/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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;
protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
// protected JRadioButtonMenuItem covariationColour = new
// JRadioButtonMenuItem();
protected JMenuItem showTranslation = new JMenuItem();
protected JMenuItem extractScores = new JMenuItem();
+
+ protected JMenuItem expandAlignment = new JMenuItem();
protected JMenu showProducts = new JMenu();
colours.add(purinePyrimidineColour);
// colours.add(covariationColour);
colours.add(tcoffeeColour);
-
+ colours.add(RNAInteractionColour);
setColourSelected(jalview.bin.Cache
.getDefault("DEFAULT_COLOUR", "None"));
purinePyrimidineColour.setSelected(true);
break;
+
+ case ColourSchemeProperty.RNAINTERACTION:
+ RNAInteractionColour.setSelected(true);
+
+ break;
/*
* case ColourSchemeProperty.COVARIATION:
* covariationColour.setSelected(true);
makeGrpsFromSelection_actionPerformed(e);
}
});
-
+ expandAlignment.setText(MessageManager.getString("action.view_flanking_regions"));
+ expandAlignment.setToolTipText(MessageManager.getString("label.view_flanking_regions"));
+ expandAlignment.addActionListener(new java.awt.event.ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ expand_newalign(e);
+ }
+ });
remove2LeftMenuItem.setText(MessageManager.getString("action.remove_left"));
remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
java.awt.event.KeyEvent.VK_L, Toolkit.getDefaultToolkit()
strandColour_actionPerformed(e);
}
});
- turnColour.setText(MessageManager.getString("Turn Propensity"));
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));
turnColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
turnColour_actionPerformed(e);
}
});
- buriedColour.setText(MessageManager.getString("Buried Index"));
+ buriedColour.setText(MessageManager.getString("label.buried_index"));
buriedColour.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
purinePyrimidineColour_actionPerformed(e);
}
});
+
+ RNAInteractionColour.setText("RNA Interaction type");
+ RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed(e);
+ }
+ });
/*
* covariationColour.setText("Covariation");
* covariationColour.addActionListener(new java.awt.event.ActionListener() {
noColourmenuItem_actionPerformed(e);
}
});
- wrapMenuItem.setText(MessageManager.getString("labe.wrap"));
+ wrapMenuItem.setText(MessageManager.getString("label.wrap"));
wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(RNAInteractionColour);
// colourMenu.add(covariationColour);
colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
- colourMenu.add(rnahelicesColour);
+ colourMenu.add(rnahelicesColour);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
sort.add(sortGroupMenuItem);
sort.add(sortPairwiseMenuItem);
sort.add(sortByTreeMenu);
- calculateTree.add(averageDistanceTreeMenuItem);
- calculateTree.add(neighbourTreeMenuItem);
- calculateTree.add(avDistanceTreeBlosumMenuItem);
- calculateTree.add(njTreeBlosumMenuItem);
jMenu2.add(htmlMenuItem);
jMenu2.add(epsFile);
jMenu2.add(createPNG);
selectMenu.add(unGroup);
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
+ calculateMenu.add(expandAlignment);
// TODO - determine if the listenToViewSelections button is needed : see bug
// JAL-574
// selectMenu.addSeparator();
protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
{
}
+
+ protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+ {
+ }
+
/*
* protected void covariationColour_actionPerformed(ActionEvent e) { }
{
}
+
+ protected void expand_newalign(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
}