/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.schemes.*;
+import jalview.schemes.ColourSchemeProperty;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.GridLayout;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JTabbedPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
public class GAlignFrame extends JInternalFrame
{
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
+
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
protected JMenu showProducts = new JMenu();
- public JMenuItem featureSettings = new JMenuItem();
+ public JMenuItem openFeatureSettings = new JMenuItem();
JMenuItem fetchSequence = new JMenuItem();
colours.add(nucleotideColour);
colours.add(purinePyrimidineColour);
// colours.add(covariationColour);
+ colours.add(tcoffeeColour);
setColourSelected(jalview.bin.Cache
.getDefault("DEFAULT_COLOUR", "None"));
break;
+ case ColourSchemeProperty.TCOFFEE:
+ tcoffeeColour.setSelected(true);
+ break;
+
case ColourSchemeProperty.PURINEPYRIMIDINE:
purinePyrimidineColour.setSelected(true);
nucleotideColour_actionPerformed(e);
}
});
+
+ tcoffeeColour.setText("T-Coffee scores");
+ tcoffeeColour.setEnabled(false);
+ tcoffeeColour.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ tcoffeeColorScheme_actionPerformed(e);
+ }
+ });
+
deleteGroups.setText("Undefine groups");
deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_U, Toolkit.getDefaultToolkit()
LoadtreeMenuItem_actionPerformed(e);
}
});
+
scaleAbove.setVisible(false);
scaleAbove.setText("Scale Above");
scaleAbove.addActionListener(new java.awt.event.ActionListener()
* public void actionPerformed(ActionEvent e) {
* showProducts_actionPerformed(e); } });
*/
- featureSettings.setText("Feature Settings...");
- featureSettings.addActionListener(new ActionListener()
+ openFeatureSettings.setText("Feature Settings...");
+ openFeatureSettings.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
}
});
sortByTree.setText("Sort Alignment With New Tree");
- sortByTree.setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
- sortByTree.setState(jalview.bin.Cache.getDefault(
- "SORT_BY_TREE", false));
+ sortByTree
+ .setToolTipText("<html>Enable this to automatically sort<br>the alignment when you open<br> a new tree.");
+ sortByTree
+ .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
});
listenToViewSelections.setText("Listen for selections");
- listenToViewSelections.setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
- listenToViewSelections.setState(false);
+ listenToViewSelections
+ .setToolTipText("<html>When selected, selections in this view will mirror<br>selections made on the same sequences in other views.");
+ listenToViewSelections.setState(false);
listenToViewSelections.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
viewMenu.add(showSeqFeatures);
// viewMenu.add(showSeqFeaturesHeight);
- viewMenu.add(featureSettings);
+ viewMenu.add(openFeatureSettings);
tooltipSettingsMenu.add(showDbRefsMenuitem);
tooltipSettingsMenu.add(showNpFeatsMenuitem);
viewMenu.add(tooltipSettingsMenu);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
// colourMenu.add(covariationColour);
+ colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
selectMenu.add(invertColSel);
selectMenu.add(deleteGroups);
selectMenu.add(grpsFromSelection);
- // TODO - determine if the listenToViewSelections button is needed : see bug JAL-574
- //selectMenu.addSeparator();
- //selectMenu.add(listenToViewSelections);
+ // TODO - determine if the listenToViewSelections button is needed : see bug
+ // JAL-574
+ // selectMenu.addSeparator();
+ // selectMenu.add(listenToViewSelections);
}
protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void listenToViewSelections_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
-
+
}
protected void showAllhidden_actionPerformed(ActionEvent e)
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
{
+
+ }
+
+ /**
+ * Template method to handle the 'load T-Coffee scores' menu event.
+ * <p>
+ * Subclasses override this method to provide a custom action.
+ *
+ * @param event
+ * The raised event
+ */
+ protected void loadScores_actionPerformed(ActionEvent event)
+ {
+
+ }
+
+ /**
+ * Template method to handle the 'Color T-Coffee scores' menu event.
+ * <p>
+ * Subclasses override this method to provide a custom action.
+ *
+ * @param event
+ * The raised event
+ */
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
+ {
+
}
protected void jpred_actionPerformed(ActionEvent e)
git://source.jalview.org / jalview.git / blobdiff