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JAL-2371 small move of code, typo correction
[jalview.git]
/
src
/
jalview
/
jbgui
/
GAlignFrame.java
diff --git
a/src/jalview/jbgui/GAlignFrame.java
b/src/jalview/jbgui/GAlignFrame.java
index
dff20d3
..
b39f4a8
100755
(executable)
--- a/
src/jalview/jbgui/GAlignFrame.java
+++ b/
src/jalview/jbgui/GAlignFrame.java
@@
-25,7
+25,7
@@
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
import jalview.bin.Cache;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
-import jalview.io.FileFormat;
+import jalview.io.FileFormats;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.MessageManager;
import jalview.util.Platform;
@@
-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 JRadioButtonMenuItem 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();
@@
-211,7
+211,7
@@
public class GAlignFrame extends JInternalFrame
setJMenuBar(alignFrameMenuBar);
// dynamically fill save as menu with available formats
setJMenuBar(alignFrameMenuBar);
// dynamically fill save as menu with available formats
- for (String ff : FileFormat.getWritableFormats(true))
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
JMenuItem item = new JMenuItem(ff);
{
JMenuItem item = new JMenuItem(ff);
@@
-1917,7
+1917,7
@@
public class GAlignFrame extends JInternalFrame
@Override
public void actionPerformed(ActionEvent e)
{
@Override
public void actionPerformed(ActionEvent e)
{
- applyToAllGroups_actionPerformed();
+ applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
}
});
}
});
@@
-1939,7
+1939,8
@@
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
+1951,7
@@
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
+2343,7
@@
public class GAlignFrame extends JInternalFrame
{
}
{
}
- protected void conservationMenuItem_actionPerformed()
+ protected void conservationMenuItem_actionPerformed(boolean selected)
{
}
{
}
@@
-2358,7
+2359,7
@@
public class GAlignFrame extends JInternalFrame
{
}
{
}
- protected void abovePIDThreshold_actionPerformed()
+ protected void abovePIDThreshold_actionPerformed(boolean selected)
{
}
{
}
@@
-2398,7
+2399,7
@@
public class GAlignFrame extends JInternalFrame
{
}
{
}
- protected void applyToAllGroups_actionPerformed()
+ protected void applyToAllGroups_actionPerformed(boolean selected)
{
}
{
}