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Merge branch 'develop' into features/JAL-1933_occupancy
[jalview.git]
/
src
/
jalview
/
jbgui
/
GAlignFrame.java
diff --git
a/src/jalview/jbgui/GAlignFrame.java
b/src/jalview/jbgui/GAlignFrame.java
index
a320a9c
..
b759d64
100755
(executable)
--- a/
src/jalview/jbgui/GAlignFrame.java
+++ b/
src/jalview/jbgui/GAlignFrame.java
@@
-65,8
+65,6
@@
public class GAlignFrame extends JInternalFrame
protected JMenuItem closeMenuItem = new JMenuItem();
protected JMenuItem closeMenuItem = new JMenuItem();
- protected JMenu colourMenu = new JMenu();
-
protected JMenu webService = new JMenu();
protected JMenuItem webServiceNoServices;
protected JMenu webService = new JMenu();
protected JMenuItem webServiceNoServices;
@@
-81,8
+79,6
@@
public class GAlignFrame extends JInternalFrame
protected JMenu outputTextboxMenu = new JMenu();
protected JMenu outputTextboxMenu = new JMenu();
- protected JRadioButtonMenuItem textColour;
-
protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
@@
-93,14
+89,10
@@
public class GAlignFrame extends JInternalFrame
protected JMenuItem redoMenuItem = new JMenuItem();
protected JMenuItem redoMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem conservationMenuItem;
-
protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem abovePIDThreshold;
-
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
JMenuItem copy = new JMenuItem();
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
JMenuItem copy = new JMenuItem();
@@
-109,8
+101,6
@@
public class GAlignFrame extends JInternalFrame
JMenu pasteMenu = new JMenu();
JMenu pasteMenu = new JMenu();
- protected JCheckBoxMenuItem applyToAllGroups;
-
protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
@@
-119,10
+109,20
@@
public class GAlignFrame extends JInternalFrame
protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
- protected JMenuItem modifyPID;
+ protected JCheckBoxMenuItem applyToAllGroups;
+
+ protected JMenu colourMenu = new JMenu();
+
+ protected JMenuItem textColour;
+
+ protected JCheckBoxMenuItem conservationMenuItem;
protected JMenuItem modifyConservation;
protected JMenuItem modifyConservation;
+ protected JCheckBoxMenuItem abovePIDThreshold;
+
+ protected JMenuItem modifyPID;
+
protected JMenuItem annotationColour;
protected JMenu sortByTreeMenu = new JMenu();
protected JMenuItem annotationColour;
protected JMenu sortByTreeMenu = new JMenu();
@@
-975,7
+975,7
@@
public class GAlignFrame extends JInternalFrame
});
JMenuItem createGroup = new JMenuItem(
});
JMenuItem createGroup = new JMenuItem(
- MessageManager.getString("action.create_groups"));
+ MessageManager.getString("action.create_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask(), false);
al = new ActionListener()
@@
-1653,6
+1653,7
@@
public class GAlignFrame extends JInternalFrame
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
+
idRightAlign.setText(MessageManager
.getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
idRightAlign.setText(MessageManager
.getString("label.right_align_sequence_id"));
idRightAlign.addActionListener(new ActionListener()
@@
-1904,6
+1905,12
@@
public class GAlignFrame extends JInternalFrame
// selectMenu.add(listenToViewSelections);
}
// selectMenu.add(listenToViewSelections);
}
+ protected void configureSelectMenu()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
/**
* Constructs the entries on the Colour menu (but does not add them to the
* menu).
/**
* Constructs the entries on the Colour menu (but does not add them to the
* menu).
@@
-1917,12
+1924,12
@@
public class GAlignFrame extends JInternalFrame
@Override
public void actionPerformed(ActionEvent e)
{
@Override
public void actionPerformed(ActionEvent e)
{
- applyToAllGroups_actionPerformed();
+ applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
}
});
}
});
- textColour = new JRadioButtonMenuItem(
- MessageManager.getString("action.set_text_colour"));
+ textColour = new JMenuItem(
+ MessageManager.getString("label.text_colour"));
textColour.addActionListener(new ActionListener()
{
@Override
textColour.addActionListener(new ActionListener()
{
@Override
@@
-1939,7
+1946,8
@@
public class GAlignFrame extends JInternalFrame
@Override
public void actionPerformed(ActionEvent e)
{
@Override
public void actionPerformed(ActionEvent e)
{
- conservationMenuItem_actionPerformed();
+ conservationMenuItem_actionPerformed(conservationMenuItem
+ .isSelected());
}
});
}
});
@@
-1950,7
+1958,7
@@
public class GAlignFrame extends JInternalFrame
@Override
public void actionPerformed(ActionEvent e)
{
@Override
public void actionPerformed(ActionEvent e)
{
- abovePIDThreshold_actionPerformed();
+ abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
}
});
modifyPID = new JMenuItem(
}
});
modifyPID = new JMenuItem(
@@
-2342,7
+2350,7
@@
public class GAlignFrame extends JInternalFrame
{
}
{
}
- protected void conservationMenuItem_actionPerformed()
+ protected void conservationMenuItem_actionPerformed(boolean selected)
{
}
{
}
@@
-2358,7
+2366,7
@@
public class GAlignFrame extends JInternalFrame
{
}
{
}
- protected void abovePIDThreshold_actionPerformed()
+ protected void abovePIDThreshold_actionPerformed(boolean selected)
{
}
{
}
@@
-2398,7
+2406,7
@@
public class GAlignFrame extends JInternalFrame
{
}
{
}
- protected void applyToAllGroups_actionPerformed()
+ protected void applyToAllGroups_actionPerformed(boolean selected)
{
}
{
}