/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*
* This file is part of Jalview.
*
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
+
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
-
JMenuItem deleteGroups = new JMenuItem();
JMenuItem delete = new JMenuItem();
protected JMenu showProducts = new JMenu();
- public JMenuItem featureSettings = new JMenuItem();
+ public JMenuItem openFeatureSettings = new JMenuItem();
JMenuItem fetchSequence = new JMenuItem();
JMenuItem annotationColour = new JMenuItem();
+ protected JMenuItem rnahelicesColour = new JMenuItem();
+
JMenuItem associatedData = new JMenuItem();
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+
protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
private JMenuItem grpsFromSelection = new JMenuItem();
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
colours.add(nucleotideColour);
+ colours.add(purinePyrimidineColour);
+ // colours.add(covariationColour);
setColourSelected(jalview.bin.Cache
.getDefault("DEFAULT_COLOUR", "None"));
break;
+ case ColourSchemeProperty.PURINEPYRIMIDINE:
+ purinePyrimidineColour.setSelected(true);
+
+ break;
+ /*
+ * case ColourSchemeProperty.COVARIATION:
+ * covariationColour.setSelected(true);
+ *
+ * break;
+ */
case ColourSchemeProperty.USER_DEFINED:
userDefinedColour.setSelected(true);
BLOSUM62Colour_actionPerformed(e);
}
});
+ nucleotideColour.setText("Nucleotide");
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideColour_actionPerformed(e);
+ }
+ });
+
+ purinePyrimidineColour.setText("Purine/Pyrimidine");
+ purinePyrimidineColour
+ .addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed(e);
+ }
+ });
+ /*
+ * covariationColour.setText("Covariation");
+ * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+ * public void actionPerformed(ActionEvent e) {
+ * covariationColour_actionPerformed(e); } });
+ */
+
avDistanceTreeBlosumMenuItem.setText("Average Distance Using BLOSUM62");
avDistanceTreeBlosumMenuItem
.addActionListener(new java.awt.event.ActionListener()
}
});
+ normaliseSequenceLogo.setText("Normalise Consensus Logo");
+ normaliseSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ normaliseSequenceLogo_actionPerformed(e);
+ }
+
+ });
applyAutoAnnotationSettings.setText("Apply to all groups");
applyAutoAnnotationSettings.setState(false);
applyAutoAnnotationSettings.setVisible(true);
* 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)
{
annotationColour_actionPerformed(e);
}
});
+
+ rnahelicesColour.setText("By RNA helices");
+ rnahelicesColour.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ rnahelicesColour_actionPerformed(e);
+ }
+ });
+
associatedData.setText("Load Features / Annotations");
associatedData.addActionListener(new ActionListener()
{
autoAnnMenu.add(applyAutoAnnotationSettings);
autoAnnMenu.add(showConsensusHistogram);
autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normaliseSequenceLogo);
autoAnnMenu.addSeparator();
autoAnnMenu.add(showGroupConservation);
autoAnnMenu.add(showGroupConsensus);
viewMenu.add(showSeqFeatures);
// viewMenu.add(showSeqFeaturesHeight);
- viewMenu.add(featureSettings);
+ viewMenu.add(openFeatureSettings);
tooltipSettingsMenu.add(showDbRefsMenuitem);
tooltipSettingsMenu.add(showNpFeatsMenuitem);
viewMenu.add(tooltipSettingsMenu);
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ // colourMenu.add(covariationColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
colourMenu.add(conservationMenuItem);
colourMenu.add(abovePIDThreshold);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
+ colourMenu.add(rnahelicesColour);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.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 purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed(ActionEvent e) { }
+ */
+
protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
}
}
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void associatedData_actionPerformed(ActionEvent e)
{