/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * 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 jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.api.SplitContainerI;
import jalview.bin.Cache;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
import jalview.gui.JvSwingUtils;
import jalview.gui.Preferences;
+import jalview.gui.UserDefinedColours;
+import jalview.io.FileFormat;
import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.awt.BorderLayout;
import java.awt.Color;
import javax.swing.JMenu;
import javax.swing.JMenuBar;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
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 class GAlignFrame extends JInternalFrame
{
+ protected static final String USER_DEFINED_COLOUR_SCHEME = "USER_DEFINED";
+
protected JMenuBar alignFrameMenuBar = new JMenuBar();
protected JMenuItem closeMenuItem = new JMenuItem();
protected JMenuItem webServiceNoServices;
- public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
protected JMenu sortByAnnotScore = new JMenu();
protected JMenu outputTextboxMenu = new JMenu();
- protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem textColour;
+
+ protected JRadioButtonMenuItem clustalColour;
- protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem zappoColour;
- protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem taylorColour;
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem hydrophobicityColour;
- protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem helixColour;
- protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem strandColour;
- protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem turnColour;
- protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem buriedColour;
- protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem userDefinedColour;
- protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem PIDColour;
- protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem BLOSUM62Colour;
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem nucleotideColour;
- protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem purinePyrimidineColour;
- protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem RNAInteractionColour;
- // protected JRadioButtonMenuItem covariationColour = new
- // JRadioButtonMenuItem();
+ // protected JRadioButtonMenuItem covariationColour;
- protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
+ protected JRadioButtonMenuItem tcoffeeColour;
- public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
protected JMenuItem undoMenuItem = new JMenuItem();
protected JMenuItem redoMenuItem = new JMenuItem();
- public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem conservationMenuItem;
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem noColourmenuItem;
- public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem abovePIDThreshold;
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
-
JMenuItem copy = new JMenuItem();
JMenuItem cut = new JMenuItem();
JMenu pasteMenu = new JMenu();
- public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem applyToAllGroups;
+
+ protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+ protected JMenuItem modifyPID;
- protected JMenuItem modifyConservation = new JMenuItem();
+ protected JMenuItem modifyConservation;
+
+ protected JMenuItem annotationColour;
protected JMenu sortByTreeMenu = new JMenu();
protected JMenuItem showTranslation = new JMenuItem();
+ protected JMenuItem showReverse = new JMenuItem();
+
+ protected JMenuItem showReverseComplement = new JMenuItem();
+
protected JMenu showProducts = new JMenu();
- protected JMenuItem rnahelicesColour = new JMenuItem();
+ protected JMenuItem runGroovy = new JMenuItem();
+
+ protected JMenuItem rnahelicesColour;
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
setJMenuBar(alignFrameMenuBar);
// dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+ for (String ff : FileFormat.getWritableFormats(true))
{
- JMenuItem item = new JMenuItem(
- jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+ JMenuItem item = new JMenuItem(ff);
item.addActionListener(new ActionListener()
{
System.err.println(e.toString());
}
- if (!jalview.util.Platform.isAMac())
+ if (!Platform.isAMac())
{
closeMenuItem.setMnemonic('C');
outputTextboxMenu.setMnemonic('T');
reload.setMnemonic('R');
}
- 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.isControlDown()
- || SwingUtilities.isRightMouseButton(evt))
- {
- 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()
- {
- @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);
- }
- }
- colours.add(noColourmenuItem);
- colours.add(clustalColour);
- colours.add(zappoColour);
- colours.add(taylorColour);
- colours.add(hydrophobicityColour);
- colours.add(helixColour);
- colours.add(strandColour);
- colours.add(turnColour);
- colours.add(buriedColour);
- colours.add(userDefinedColour);
- colours.add(PIDColour);
- colours.add(BLOSUM62Colour);
- colours.add(nucleotideColour);
- colours.add(purinePyrimidineColour);
- // colours.add(covariationColour);
- colours.add(tcoffeeColour);
- colours.add(RNAInteractionColour);
- setColourSelected(jalview.bin.Cache.getDefault(
- Preferences.DEFAULT_COLOUR, "None"));
+ // Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
+ // .getUserColourSchemes();
+ // if (userColourSchemes != null)
+ // {
+ // int insertionPoint = findUserDefinedColourPosition();
+ // for (String userColour : userColourSchemes.keySet())
+ // {
+ // final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+ // userColour);
+ // radioItem.setName(USER_DEFINED_COLOUR_SCHEME);
+ // radioItem.addMouseListener(new MouseAdapter()
+ // {
+ // @Override
+ // public void mousePressed(MouseEvent evt)
+ // {
+ // if (evt.isPopupTrigger()) // Mac
+ // {
+ // offerRemoval();
+ // }
+ // }
+ //
+ // @Override
+ // public void mouseReleased(MouseEvent evt)
+ // {
+ // if (evt.isPopupTrigger()) // Windows
+ // {
+ // offerRemoval();
+ // }
+ // }
+ //
+ // void offerRemoval()
+ // {
+ // radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+ //
+ // int option = JvOptionPane.showInternalConfirmDialog(
+ // 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)
+ // {
+ // 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, insertionPoint);
+ // insertionPoint++;
+ // colours.add(radioItem);
+ // }
+ // }
+ //
+ // /*
+ // * add colours to a ButtonGroup to make their
+ // * selection mutually exclusive
+ // */
+ // colours.add(noColourmenuItem);
+ // colours.add(clustalColour);
+ // colours.add(zappoColour);
+ // colours.add(taylorColour);
+ // colours.add(hydrophobicityColour);
+ // colours.add(helixColour);
+ // colours.add(strandColour);
+ // colours.add(turnColour);
+ // colours.add(buriedColour);
+ // colours.add(userDefinedColour);
+ // colours.add(PIDColour);
+ // colours.add(BLOSUM62Colour);
+ // colours.add(nucleotideColour);
+ // colours.add(purinePyrimidineColour);
+ // // colours.add(covariationColour);
+ // colours.add(tcoffeeColour);
+ // colours.add(RNAInteractionColour);
+ // setColourSelected(Cache.getDefault(Preferences.DEFAULT_COLOUR, "None"));
}
public void setColourSelected(String defaultColour)
private void jbInit() throws Exception
{
+ initColourMenu();
+ buildColourMenu();
+
JMenuItem saveAs = new JMenuItem(
MessageManager.getString("action.save_as"));
ActionListener al = new ActionListener()
saveAs_actionPerformed(e);
}
};
+
+ // FIXME getDefaultToolkit throws an exception in Headless mode
KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
.getDefaultToolkit().getMenuShortcutKeyMask()
| KeyEvent.SHIFT_MASK, false);
statusBar.setText(MessageManager.getString("label.status_bar"));
outputTextboxMenu.setText(MessageManager
.getString("label.out_to_textbox"));
- clustalColour.setText(MessageManager.getString("label.clustalx"));
- clustalColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- clustalColour_actionPerformed(e);
- }
- });
- zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- zappoColour_actionPerformed(e);
- }
- });
- taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- taylorColour_actionPerformed(e);
- }
- });
- hydrophobicityColour.setText(MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed(e);
- }
- });
- helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- helixColour_actionPerformed(e);
- }
- });
- strandColour.setText(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- strandColour_actionPerformed(e);
- }
- });
- turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- turnColour_actionPerformed(e);
- }
- });
- buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- buriedColour_actionPerformed(e);
- }
- });
- 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.percentage_identity"));
- PIDColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- PIDColour_actionPerformed(e);
- }
- });
- BLOSUM62Colour
- .setText(MessageManager.getString("label.blosum62_score"));
- BLOSUM62Colour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- BLOSUM62Colour_actionPerformed(e);
- }
- });
- nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- nucleotideColour_actionPerformed(e);
- }
- });
-
- purinePyrimidineColour.setText(MessageManager
- .getString("label.purine_pyrimidine"));
- purinePyrimidineColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed(e);
- }
- });
- RNAInteractionColour.setText("RNA Interaction type");
- RNAInteractionColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- RNAInteractionColour_actionPerformed(e);
- }
- });
- /*
- * covariationColour.setText("Covariation");
- * covariationColour.addActionListener(new ActionListener() { public void
- * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
- * });
- */
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
MessageManager.getString("label.average_distance_bloslum62"));
sortAnnotations_actionPerformed();
}
});
- colourTextMenuItem.setText(MessageManager
+ colourTextMenuItem = new JCheckBoxMenuItem(
+ MessageManager
.getString("label.colour_text"));
colourTextMenuItem.addActionListener(new ActionListener()
{
};
addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
- conservationMenuItem.setText(MessageManager
- .getString("action.by_conservation"));
- conservationMenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed(e);
- }
- });
- noColourmenuItem.setText(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- noColourmenuItem_actionPerformed(e);
- }
- });
wrapMenuItem.setText(MessageManager.getString("label.wrap"));
wrapMenuItem.addActionListener(new ActionListener()
{
};
addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
- abovePIDThreshold.setText(MessageManager
- .getString("label.above_identity_threshold"));
- abovePIDThreshold.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- abovePIDThreshold_actionPerformed(e);
- }
- });
showSeqFeatures.setText(MessageManager
.getString("label.show_sequence_features"));
showSeqFeatures.addActionListener(new ActionListener()
MessageManager.getString("label.show_last"));
buttonGroup.add(showAutoFirst);
buttonGroup.add(showAutoLast);
- showAutoFirst.setSelected(Cache.getDefault(
- Preferences.SHOW_AUTOCALC_ABOVE, false));
+ final boolean autoFirst = Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false);
+ showAutoFirst.setSelected(autoFirst);
+ setShowAutoCalculatedAbove(autoFirst);
showAutoFirst.addActionListener(new ActionListener()
{
@Override
}
});
- nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
- nucleotideColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- nucleotideColour_actionPerformed(e);
- }
- });
-
- tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
- tcoffeeColour.setEnabled(false);
- tcoffeeColour.addActionListener(new ActionListener()
- {
-
- @Override
- public void actionPerformed(ActionEvent e)
- {
- tcoffeeColorScheme_actionPerformed(e);
- }
- });
-
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
};
addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
+ JMenuItem annotationColumn = new JMenuItem(
+ MessageManager.getString("action.select_by_annotation"));
+ annotationColumn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColumn_actionPerformed(e);
+ }
+ });
+
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
};
addMenuActionAndAccelerator(keyStroke, pasteThis, al);
- applyToAllGroups.setText(MessageManager
- .getString("label.apply_colour_to_all_groups"));
- applyToAllGroups.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- applyToAllGroups_actionPerformed(e);
- }
- });
JMenuItem createPNG = new JMenuItem("PNG");
createPNG.addActionListener(new ActionListener()
{
});
- JMenuItem modifyPID = new JMenuItem(
- MessageManager.getString("label.modify_identity_thereshold"));
- modifyPID.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- modifyPID_actionPerformed(e);
- }
- });
- modifyConservation.setText(MessageManager
- .getString("label.modify_conservation_thereshold"));
- modifyConservation.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- modifyConservation_actionPerformed(e);
- }
- });
sortByTreeMenu
.setText(MessageManager.getString("action.by_tree_order"));
sort.setText(MessageManager.getString("action.sort"));
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()
}
});
- JMenuItem annotationColour = new JMenuItem(
- MessageManager.getString("action.by_annotation"));
- annotationColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- annotationColour_actionPerformed(e);
- }
- });
-
- JMenuItem annotationColumn = new JMenuItem(
- MessageManager.getString("action.select_by_annotation"));
- annotationColumn.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- annotationColumn_actionPerformed(e);
- }
- });
-
- rnahelicesColour.setText(MessageManager
- .getString("action.by_rna_helixes"));
- rnahelicesColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- rnahelicesColour_actionPerformed(e);
- }
- });
-
JMenuItem associatedData = new JMenuItem(
MessageManager.getString("label.load_features_annotations"));
associatedData.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()
tabbedPane.setToolTipText("<html><i>"
+ MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ "</i></html>");
- JMenuItem textColour = new JMenuItem(
- MessageManager.getString("action.set_text_colour"));
- textColour.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- textColour_actionPerformed(e);
- }
- });
+
formatMenu.setText(MessageManager.getString("action.format"));
JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
idRightAlign.setText(MessageManager
alignmentProperties();
}
});
+ JMenuItem selectHighlighted = new JMenuItem(
+ MessageManager.getString("action.select_highlighted_columns"));
+ selectHighlighted.setToolTipText(MessageManager
+ .getString("tooltip.select_highlighted_columns"));
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ selectHighlightedColumns_actionPerformed(actionEvent);
+ }
+ };
+ selectHighlighted.addActionListener(al);
JMenu tooltipSettingsMenu = new JMenu(
MessageManager.getString("label.sequence_id_tooltip"));
JMenu autoAnnMenu = new JMenu(
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);
autoAnnMenu.add(showGroupConsensus);
annotationsMenu.add(autoAnnMenu);
- colourMenu.add(applyToAllGroups);
- colourMenu.add(textColour);
- colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideColour);
- colourMenu.add(purinePyrimidineColour);
- colourMenu.add(RNAInteractionColour);
- // colourMenu.add(covariationColour);
- colourMenu.add(tcoffeeColour);
- colourMenu.add(userDefinedColour);
- colourMenu.addSeparator();
- colourMenu.add(conservationMenuItem);
- colourMenu.add(modifyConservation);
- colourMenu.add(abovePIDThreshold);
- 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);
+ selectMenu.add(selectHighlighted);
// TODO - determine if the listenToViewSelections button is needed : see bug
// JAL-574
// selectMenu.addSeparator();
}
/**
+ * Rebuilds the Colour menu, including any user-defined colours which have
+ * been loaded either on startup or during the session
+ */
+ public void buildColourMenu()
+ {
+ colourMenu.removeAll();
+ colours = new ButtonGroup();
+
+ colourMenu.add(applyToAllGroups);
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+ colourMenu.add(noColourmenuItem);
+ colourMenu.add(clustalColour);
+ colourMenu.add(BLOSUM62Colour);
+ colourMenu.add(PIDColour);
+ colourMenu.add(zappoColour);
+ colourMenu.add(taylorColour);
+ colourMenu.add(hydrophobicityColour);
+ colourMenu.add(helixColour);
+ colourMenu.add(strandColour);
+ colourMenu.add(turnColour);
+ colourMenu.add(buriedColour);
+ colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ // colourMenu.add(RNAInteractionColour);
+ // colourMenu.add(covariationColour);
+ colourMenu.add(tcoffeeColour);
+
+ /*
+ * add any user-defined colours
+ */
+ Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
+ .getUserColourSchemes();
+ if (userColourSchemes != null)
+ {
+ for (String userColour : userColourSchemes.keySet())
+ {
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
+ userColour);
+ radioItem.setName(USER_DEFINED_COLOUR_SCHEME);
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Mac
+ {
+ offerRemoval();
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (evt.isPopupTrigger()) // Windows
+ {
+ offerRemoval();
+ }
+ }
+
+ void offerRemoval()
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JvOptionPane.showInternalConfirmDialog(
+ 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)
+ {
+ 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.add(radioItem);
+ colours.add(radioItem);
+ }
+ }
+
+ colourMenu.add(userDefinedColour);
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDThreshold);
+ colourMenu.add(modifyPID);
+ colourMenu.add(annotationColour);
+ colourMenu.add(rnahelicesColour);
+
+ /*
+ * add colours to a ButtonGroup to make their
+ * selection mutually exclusive
+ */
+ colours.add(noColourmenuItem);
+ colours.add(clustalColour);
+ colours.add(zappoColour);
+ colours.add(taylorColour);
+ colours.add(hydrophobicityColour);
+ colours.add(helixColour);
+ colours.add(strandColour);
+ colours.add(turnColour);
+ colours.add(buriedColour);
+ colours.add(userDefinedColour);
+ colours.add(PIDColour);
+ colours.add(BLOSUM62Colour);
+ colours.add(nucleotideColour);
+ colours.add(purinePyrimidineColour);
+ // colours.add(covariationColour);
+ colours.add(tcoffeeColour);
+ colours.add(RNAInteractionColour);
+ setColourSelected(Cache.getDefault(Preferences.DEFAULT_COLOUR, "None"));
+
+ }
+
+ /**
+ * Constructs the entries on the Colour menu (but does not add them to the
+ * menu)
+ */
+ protected void initColourMenu()
+ {
+ applyToAllGroups = new JCheckBoxMenuItem(
+ MessageManager.getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ applyToAllGroups_actionPerformed();
+ }
+ });
+
+ textColour = new JRadioButtonMenuItem(
+ MessageManager.getString("action.set_text_colour"));
+ textColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed();
+ }
+ });
+ clustalColour = new JRadioButtonMenuItem(
+ MessageManager.getString("label.clustalx"));
+ clustalColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ clustalColour_actionPerformed();
+ }
+ });
+ zappoColour = new JRadioButtonMenuItem(
+ MessageManager.getString("label.zappo"));
+ zappoColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ zappoColour_actionPerformed();
+ }
+ });
+ taylorColour = new JRadioButtonMenuItem(
+ MessageManager.getString("label.taylor"));
+ taylorColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ taylorColour_actionPerformed();
+ }
+ });
+ hydrophobicityColour = new JRadioButtonMenuItem(
+ MessageManager
+ .getString("label.hydrophobicity"));
+ hydrophobicityColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed();
+ }
+ });
+ helixColour = new JRadioButtonMenuItem(
+ MessageManager.getString("label.helix_propensity"));
+ helixColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ helixColour_actionPerformed();
+ }
+ });
+ strandColour = new JRadioButtonMenuItem(
+ MessageManager
+ .getString("label.strand_propensity"));
+ strandColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ strandColour_actionPerformed();
+ }
+ });
+ turnColour = new JRadioButtonMenuItem(
+ MessageManager.getString("label.turn_propensity"));
+ turnColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ turnColour_actionPerformed();
+ }
+ });
+ buriedColour = new JRadioButtonMenuItem(
+ MessageManager.getString("label.buried_index"));
+ buriedColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ buriedColour_actionPerformed();
+ }
+ });
+ userDefinedColour = new JRadioButtonMenuItem(
+ MessageManager
+ .getString("action.user_defined"));
+ userDefinedColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ userDefinedColour_actionPerformed(e);
+ }
+ });
+ PIDColour = new JRadioButtonMenuItem(
+ MessageManager.getString("label.percentage_identity"));
+ PIDColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ PIDColour_actionPerformed();
+ }
+ });
+ BLOSUM62Colour = new JRadioButtonMenuItem(
+ MessageManager.getString("label.blosum62_score"));
+ BLOSUM62Colour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ BLOSUM62Colour_actionPerformed();
+ }
+ });
+ nucleotideColour = new JRadioButtonMenuItem(
+ MessageManager.getString("label.nucleotide"));
+ nucleotideColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ nucleotideColour_actionPerformed();
+ }
+ });
+ purinePyrimidineColour = new JRadioButtonMenuItem(
+ MessageManager.getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed();
+ }
+ });
+
+ tcoffeeColour = new JRadioButtonMenuItem(
+ MessageManager.getString("label.tcoffee_scores"));
+ tcoffeeColour.setEnabled(false);
+ tcoffeeColour.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ tcoffeeColorScheme_actionPerformed();
+ }
+ });
+
+ RNAInteractionColour = new JRadioButtonMenuItem("RNA Interaction type");
+ RNAInteractionColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ RNAInteractionColour_actionPerformed();
+ }
+ });
+ /*
+ * covariationColour = new JRadioButtonMenuItem("Covariation");
+ * covariationColour.addActionListener(new ActionListener() { public void
+ * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(); }
+ * });
+ */
+
+ conservationMenuItem = new JCheckBoxMenuItem(
+ MessageManager
+ .getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ });
+ noColourmenuItem = new JRadioButtonMenuItem(
+ MessageManager.getString("label.none"));
+ noColourmenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ noColourmenuItem_actionPerformed();
+ }
+ });
+
+ abovePIDThreshold = new JCheckBoxMenuItem(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDThreshold_actionPerformed();
+ }
+ });
+ modifyPID = new JMenuItem(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed();
+ }
+ });
+ modifyConservation = new JMenuItem(
+ MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed();
+ }
+ });
+
+ annotationColour = new JMenuItem(
+ MessageManager.getString("action.by_annotation"));
+ annotationColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColour_actionPerformed();
+ }
+ });
+
+ rnahelicesColour = new JMenuItem(
+ MessageManager.getString("action.by_rna_helixes"));
+ rnahelicesColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ rnahelicesColour_actionPerformed();
+ }
+ });
+ }
+
+ protected void selectHighlightedColumns_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ /**
+ * 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
{
}
- protected void clustalColour_actionPerformed(ActionEvent e)
+ protected void clustalColour_actionPerformed()
{
}
- protected void zappoColour_actionPerformed(ActionEvent e)
+ protected void zappoColour_actionPerformed()
{
}
- protected void taylorColour_actionPerformed(ActionEvent e)
+ protected void taylorColour_actionPerformed()
{
}
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ protected void hydrophobicityColour_actionPerformed()
{
}
- protected void helixColour_actionPerformed(ActionEvent e)
+ protected void helixColour_actionPerformed()
{
}
- protected void strandColour_actionPerformed(ActionEvent e)
+ protected void strandColour_actionPerformed()
{
}
- protected void turnColour_actionPerformed(ActionEvent e)
+ protected void turnColour_actionPerformed()
{
}
- protected void buriedColour_actionPerformed(ActionEvent e)
+ protected void buriedColour_actionPerformed()
{
}
{
}
- protected void PIDColour_actionPerformed(ActionEvent e)
+ protected void PIDColour_actionPerformed()
{
}
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ protected void BLOSUM62Colour_actionPerformed()
{
}
- protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ protected void purinePyrimidineColour_actionPerformed()
{
}
- protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+ protected void RNAInteractionColour_actionPerformed()
{
}
/*
- * protected void covariationColour_actionPerformed(ActionEvent e) { }
+ * protected void covariationColour_actionPerformed() { }
*/
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ protected void noColourmenuItem_actionPerformed()
{
}
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ protected void conservationMenuItem_actionPerformed()
{
}
{
}
- protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+ protected void abovePIDThreshold_actionPerformed()
{
}
{
}
- protected void nucleotideColour_actionPerformed(ActionEvent e)
+ protected void nucleotideColour_actionPerformed()
{
}
{
}
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed()
{
}
* Template method to handle the 'Color T-Coffee scores' menu event.
* <p>
* Subclasses override this method to provide a custom action.
- *
- * @param event
- * The raised event
*/
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
+ protected void tcoffeeColorScheme_actionPerformed()
{
}
{
}
- protected void modifyPID_actionPerformed(ActionEvent e)
+ protected void modifyPID_actionPerformed()
{
}
- protected void modifyConservation_actionPerformed(ActionEvent e)
+ protected void modifyConservation_actionPerformed()
{
}
}
- public void annotationColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
-
}
public void annotationColumn_actionPerformed(ActionEvent e)
{
-
}
- public void rnahelicesColour_actionPerformed(ActionEvent e)
+ public void rnahelicesColour_actionPerformed()
{
}
}
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
}
return this.splitFrame;
}
- protected void showComplement_actionPerformed(boolean state)
+ protected void showComplement_actionPerformed(boolean complement)
{
}
}
git://source.jalview.org / jalview.git / blobdiff