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Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
[jalview.git]
/
src
/
jalview
/
gui
/
AppVarnaBinding.java
diff --git
a/src/jalview/gui/AppVarnaBinding.java
b/src/jalview/gui/AppVarnaBinding.java
index
25af7d1
..
8951df0
100644
(file)
--- a/
src/jalview/gui/AppVarnaBinding.java
+++ b/
src/jalview/gui/AppVarnaBinding.java
@@
-113,7
+113,8
@@
public class AppVarnaBinding extends JalviewVarnaBinding
_sideList.addMouseListener(new MouseAdapter()
{
@Override
_sideList.addMouseListener(new MouseAdapter()
{
@Override
- public void mouseClicked(MouseEvent e) {
+ public void mouseClicked(MouseEvent e)
+ {
AppVarnaBinding.this.mouseClicked(e);
}
});
AppVarnaBinding.this.mouseClicked(e);
}
});
@@
-150,7
+151,8
@@
public class AppVarnaBinding extends JalviewVarnaBinding
_listPanel.add(j, BorderLayout.NORTH);
_listPanel.add(listScroller, BorderLayout.CENTER);
_listPanel.add(j, BorderLayout.NORTH);
_listPanel.add(listScroller, BorderLayout.CENTER);
- new DropTarget(vp, new DropTargetAdapter() {
+ new DropTarget(vp, new DropTargetAdapter()
+ {
@Override
public void drop(DropTargetDropEvent dtde)
{
@Override
public void drop(DropTargetDropEvent dtde)
{
@@
-198,8
+200,7
@@
public class AppVarnaBinding extends JalviewVarnaBinding
public String[][] getParameterInfo()
{
public String[][] getParameterInfo()
{
- String[][] info =
- {
+ String[][] info = {
// Parameter Name Kind of Value Description,
{ "sequenceDBN", "String", "A raw RNA sequence" },
{ "structureDBN", "String",
// Parameter Name Kind of Value Description,
{ "sequenceDBN", "String", "A raw RNA sequence" },
{ "structureDBN", "String",
@@
-280,14
+281,17
@@
public class AppVarnaBinding extends JalviewVarnaBinding
String name = r.getName();
if (name.equals(""))
{
String name = r.getName();
if (name.equals(""))
{
- name = path.substring(path
- .lastIndexOf(File.separatorChar) + 1);
+ name = path.substring(
+ path.lastIndexOf(File.separatorChar) + 1);
}
if (mdls.size() > 1)
{
name += " (Model " + mn++ + ")";
}
}
if (mdls.size() > 1)
{
name += " (Model " + mn++ + ")";
}
- _rnaList.add(varnaPanel.getConfig().clone(), r, name, true);
+ _rnaList.add(varnaPanel.getConfig().clone(), r, name,
+ true);
+ // BH 2018 SwingJS clone of varnaPanel or its config will
+ // be the object itself, not a clone
}
}
}
}
}
}
@@
-372,9
+376,9
@@
public class AppVarnaBinding extends JalviewVarnaBinding
_sideList.ensureIndexIsVisible(index);
/*
_sideList.ensureIndexIsVisible(index);
/*
- * TODO Object newName = JOptionPane.showInputDialog( this,
+ * TODO Object newName = JvOptionPane.showInputDialog( this,
* "Specify a new name for this RNA", "Rename RNA",
* "Specify a new name for this RNA", "Rename RNA",
- * JOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if
+ * JvOptionPane.QUESTION_MESSAGE, (Icon)null, null, item.toString()); if
* (newName!=null) { item.name = newName.toString();
* this._sideList.repaint(); }
*/
* (newName!=null) { item.name = newName.toString();
* this._sideList.repaint(); }
*/
@@
-382,7
+386,7
@@
public class AppVarnaBinding extends JalviewVarnaBinding
}
@Override
}
@Override
- public String[] getPdbFile()
+ public String[] getStructureFiles()
{
return null;
}
{
return null;
}
@@
-482,7
+486,7
@@
public class AppVarnaBinding extends JalviewVarnaBinding
* restore the previous display
*/
vp.showRNA(sel.rna, sel.config);
* restore the previous display
*/
vp.showRNA(sel.rna, sel.config);
-
+
return filePath;
} catch (IOException e)
{
return filePath;
} catch (IOException e)
{
@@
-500,7
+504,8
@@
public class AppVarnaBinding extends JalviewVarnaBinding
*
* @param evt
*/
*
* @param evt
*/
- protected void changeSelectedStructure_actionPerformed(ListSelectionEvent evt)
+ protected void changeSelectedStructure_actionPerformed(
+ ListSelectionEvent evt)
{
if (!evt.getValueIsAdjusting())
{
{
if (!evt.getValueIsAdjusting())
{
@@
-542,7
+547,8
@@
public class AppVarnaBinding extends JalviewVarnaBinding
*/
public void addStructure(RNA rna)
{
*/
public void addStructure(RNA rna)
{
- VARNAConfig config = vp.getConfig().clone();
+ VARNAConfig config = vp.getConfig().clone(); // BH 2018 this will NOT be a
+ // clone in SwingJS
addStructure(rna, config);
}
addStructure(rna, config);
}
@@
-568,7
+574,7
@@
public class AppVarnaBinding extends JalviewVarnaBinding
} catch (ExceptionNAViewAlgorithm e)
{
// only throwable for draw mode = 3 NAView
} catch (ExceptionNAViewAlgorithm e)
{
// only throwable for draw mode = 3 NAView
- System.err.println("Error drawing RNA: " + e.getMessage());
+ jalview.bin.Console.errPrintln("Error drawing RNA: " + e.getMessage());
}
}
}
}
}
}