ for (int i = 0; i < hetatmMenu.getItemCount(); i++)
{
{
- ((JCheckBoxMenuItem) hetatmMenu.getItem(i)).setSelected(false);
+ if (hetatmMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ {
+ ((JCheckBoxMenuItem) hetatmMenu.getItem(i))
+ .setSelected(false);
+ }
}
}
+ allHetatmBeingSelected = false;
+ showSelectedHetatms();
}
}
- allHetatmBeingSelected=false;
- showSelectedHetatms();
}
}
- }});
+ });
hetatmMenu.add(noneMenuItem);
hetatmMenu.add(allMenuItem);
for (Map.Entry<String, String> chain : hetatmNames.entrySet())
{
hetatmMenu.add(noneMenuItem);
hetatmMenu.add(allMenuItem);
for (Map.Entry<String, String> chain : hetatmNames.entrySet())
{
- JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem(chain.getKey(), false);
+ JCheckBoxMenuItem menuItem = new JCheckBoxMenuItem(chain.getKey(),
+ false);
menuItem.setToolTipText(chain.getValue());
menuItem.addItemListener(new ItemListener()
{
menuItem.setToolTipText(chain.getValue());
menuItem.addItemListener(new ItemListener()
{
@@
-671,7
+679,7
@@
public abstract class StructureViewerBase extends GStructureViewer
public void itemStateChanged(ItemEvent evt)
{
if (!allHetatmBeingSelected)
public void itemStateChanged(ItemEvent evt)
{
if (!allHetatmBeingSelected)
- {
+ {
// update viewer only when we were clicked, not programmatically
// checked/unchecked
showSelectedHetatms();
// update viewer only when we were clicked, not programmatically
// checked/unchecked
showSelectedHetatms();
@@
-1237,6
+1245,7
@@
public abstract class StructureViewerBase extends GStructureViewer
}
getBinding().showChains(toshow);
}
}
getBinding().showChains(toshow);
}
+
/**
* Display selected hetatms in viewer
*/
/**
* Display selected hetatms in viewer
*/
@@
-1256,6
+1265,7
@@
public abstract class StructureViewerBase extends GStructureViewer
}
getBinding().showHetatms(toshow);
}
}
getBinding().showHetatms(toshow);
}
+
/**
* Tries to fetch a PDB file and save to a temporary local file. Returns the
* saved file path if successful, or null if not.
/**
* Tries to fetch a PDB file and save to a temporary local file. Returns the
* saved file path if successful, or null if not.
@@
-1459,12
+1469,15
@@
public abstract class StructureViewerBase extends GStructureViewer
// TODO: check for memory leaks where instance isn't finalised because jmb
// holds a reference to the window
// jmb = null;
// TODO: check for memory leaks where instance isn't finalised because jmb
// holds a reference to the window
// jmb = null;
-
- try {
+
+ try
+ {
svbs.remove(this);
} catch (Throwable t)
{
svbs.remove(this);
} catch (Throwable t)
{
- Console.info("Unexpected exception when deregistering structure viewer",t);
+ Console.info(
+ "Unexpected exception when deregistering structure viewer",
+ t);
}
dispose();
}
}
dispose();
}