import java.awt.event.ItemListener;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.print.PageFormat;
import java.awt.print.PrinterJob;
import javax.swing.JLayeredPane;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JRadioButtonMenuItem;
import javax.swing.JScrollPane;
import javax.swing.SwingUtilities;
conservationMenuItem.setEnabled(!nucleotide);
modifyConservation.setEnabled(!nucleotide);
showGroupConservation.setEnabled(!nucleotide);
+ clustalColour.setEnabled(!nucleotide);
+ zappoColour.setEnabled(!nucleotide);
+ taylorColour.setEnabled(!nucleotide);
+ hydrophobicityColour.setEnabled(!nucleotide);
+ helixColour.setEnabled(!nucleotide);
+ strandColour.setEnabled(!nucleotide);
+ turnColour.setEnabled(!nucleotide);
+ buriedColour.setEnabled(!nucleotide);
rnahelicesColour.setEnabled(nucleotide);
nucleotideColour.setEnabled(nucleotide);
purinePyrimidineColour.setEnabled(nucleotide);
showComplementMenuItem.setText(nucleotide ? MessageManager
.getString("label.protein") : MessageManager
.getString("label.nucleotide"));
- setColourSelected(jalview.bin.Cache.getDefault(
+ String selectedColourScheme = Cache.getDefault(
nucleotide ? Preferences.DEFAULT_COLOUR_NUC
- : Preferences.DEFAULT_COLOUR_PROT, "None"));
+ : Preferences.DEFAULT_COLOUR_PROT, "None");
+ setColourSelected(selectedColourScheme);
}
/**
}
@Override
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
new TextColourChooser().chooseColour(alignPanel, null);
}
* DOCUMENT ME!
*/
@Override
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ protected void noColourmenuItem_actionPerformed()
{
changeColour(null);
}
* DOCUMENT ME!
*/
@Override
- public void clustalColour_actionPerformed(ActionEvent e)
+ public void clustalColour_actionPerformed()
{
changeColour(new ClustalxColourScheme(viewport.getAlignment(),
viewport.getHiddenRepSequences()));
* DOCUMENT ME!
*/
@Override
- public void zappoColour_actionPerformed(ActionEvent e)
+ public void zappoColour_actionPerformed()
{
changeColour(new ZappoColourScheme());
}
* DOCUMENT ME!
*/
@Override
- public void taylorColour_actionPerformed(ActionEvent e)
+ public void taylorColour_actionPerformed()
{
changeColour(new TaylorColourScheme());
}
* DOCUMENT ME!
*/
@Override
- public void hydrophobicityColour_actionPerformed(ActionEvent e)
+ public void hydrophobicityColour_actionPerformed()
{
changeColour(new HydrophobicColourScheme());
}
* DOCUMENT ME!
*/
@Override
- public void helixColour_actionPerformed(ActionEvent e)
+ public void helixColour_actionPerformed()
{
changeColour(new HelixColourScheme());
}
* DOCUMENT ME!
*/
@Override
- public void strandColour_actionPerformed(ActionEvent e)
+ public void strandColour_actionPerformed()
{
changeColour(new StrandColourScheme());
}
* DOCUMENT ME!
*/
@Override
- public void turnColour_actionPerformed(ActionEvent e)
+ public void turnColour_actionPerformed()
{
changeColour(new TurnColourScheme());
}
* DOCUMENT ME!
*/
@Override
- public void buriedColour_actionPerformed(ActionEvent e)
+ public void buriedColour_actionPerformed()
{
changeColour(new BuriedColourScheme());
}
* DOCUMENT ME!
*/
@Override
- public void nucleotideColour_actionPerformed(ActionEvent e)
+ public void nucleotideColour_actionPerformed()
{
changeColour(new NucleotideColourScheme());
}
@Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ public void purinePyrimidineColour_actionPerformed()
{
changeColour(new PurinePyrimidineColourScheme());
}
/*
- * public void covariationColour_actionPerformed(ActionEvent e) {
+ * public void covariationColour_actionPerformed() {
* changeColour(new
* CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
* ()[0])); }
*/
@Override
- public void annotationColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
new AnnotationColourChooser(viewport, alignPanel);
}
}
@Override
- public void rnahelicesColour_actionPerformed(ActionEvent e)
+ public void rnahelicesColour_actionPerformed()
{
new RNAHelicesColourChooser(viewport, alignPanel);
}
/**
* DOCUMENT ME!
*
- * @param e
- * DOCUMENT ME!
*/
@Override
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed()
{
viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());
}
* DOCUMENT ME!
*/
@Override
- protected void modifyPID_actionPerformed(ActionEvent e)
+ protected void modifyPID_actionPerformed()
{
if (viewport.getAbovePIDThreshold()
&& viewport.getGlobalColourScheme() != null)
* DOCUMENT ME!
*/
@Override
- protected void modifyConservation_actionPerformed(ActionEvent e)
+ protected void modifyConservation_actionPerformed()
{
if (viewport.getConservationSelected()
&& viewport.getGlobalColourScheme() != null)
* DOCUMENT ME!
*/
@Override
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ protected void conservationMenuItem_actionPerformed()
{
viewport.setConservationSelected(conservationMenuItem.isSelected());
changeColour(viewport.getGlobalColourScheme());
- modifyConservation_actionPerformed(null);
+ modifyConservation_actionPerformed();
}
/**
* DOCUMENT ME!
*/
@Override
- public void abovePIDThreshold_actionPerformed(ActionEvent e)
+ public void abovePIDThreshold_actionPerformed()
{
viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());
changeColour(viewport.getGlobalColourScheme());
- modifyPID_actionPerformed(null);
+ modifyPID_actionPerformed();
}
/**
}
else
{
- UserColourScheme udc = (UserColourScheme) UserDefinedColours
+ UserColourScheme udc = UserDefinedColours
.getUserColourSchemes().get(e.getActionCommand());
changeColour(udc);
}
}
- public void updateUserColourMenu()
- {
-
- Component[] menuItems = colourMenu.getMenuComponents();
- int iSize = menuItems.length;
- for (int i = 0; i < iSize; i++)
- {
- if (menuItems[i].getName() != null
- && menuItems[i].getName().equals("USER_DEFINED"))
- {
- colourMenu.remove(menuItems[i]);
- iSize--;
- }
- }
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours
- .getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- @Override
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Mac
- {
- offerRemoval(radioItem);
- }
- }
-
- @Override
- public void mouseReleased(MouseEvent evt)
- {
- if (evt.isPopupTrigger()) // Windows
- {
- offerRemoval(radioItem);
- }
- }
-
- /**
- * @param radioItem
- */
- void offerRemoval(final JRadioButtonMenuItem radioItem)
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JvOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop, MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JvOptionPane.YES_NO_OPTION);
- if (option == JvOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
-
- colourMenu.insert(radioItem, 15);
- colours.add(radioItem);
- }
- }
- }
-
/**
* DOCUMENT ME!
*
* DOCUMENT ME!
*/
@Override
- public void PIDColour_actionPerformed(ActionEvent e)
+ public void PIDColour_actionPerformed()
{
changeColour(new PIDColourScheme());
}
* DOCUMENT ME!
*/
@Override
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ public void BLOSUM62Colour_actionPerformed()
{
changeColour(new Blosum62ColourScheme());
}
}
@Override
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
+ protected void tcoffeeColorScheme_actionPerformed()
{
changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
}
}
AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
.size()]));
- AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
+ GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
cdna.alignAs(alignment);
String newtitle = "cDNA " + MessageManager.getString("label.for") + " "