- @Override
- public void actionPerformed(ActionEvent e)
- {
- abovePIDColour_actionPerformed();
- }
- });
- userDefinedColour.setText(MessageManager
- .getString("action.user_defined"));
- userDefinedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- userDefinedColour_actionPerformed(e);
- }
- });
- PIDColour
-.setText(MessageManager
- .getString("label.colourScheme_%_identity"));
- PIDColour.setName(JalviewColourScheme.PID.toString());
- PIDColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- PIDColour_actionPerformed();
- }
- });
- BLOSUM62Colour
-.setText(MessageManager
- .getString("label.colourScheme_blosum62"));
- BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
- BLOSUM62Colour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed();
- }
- });
- nucleotideColour.setText(MessageManager
- .getString("label.colourScheme_nucleotide"));
- nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString());
- nucleotideColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- nucleotideMenuItem_actionPerformed();
- }
- });
- purinePyrimidineColour.setText(MessageManager
- .getString("label.colourScheme_purine/pyrimidine"));
- purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine
- .toString());
- purinePyrimidineColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed();
- }
- });
-
- tcoffeeColour.setText(MessageManager
- .getString("label.colourScheme_t-coffee_scores"));
- tcoffeeColour.setName(JalviewColourScheme.TCoffee.toString());
- tcoffeeColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- tcoffeeColorScheme_actionPerformed();
- }
- });
-
- /*
- * covariationColour.addActionListener(new ActionListener() {
- * public void actionPerformed(ActionEvent e) {
- * covariationColour_actionPerformed(); } });
- */
-
- conservationMenuItem.setText(MessageManager
- .getString("action.by_conservation"));
- conservationMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed();
- }
- });
- }
-
- /**
- * Builds the group colour sub-menu, including any user-defined colours which
- * were loaded at startup or during the Jalview session
- */
- protected void buildColourMenu()
- {
- SequenceGroup sg = getGroup();
- colourMenu.removeAll();
- colourMenu.add(textColour);
- colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- // in Java 8, isApplicableTo can be a static method on the interface
- clustalColour.setEnabled(new ClustalxColourScheme(sg, null)
- .isApplicableTo(sg));
- colourMenu.add(BLOSUM62Colour);
- BLOSUM62Colour
- .setEnabled(new Blosum62ColourScheme().isApplicableTo(sg));
- colourMenu.add(PIDColour);
- PIDColour.setEnabled(new PIDColourScheme().isApplicableTo(sg));
- colourMenu.add(zappoColour);
- zappoColour.setEnabled(new ZappoColourScheme().isApplicableTo(sg));
- colourMenu.add(taylorColour);
- taylorColour.setEnabled(new TaylorColourScheme().isApplicableTo(sg));
- colourMenu.add(hydrophobicityColour);
- hydrophobicityColour.setEnabled(new HydrophobicColourScheme()
- .isApplicableTo(sg));
- colourMenu.add(helixColour);
- helixColour.setEnabled(new HelixColourScheme().isApplicableTo(sg));
- colourMenu.add(strandColour);
- strandColour.setEnabled(new StrandColourScheme().isApplicableTo(sg));
- colourMenu.add(turnColour);
- turnColour.setEnabled(new TurnColourScheme().isApplicableTo(sg));
- colourMenu.add(buriedColour);
- buriedColour.setEnabled(new BuriedColourScheme().isApplicableTo(sg));
- colourMenu.add(nucleotideColour);
- nucleotideColour.setEnabled(new NucleotideColourScheme()
- .isApplicableTo(sg));
- colourMenu.add(purinePyrimidineColour);
- purinePyrimidineColour.setEnabled(new PurinePyrimidineColourScheme()
- .isApplicableTo(sg));
- colourMenu.add(tcoffeeColour);
- tcoffeeColour
- .setEnabled(new TCoffeeColourScheme(sg).isApplicableTo(sg));
-
- /*
- * add some of these items to a ButtonGroup so their
- * selection is mutually exclusive
- */
- ButtonGroup colours = new ButtonGroup();
-
- /*
- * add any user-defined colours loaded on startup or
- * during the application session
- */
- SortedMap<String, UserColourScheme> userColourSchemes = UserDefinedColours
- .getUserColourSchemes();
- if (userColourSchemes != null)
- {
- for (String userColour : userColourSchemes.keySet())
- {
- JRadioButtonMenuItem item = new JRadioButtonMenuItem(userColour);
- item.setName(userColour); // button name identifies selected colour
- item.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- colourMenu.add(item);
- colours.add(item);
- }