protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+ MenuItem modifyPID = new MenuItem();
+
protected CheckboxMenuItem conservationColour = new CheckboxMenuItem();
+ MenuItem modifyConservation = new MenuItem();
+
+ MenuItem noColourmenuItem = new MenuItem();
+
final AlignmentPanel ap;
MenuItem unGroupMenuItem = new MenuItem();
{
abovePIDColour.setState(sg.cs.getThreshold() > 0);
conservationColour.setState(sg.cs.conservationApplied());
+ modifyPID.setEnabled(abovePIDColour.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
}
}
setSelectedColour(sg.cs);
{
userDefinedColour_actionPerformed();
}
+ else if (source == modifyConservation)
+ {
+ conservationMenuItem_itemStateChanged();
+ }
+ else if (source == modifyPID)
+ {
+ abovePIDColour_itemStateChanged();
+ }
else if (source == unGroupMenuItem)
{
unGroupMenuItem_actionPerformed();
void addPDB()
{
Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
- if (pdbs != null&& !pdbs.isEmpty())
+ if (pdbs != null && !pdbs.isEmpty())
{
PDBEntry entry = pdbs.firstElement();
if (ap.av.applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
- null, ap, DataSourceType.URL);
+ new AppletJmol(entry, new SequenceI[] { seq }, null, ap,
+ DataSourceType.URL);
}
else
{
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.paste_pdb_file_for_sequence",
new Object[] { seq.getName() }), 400, 300);
}
colourMenu.add(purinePyrimidineColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
- colourMenu.add(abovePIDColour);
colourMenu.add(conservationColour);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
noColour.setLabel(MessageManager.getString("label.none"));
noColour.addItemListener(this);
abovePIDColour.setLabel(MessageManager
.getString("label.above_identity_threshold"));
abovePIDColour.addItemListener(this);
+ modifyPID.setLabel(MessageManager
+ .getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(this);
conservationColour.setLabel(MessageManager
- .getString("label.conservation"));
+ .getString("action.by_conservation"));
conservationColour.addItemListener(this);
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(this);
editMenu.add(copy);
copy.addActionListener(this);
else
// remove PIDColouring
{
+ SliderPanel.hidePIDSlider();
sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
-
+ modifyPID.setEnabled(abovePIDColour.getState());
refresh();
-
}
protected void userDefinedColour_actionPerformed()
else
// remove ConservationColouring
{
+ SliderPanel.hideConservationSlider();
sg.cs.setConservation(null);
}
-
+ modifyConservation.setEnabled(conservationColour.getState());
refresh();
}