/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import javax.swing.JRadioButtonMenuItem;
import javax.swing.JTabbedPane;
import javax.swing.KeyStroke;
-import javax.swing.SwingUtilities;
import javax.swing.event.ChangeEvent;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
-
JMenuItem copy = new JMenuItem();
JMenuItem cut = new JMenuItem();
protected JMenuItem showTranslation = new JMenuItem();
+ protected JMenuItem showReverse = new JMenuItem();
+
+ protected JMenuItem showReverseComplement = new JMenuItem();
+
protected JMenu showProducts = new JMenu();
+ protected JMenuItem runGroovy = new JMenuItem();
+
protected JMenuItem rnahelicesColour = new JMenuItem();
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
@Override
public void mousePressed(MouseEvent evt)
{
- if (evt.isControlDown()
- || SwingUtilities.isRightMouseButton(evt))
+ if (evt.isPopupTrigger()) // Mac
{
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JOptionPane.showInternalConfirmDialog(
- jalview.gui.Desktop.desktop,
- MessageManager
- .getString("label.remove_from_default_list"),
- MessageManager
- .getString("label.remove_user_defined_colour"),
- JOptionPane.YES_NO_OPTION);
- if (option == JOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours
- .removeColourFromDefaults(radioItem.getText());
- colourMenu.remove(radioItem);
- }
- else
+ 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 = JOptionPane.showInternalConfirmDialog(
+ jalview.gui.Desktop.desktop, MessageManager
+ .getString("label.remove_from_default_list"),
+ MessageManager
+ .getString("label.remove_user_defined_colour"),
+ JOptionPane.YES_NO_OPTION);
+ if (option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours
+ .removeColourFromDefaults(radioItem.getText());
+ colourMenu.remove(radioItem);
+ }
+ else
+ {
+ radioItem.addActionListener(new ActionListener()
{
- radioItem.addActionListener(new ActionListener()
+ @Override
+ public void actionPerformed(ActionEvent evt)
{
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
+ userDefinedColour_actionPerformed(evt);
+ }
+ });
}
}
});
});
JMenuItem modifyPID = new JMenuItem(
- MessageManager.getString("label.modify_identity_thereshold"));
+ MessageManager.getString("label.modify_identity_threshold"));
modifyPID.addActionListener(new ActionListener()
{
@Override
}
});
modifyConservation.setText(MessageManager
- .getString("label.modify_conservation_thereshold"));
+ .getString("label.modify_conservation_threshold"));
modifyConservation.addActionListener(new ActionListener()
{
@Override
showTranslation_actionPerformed(e);
}
});
+ showReverse.setText(MessageManager.getString("label.reverse"));
+ showReverse.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showReverse_actionPerformed(false);
+ }
+ });
+ showReverseComplement.setText(MessageManager
+ .getString("label.reverse_complement"));
+ showReverseComplement.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showReverse_actionPerformed(true);
+ }
+ });
JMenuItem extractScores = new JMenuItem(
MessageManager.getString("label.extract_scores"));
// for show products actions see AlignFrame.canShowProducts
showProducts.setText(MessageManager.getString("label.get_cross_refs"));
+ runGroovy.setText(MessageManager.getString("label.run_groovy"));
+ runGroovy.setToolTipText(MessageManager
+ .getString("label.run_groovy_tip"));
+ runGroovy.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ runGroovy_actionPerformed();
+ }
+ });
+
JMenuItem openFeatureSettings = new JMenuItem(
MessageManager.getString("action.feature_settings"));
openFeatureSettings.addActionListener(new ActionListener()
@Override
public void mousePressed(MouseEvent e)
{
- tabbedPane_mousePressed(e);
+ if (e.isPopupTrigger()) // Mac
+ {
+ tabbedPane_mousePressed(e);
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ if (e.isPopupTrigger()) // Windows
+ {
+ tabbedPane_mousePressed(e);
+ }
}
});
tabbedPane.addFocusListener(new FocusAdapter()
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
alignFrameMenuBar.add(webService);
+
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
fileMenu.add(reload);
fileMenu.add(associatedData);
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
+
+ pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
editMenu.add(undoMenuItem);
editMenu.add(redoMenuItem);
editMenu.add(cut);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
+ showMenu.add(showAllColumns);
+ showMenu.add(showAllSeqs);
+ showMenu.add(showAllhidden);
+ hideMenu.add(hideSelColumns);
+ hideMenu.add(hideSelSequences);
+ hideMenu.add(hideAllSelection);
+ hideMenu.add(hideAllButSelection);
viewMenu.add(newView);
viewMenu.add(expandViews);
viewMenu.add(gatherViews);
colourMenu.add(modifyPID);
colourMenu.add(annotationColour);
colourMenu.add(rnahelicesColour);
+
+ sort.add(sortIDMenuItem);
+ sort.add(sortLengthMenuItem);
+ sort.add(sortGroupMenuItem);
+ sort.add(sortPairwiseMenuItem);
+ sort.add(sortByTreeMenu);
calculateMenu.add(sort);
calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
calculateMenu.add(showTranslation);
+ calculateMenu.add(showReverse);
+ calculateMenu.add(showReverseComplement);
calculateMenu.add(showProducts);
calculateMenu.add(autoCalculate);
calculateMenu.add(sortByTree);
calculateMenu.addSeparator();
+ calculateMenu.add(expandAlignment);
calculateMenu.add(extractScores);
+ calculateMenu.addSeparator();
+ calculateMenu.add(runGroovy);
+
webServiceNoServices = new JMenuItem(
MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
- pasteMenu.add(pasteNew);
- pasteMenu.add(pasteThis);
- sort.add(sortIDMenuItem);
- sort.add(sortLengthMenuItem);
- sort.add(sortGroupMenuItem);
- sort.add(sortPairwiseMenuItem);
- sort.add(sortByTreeMenu);
exportImageMenu.add(htmlMenuItem);
exportImageMenu.add(epsFile);
exportImageMenu.add(createPNG);
this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
statusPanel.add(statusBar, null);
this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
- showMenu.add(showAllColumns);
- showMenu.add(showAllSeqs);
- showMenu.add(showAllhidden);
- hideMenu.add(hideSelColumns);
- hideMenu.add(hideSelSequences);
- hideMenu.add(hideAllSelection);
- hideMenu.add(hideAllButSelection);
formatMenu.add(font);
formatMenu.addSeparator();
selectMenu.add(grpsFromSelection);
selectMenu.add(deleteGroups);
selectMenu.add(annotationColumn);
- calculateMenu.add(expandAlignment);
// TODO - determine if the listenToViewSelections button is needed : see bug
// JAL-574
// selectMenu.addSeparator();
}
/**
+ * Generate the reverse sequence (or reverse complement if the flag is true)
+ * and add it to the alignment
+ *
+ * @param complement
+ */
+ protected void showReverse_actionPerformed(boolean complement)
+ {
+ }
+
+ /**
+ * Try to run script in a Groovy console, having first ensured that this
+ * alignframe is set as currentAlignFrame in Desktop
+ */
+ protected void runGroovy_actionPerformed()
+ {
+
+ }
+
+ /**
* Adds the given action listener and key accelerator to the given menu item.
* Also saves in a lookup table to support lookup of action by key stroke.
*
}
- protected void showSeqFeaturesHeight_actionPerformed(
- ActionEvent actionEvent)
- {
- // TODO Auto-generated method stub
-
- }
-
protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
// TODO Auto-generated method stub
return this.splitFrame;
}
- protected void showComplement_actionPerformed(boolean state)
+ protected void showComplement_actionPerformed(boolean complement)
{
}
}
git://source.jalview.org / jalview.git / blobdiff