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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git]
/
src
/
jalview
/
appletgui
/
AppletJmol.java
diff --git
a/src/jalview/appletgui/AppletJmol.java
b/src/jalview/appletgui/AppletJmol.java
index
d894a47
..
b925284
100644
(file)
--- a/
src/jalview/appletgui/AppletJmol.java
+++ b/
src/jalview/appletgui/AppletJmol.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-25,6
+25,7
@@
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
+import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
@@
-59,7
+60,6
@@
import java.awt.event.KeyListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.ArrayList;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.util.ArrayList;
-import java.util.Hashtable;
import java.util.List;
import java.util.Vector;
import java.util.List;
import java.util.Vector;
@@
-204,7
+204,7
@@
public class AppletJmol extends EmbmenuFrame implements
String alreadyMapped = StructureSelectionManager
.getStructureSelectionManager(ap.av.applet)
.alreadyMappedToFile(pdbentry.getId());
String alreadyMapped = StructureSelectionManager
.getStructureSelectionManager(ap.av.applet)
.alreadyMappedToFile(pdbentry.getId());
- MCview.PDBfile reader = null;
+ StructureFile reader = null;
if (alreadyMapped != null)
{
reader = StructureSelectionManager.getStructureSelectionManager(
if (alreadyMapped != null)
{
reader = StructureSelectionManager.getStructureSelectionManager(
@@
-283,16
+283,14
@@
public class AppletJmol extends EmbmenuFrame implements
this.addWindowListener(new WindowAdapter()
{
this.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent evt)
{
closeViewer();
}
});
public void windowClosing(WindowEvent evt)
{
closeViewer();
}
});
- if (pdbentry.getProperty() == null)
- {
- pdbentry.setProperty(new Hashtable());
- pdbentry.getProperty().put("protocol", protocol);
- }
+ pdbentry.setProperty("protocol", protocol);
+
if (pdbentry.getFile() != null)
{
// import structure data from pdbentry.getFile based on given protocol
if (pdbentry.getFile() != null)
{
// import structure data from pdbentry.getFile based on given protocol
@@
-415,6
+413,7
@@
public class AppletJmol extends EmbmenuFrame implements
this.setVisible(false);
}
this.setVisible(false);
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == mappingMenuItem)
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == mappingMenuItem)
@@
-535,6
+534,7
@@
public class AppletJmol extends EmbmenuFrame implements
jmb.setColourBySequence(itm == seqColour);
}
jmb.setColourBySequence(itm == seqColour);
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == jmolColour)
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == jmolColour)
@@
-553,6
+553,7
@@
public class AppletJmol extends EmbmenuFrame implements
}
}
}
}
+ @Override
public void keyPressed(KeyEvent evt)
{
if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
public void keyPressed(KeyEvent evt)
{
if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
@@
-564,10
+565,12
@@
public class AppletJmol extends EmbmenuFrame implements
}
}
+ @Override
public void keyTyped(KeyEvent evt)
{
}
public void keyTyped(KeyEvent evt)
{
}
+ @Override
public void keyReleased(KeyEvent evt)
{
}
public void keyReleased(KeyEvent evt)
{
}
@@
-641,11
+644,13
@@
public class AppletJmol extends EmbmenuFrame implements
{
Dimension currentSize = new Dimension();
{
Dimension currentSize = new Dimension();
+ @Override
public void update(Graphics g)
{
paint(g);
}
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
currentSize = this.getSize();
public void paint(Graphics g)
{
currentSize = this.getSize();