-/********************
- * 2004 Jalview Reengineered
- * Barton Group
- * Dundee University
- *
- * AM Waterhouse
- *******************/
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.jbgui;
-import javax.swing.*;
-import java.awt.event.*;
-import java.awt.*;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.api.SplitContainerI;
+import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
+import jalview.io.FileFormat;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.GridLayout;
+import java.awt.Toolkit;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JTabbedPane;
+import javax.swing.KeyStroke;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.MenuEvent;
+import javax.swing.event.MenuListener;
public class GAlignFrame extends JInternalFrame
{
protected JMenuBar alignFrameMenuBar = new JMenuBar();
- protected JMenu fileMenu = new JMenu();
+
protected JMenuItem closeMenuItem = new JMenuItem();
- protected JMenu editMenu = new JMenu();
- protected JMenu viewMenu = new JMenu();
+
protected JMenu colourMenu = new JMenu();
- protected JMenu calculateMenu = new JMenu();
- protected JMenu alignMenu = new JMenu();
- protected JMenuItem groupsMenuItem = new JMenuItem();
- protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
- protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
- protected JMenuItem invertSequenceMenuItem = new JMenuItem();
- protected JMenuItem deselectAllColumnsMenuItem = new JMenuItem();
- protected JMenuItem remove2LeftMenuItem = new JMenuItem();
- protected JMenuItem remove2RightMenuItem = new JMenuItem();
- protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
- protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
- protected JMenuItem setGapCharMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
- protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
- protected JMenuItem sortIDMenuItem = new JMenuItem();
- protected JMenuItem sortGroupMenuItem = new JMenuItem();
- protected JMenuItem sortTreeOrderMenuItem = new JMenuItem();
- protected JMenuItem removeRedundancyMenuItem = new JMenuItem();
- protected JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
- protected JMenuItem PCAMenuItem = new JMenuItem();
- protected JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
- protected JMenuItem neighbourTreeMenuItem = new JMenuItem();
- protected JMenuItem clustalAlignMenuItem = new JMenuItem();
- BorderLayout borderLayout1 = new BorderLayout();
+
+ protected JMenu webService = new JMenu();
+
+ protected JMenuItem webServiceNoServices;
+
+ public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+
+ protected JMenu sortByAnnotScore = new JMenu();
+
public JLabel statusBar = new JLabel();
- protected JMenu saveAlignmentMenu = new JMenu();
+
protected JMenu outputTextboxMenu = new JMenu();
+
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
- JMenuItem njTreeBlosumMenuItem = new JMenuItem();
- JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
- JMenuItem htmlMenuItem = new JMenuItem();
- JMenuItem overviewMenuItem = new JMenuItem();
+
+ protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+
+ // protected JRadioButtonMenuItem covariationColour = new
+ // JRadioButtonMenuItem();
+
+ protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
+
+ public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
+
protected JMenuItem undoMenuItem = new JMenuItem();
+
protected JMenuItem redoMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
- protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
- JMenuItem printMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
- JMenuItem findMenuItem = new JMenuItem();
- JMenu searchMenu = new JMenu();
- protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
- JMenuItem deleteGroups = new JMenuItem();
- JMenuItem delete = new JMenuItem();
+
+ public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
+
JMenuItem copy = new JMenuItem();
+
JMenuItem cut = new JMenuItem();
- JMenu jMenu1 = new JMenu();
- JMenuItem pasteNew = new JMenuItem();
- JMenuItem pasteThis = new JMenuItem();
- protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
- JMenuItem createPNG = new JMenuItem();
- protected JMenuItem font = new JMenuItem();
- protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
- JMenuItem epsFile = new JMenuItem();
- JMenuItem LoadtreeMenuItem = new JMenuItem();
- public GAlignFrame()
- {
+ JMenu pasteMenu = new JMenu();
+
+ public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+
+ public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+
+ protected JMenuItem modifyConservation = new JMenuItem();
+
+ protected JMenu sortByTreeMenu = new JMenu();
+
+ protected JMenu sort = new JMenu();
+
+ protected JMenu calculateTree = new JMenu();
+
+ protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
+
+ protected ButtonGroup colours = new ButtonGroup();
+
+ 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();
+
+ protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
+
+ protected JPanel statusPanel = new JPanel();
+
+ protected JMenuItem showAllSeqAnnotations = new JMenuItem();
+
+ protected JMenuItem hideAllSeqAnnotations = new JMenuItem();
+
+ protected JMenuItem showAllAlAnnotations = new JMenuItem();
+
+ protected JMenuItem hideAllAlAnnotations = new JMenuItem();
+
+ protected JCheckBoxMenuItem showComplementMenuItem = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem hiddenMarkers = new JCheckBoxMenuItem();
+
+ protected JTabbedPane tabbedPane = new JTabbedPane();
+
+ protected JMenuItem reload = new JMenuItem();
+
+ protected JMenu formatMenu = new JMenu();
+
+ protected JCheckBoxMenuItem idRightAlign = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem centreColumnLabelsMenuItem = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem followHighlightMenuItem = new JCheckBoxMenuItem();
+
+ protected JMenuItem gatherViews = new JMenuItem();
+
+ protected JMenuItem expandViews = new JMenuItem();
+
+ protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
+
+ private SequenceAnnotationOrder annotationSortOrder;
+
+ private boolean showAutoCalculatedAbove = false;
+
+ private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+
+ private SplitContainerI splitFrame;
+
+ public GAlignFrame()
+ {
try
{
jbInit();
setJMenuBar(alignFrameMenuBar);
- JMenuItem item;
// dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.FormatProperties.getFormats().size(); i++) {
- item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
- saveAlignmentMenu.add( item );
- item.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- saveAs_actionPerformed(e);
- }
- });
+ for (String ff : FileFormat.getWritableFormats(true))
+ {
+ JMenuItem item = new JMenuItem(ff);
- item = new JMenuItem((String) jalview.io.FormatProperties.getFormats().elementAt(i));
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
outputText_actionPerformed(e);
}
});
- outputTextboxMenu.add( item );
+ outputTextboxMenu.add(item);
}
-
+ } catch (Exception e)
+ {
+ System.err.println(e.toString());
}
- catch(Exception e)
+
+ if (!jalview.util.Platform.isAMac())
{
- e.printStackTrace();
+ closeMenuItem.setMnemonic('C');
+ outputTextboxMenu.setMnemonic('T');
+ undoMenuItem.setMnemonic('Z');
+ redoMenuItem.setMnemonic('0');
+ copy.setMnemonic('C');
+ cut.setMnemonic('U');
+ pasteMenu.setMnemonic('P');
+ reload.setMnemonic('R');
}
- ButtonGroup colours = new ButtonGroup();
+ 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);
+ }
+ }
colours.add(noColourmenuItem);
colours.add(clustalColour);
colours.add(zappoColour);
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"));
+ }
+
+ public void setColourSelected(String defaultColour)
+ {
+
+ if (defaultColour != null)
+ {
+ int index = ColourSchemeProperty
+ .getColourIndexFromName(defaultColour);
+
+ switch (index)
+ {
+ case ColourSchemeProperty.CLUSTAL:
+ clustalColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.BLOSUM:
+ BLOSUM62Colour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.PID:
+ PIDColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.ZAPPO:
+ zappoColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.TAYLOR:
+ taylorColour.setSelected(true);
+ break;
+
+ case ColourSchemeProperty.HYDROPHOBIC:
+ hydrophobicityColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.HELIX:
+ helixColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.STRAND:
+ strandColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.TURN:
+ turnColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.BURIED:
+ buriedColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.NUCLEOTIDE:
+ nucleotideColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.TCOFFEE:
+ tcoffeeColour.setSelected(true);
+ break;
+
+ case ColourSchemeProperty.PURINEPYRIMIDINE:
+ purinePyrimidineColour.setSelected(true);
+
+ break;
+
+ case ColourSchemeProperty.RNAINTERACTION:
+ RNAInteractionColour.setSelected(true);
+
+ break;
+ /*
+ * case ColourSchemeProperty.COVARIATION:
+ * covariationColour.setSelected(true);
+ *
+ * break;
+ */
+ case ColourSchemeProperty.USER_DEFINED:
+ userDefinedColour.setSelected(true);
+
+ break;
+ case ColourSchemeProperty.NONE:
+ default:
+ noColourmenuItem.setSelected(true);
+ break;
+
+ }
+ }
+
}
+
private void jbInit() throws Exception
{
- fileMenu.setMnemonic('F');
- fileMenu.setText("File");
- saveAlignmentMenu.setMnemonic('L');
- saveAlignmentMenu.setText("Save alignment to local file");
- closeMenuItem.setMnemonic('C');
- closeMenuItem.setText("Close");
- closeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem saveAs = new JMenuItem(
+ MessageManager.getString("action.save_as"));
+ ActionListener al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- closeMenuItem_actionPerformed(e);
- }
- });
- editMenu.setText("Edit");
- viewMenu.setText("View");
- colourMenu.setText("Colour");
- calculateMenu.setText("Calculate");
- alignMenu.setText("Web Service");
- groupsMenuItem.setVisible(false);
- groupsMenuItem.setText("Groups");
- groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ saveAs_actionPerformed(e);
+ }
+ };
+ KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ addMenuActionAndAccelerator(keyStroke, saveAs, al);
+
+ closeMenuItem.setText(MessageManager.getString("action.close"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- groupsMenuItem_actionPerformed(e);
- }
- });
- selectAllSequenceMenuItem.setText("Select all");
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ closeMenuItem_actionPerformed(false);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
+
+ JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
+ JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
+ JMenu annotationsMenu = new JMenu(
+ MessageManager.getString("action.annotations"));
+ JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
+ colourMenu.setText(MessageManager.getString("action.colour"));
+ JMenu calculateMenu = new JMenu(
+ MessageManager.getString("action.calculate"));
+ webService.setText(MessageManager.getString("action.web_service"));
+ JMenuItem selectAllSequenceMenuItem = new JMenuItem(
+ MessageManager.getString("action.select_all"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
selectAllSequenceMenuItem_actionPerformed(e);
}
- });
- deselectAllSequenceMenuItem.setText("Clear selection");
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
+
+ JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
+ MessageManager.getString("action.deselect_all"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
deselectAllSequenceMenuItem_actionPerformed(e);
}
- });
- invertSequenceMenuItem.setText("Invert sequence selection");
- invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
+
+ JMenuItem invertSequenceMenuItem = new JMenuItem(
+ MessageManager.getString("action.invert_sequence_selection"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
invertSequenceMenuItem_actionPerformed(e);
}
+ };
+ addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
+
+ JMenuItem grpsFromSelection = new JMenuItem(
+ MessageManager.getString("action.make_groups_selection"));
+ grpsFromSelection.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ makeGrpsFromSelection_actionPerformed(e);
+ }
});
- deselectAllColumnsMenuItem.setText("Deselect all columns");
- deselectAllColumnsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem expandAlignment = new JMenuItem(
+ MessageManager.getString("action.view_flanking_regions"));
+ expandAlignment.setToolTipText(MessageManager
+ .getString("label.view_flanking_regions"));
+ expandAlignment.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- deselectAllColumnsMenuItem_actionPerformed(e);
+ expand_newalign(e);
}
});
- remove2LeftMenuItem.setText("Remove sequence <- left of selected column");
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem remove2LeftMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_left"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
remove2LeftMenuItem_actionPerformed(e);
}
- });
- remove2RightMenuItem.setText("Remove sequence -> right of selected column");
- remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
+
+ JMenuItem remove2RightMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_right"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
remove2RightMenuItem_actionPerformed(e);
}
- });
- removeGappedColumnMenuItem.setText("Remove gapped columns");
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
+
+ JMenuItem removeGappedColumnMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_empty_columns"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
removeGappedColumnMenuItem_actionPerformed(e);
}
- });
- removeAllGapsMenuItem.setText("Remove all gaps");
- removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
+
+ JMenuItem removeAllGapsMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_all_gaps"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
removeAllGapsMenuItem_actionPerformed(e);
}
+ };
+ addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
+
+ JMenuItem justifyLeftMenuItem = new JMenuItem(
+ MessageManager.getString("action.left_justify_alignment"));
+ justifyLeftMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ justifyLeftMenuItem_actionPerformed(e);
+ }
});
- setGapCharMenuItem.setText("Set gap character to \".\"");
- setGapCharMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem justifyRightMenuItem = new JMenuItem(
+ MessageManager.getString("action.right_justify_alignment"));
+ justifyRightMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- setGapCharMenuItem_actionPerformed(e);
+ justifyRightMenuItem_actionPerformed(e);
}
});
- viewBoxesMenuItem.setText("Boxes");
+ viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+ viewBoxesMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
viewBoxesMenuItem_actionPerformed(e);
}
});
- viewTextMenuItem.setText("Text");
+ viewTextMenuItem.setText(MessageManager.getString("action.text"));
viewTextMenuItem.setState(true);
- viewTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ viewTextMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
viewTextMenuItem_actionPerformed(e);
}
});
- sortPairwiseMenuItem.setText("Sort by pairwise identity");
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
+ showNonconservedMenuItem.setText(MessageManager
+ .getString("label.show_non_conversed"));
+ showNonconservedMenuItem.setState(false);
+ showNonconservedMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showUnconservedMenuItem_actionPerformed(e);
+ }
+ });
+ JMenuItem sortPairwiseMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortPairwiseMenuItem_actionPerformed(e);
}
});
- sortIDMenuItem.setText("Sort by ID");
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem sortIDMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_id"));
+ sortIDMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
sortIDMenuItem_actionPerformed(e);
}
});
- sortGroupMenuItem.setText("Sort by group");
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem sortLengthMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_length"));
+ sortLengthMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- sortGroupMenuItem_actionPerformed(e);
+ sortLengthMenuItem_actionPerformed(e);
}
});
- sortTreeOrderMenuItem.setText("Sort by tree order");
- sortTreeOrderMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem sortGroupMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_group"));
+ sortGroupMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- sortTreeOrderMenuItem_actionPerformed(e);
+ sortGroupMenuItem_actionPerformed(e);
}
});
- removeRedundancyMenuItem.setText("Remove redundancy");
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem removeRedundancyMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_redundancy"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
removeRedundancyMenuItem_actionPerformed(e);
}
- });
- pairwiseAlignmentMenuItem.setText("Pairwise alignments");
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
+
+ JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
+ MessageManager.getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pairwiseAlignmentMenuItem_actionPerformed(e);
}
});
- PCAMenuItem.setText("Principal component analysis");
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem PCAMenuItem = new JMenuItem(
+ MessageManager.getString("label.principal_component_analysis"));
+ PCAMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
PCAMenuItem_actionPerformed(e);
}
});
- averageDistanceTreeMenuItem.setText("Average distance tree using PID");
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
+ MessageManager.getString("label.average_distance_identity"));
+ averageDistanceTreeMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
averageDistanceTreeMenuItem_actionPerformed(e);
}
});
- neighbourTreeMenuItem.setText("Neighbour joining tree using PID");
- neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem neighbourTreeMenuItem = new JMenuItem(
+ MessageManager.getString("label.neighbour_joining_identity"));
+ neighbourTreeMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
neighbourTreeMenuItem_actionPerformed(e);
}
});
- clustalAlignMenuItem.setText("Clustal alignment");
- clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- clustalAlignMenuItem_actionPerformed(e);
- }
- });
- this.getContentPane().setLayout(borderLayout1);
+
+ this.getContentPane().setLayout(new BorderLayout());
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBackground(Color.white);
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
- statusBar.setText("Status bar");
- outputTextboxMenu.setMnemonic('T');
- outputTextboxMenu.setText("Output alignment via textbox");
- clustalColour.setSelected(false);
- clustalColour.setText("Clustalx colours");
- clustalColour.addActionListener(new java.awt.event.ActionListener()
+ 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("Zappo colour scheme");
- zappoColour.addActionListener(new java.awt.event.ActionListener()
+ zappoColour.setText(MessageManager.getString("label.zappo"));
+ zappoColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
zappoColour_actionPerformed(e);
}
});
- taylorColour.setText("Taylor colour scheme");
- taylorColour.addActionListener(new java.awt.event.ActionListener()
+ taylorColour.setText(MessageManager.getString("label.taylor"));
+ taylorColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
taylorColour_actionPerformed(e);
}
});
- hydrophobicityColour.setText("By hydrophobicity");
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
+ hydrophobicityColour.setText(MessageManager
+ .getString("label.hydrophobicity"));
+ hydrophobicityColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
hydrophobicityColour_actionPerformed(e);
}
});
- helixColour.setText("Helix propensity");
- helixColour.addActionListener(new java.awt.event.ActionListener()
+ helixColour.setText(MessageManager.getString("label.helix_propensity"));
+ helixColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
helixColour_actionPerformed(e);
}
});
- strandColour.setText("Strand propensity");
- strandColour.addActionListener(new java.awt.event.ActionListener()
+ strandColour.setText(MessageManager
+ .getString("label.strand_propensity"));
+ strandColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
strandColour_actionPerformed(e);
}
});
- turnColour.setText("Turn propensity");
- turnColour.addActionListener(new java.awt.event.ActionListener()
+ turnColour.setText(MessageManager.getString("label.turn_propensity"));
+ turnColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
turnColour_actionPerformed(e);
}
});
- buriedColour.setText("Buried index");
- buriedColour.addActionListener(new java.awt.event.ActionListener()
+ buriedColour.setText(MessageManager.getString("label.buried_index"));
+ buriedColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
buriedColour_actionPerformed(e);
}
});
- userDefinedColour.setText("User defined colours");
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ userDefinedColour.setText(MessageManager
+ .getString("action.user_defined"));
+ userDefinedColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
userDefinedColour_actionPerformed(e);
}
});
- PIDColour.setText("Percentage Identity");
- PIDColour.addActionListener(new java.awt.event.ActionListener()
+ PIDColour
+ .setText(MessageManager.getString("label.percentage_identity"));
+ PIDColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
PIDColour_actionPerformed(e);
}
});
- BLOSUM62Colour.setText("BLOSUM62 score");
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ BLOSUM62Colour
+ .setText(MessageManager.getString("label.blosum62_score"));
+ BLOSUM62Colour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
BLOSUM62Colour_actionPerformed(e);
}
});
- avDistanceTreeBlosumMenuItem.setText("Average distance tree using BLOSUM62");
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+ nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
+ nucleotideColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- avTreeBlosumMenuItem_actionPerformed(e);
+ nucleotideColour_actionPerformed(e);
}
});
- njTreeBlosumMenuItem.setText("Neighbour joining tree using BLOSUM62");
- njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ purinePyrimidineColour.setText(MessageManager
+ .getString("label.purine_pyrimidine"));
+ purinePyrimidineColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- njTreeBlosumMenuItem_actionPerformed(e);
+ purinePyrimidineColour_actionPerformed(e);
}
});
- consensusGraphMenuItem.setActionCommand("");
- consensusGraphMenuItem.setText("Consensus graph");
- consensusGraphMenuItem.setState(true);
- consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ RNAInteractionColour.setText("RNA Interaction type");
+ RNAInteractionColour.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- consensusGraphMenuItem_actionPerformed(e);
+ RNAInteractionColour_actionPerformed(e);
}
});
- colourTextMenuItem.setText("Colour text");
- colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+ /*
+ * 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"));
+ avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- colourTextMenuItem_actionPerformed(e);
+ avTreeBlosumMenuItem_actionPerformed(e);
}
});
- htmlMenuItem.setText("Output as HTML");
- htmlMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem njTreeBlosumMenuItem = new JMenuItem(
+ MessageManager.getString("label.neighbour_blosum62"));
+ njTreeBlosumMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- htmlMenuItem_actionPerformed(e);
+ njTreeBlosumMenuItem_actionPerformed(e);
}
});
- overviewMenuItem.setText("Overview window");
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+ annotationPanelMenuItem.setActionCommand("");
+ annotationPanelMenuItem.setText(MessageManager
+ .getString("label.show_annotations"));
+ annotationPanelMenuItem.setState(Cache.getDefault("SHOW_ANNOTATIONS",
+ true));
+ annotationPanelMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- overviewMenuItem_actionPerformed(e);
+ annotationPanelMenuItem_actionPerformed(e);
}
});
- undoMenuItem.setEnabled(false);
- undoMenuItem.setMnemonic('Z');
- undoMenuItem.setText("Undo");
- undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ showAllAlAnnotations.setText(MessageManager
+ .getString("label.show_all_al_annotations"));
+ final boolean isAnnotationPanelShown = annotationPanelMenuItem
+ .getState();
+ showAllAlAnnotations.setEnabled(isAnnotationPanelShown);
+ showAllAlAnnotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- undoMenuItem_actionPerformed(e);
+ showAllAnnotations_actionPerformed(false, true);
}
});
- redoMenuItem.setEnabled(false);
- redoMenuItem.setMnemonic('0');
- redoMenuItem.setText("Redo");
- redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ hideAllAlAnnotations.setText(MessageManager
+ .getString("label.hide_all_al_annotations"));
+ hideAllAlAnnotations.setEnabled(isAnnotationPanelShown);
+ hideAllAlAnnotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- redoMenuItem_actionPerformed(e);
+ hideAllAnnotations_actionPerformed(false, true);
}
});
- conservationMenuItem.setText("By conservation");
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+ showAllSeqAnnotations.setText(MessageManager
+ .getString("label.show_all_seq_annotations"));
+ showAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
+ showAllSeqAnnotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- conservationMenuItem_actionPerformed(e);
+ showAllAnnotations_actionPerformed(true, false);
}
});
- noColourmenuItem.setText("None");
- noColourmenuItem.setSelected(true);
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ hideAllSeqAnnotations.setText(MessageManager
+ .getString("label.hide_all_seq_annotations"));
+ hideAllSeqAnnotations.setEnabled(isAnnotationPanelShown);
+ hideAllSeqAnnotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- noColourmenuItem_actionPerformed(e);
+ hideAllAnnotations_actionPerformed(true, false);
}
});
- wrapMenuItem.setText("Wrap alignment");
- wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+ SequenceAnnotationOrder sortAnnotationsBy = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ final JCheckBoxMenuItem sortAnnBySequence = new JCheckBoxMenuItem(
+ MessageManager.getString("label.sort_annotations_by_sequence"));
+ final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
+ MessageManager.getString("label.sort_annotations_by_label"));
+
+ sortAnnBySequence
+ .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+ sortAnnBySequence.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- wrapMenuItem_actionPerformed(e);
+ boolean newState = sortAnnBySequence.getState();
+ sortAnnByLabel.setSelected(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
+ sortAnnotations_actionPerformed();
}
});
- printMenuItem.setText("Print");
- printMenuItem.addActionListener(new java.awt.event.ActionListener()
+ sortAnnByLabel
+ .setSelected(sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ sortAnnByLabel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- printMenuItem_actionPerformed(e);
+ boolean newState = sortAnnByLabel.getState();
+ sortAnnBySequence.setSelected(false);
+ setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
+ sortAnnotations_actionPerformed();
}
});
- renderGapsMenuItem.setText("Render gaps");
- renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ colourTextMenuItem.setText(MessageManager
+ .getString("label.colour_text"));
+ colourTextMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- renderGapsMenuItem_actionPerformed(e);
+ colourTextMenuItem_actionPerformed(e);
}
});
- findMenuItem.setText("Find");
- findMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem htmlMenuItem = new JMenuItem(
+ MessageManager.getString("label.html"));
+ htmlMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- findMenuItem_actionPerformed(e);
+ htmlMenuItem_actionPerformed(e);
}
});
- searchMenu.setText("Search");
- abovePIDThreshold.setText("Above PID threshold");
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener() {
- public void actionPerformed(ActionEvent e) {
- abovePIDThreshold_actionPerformed(e);
- }
- });
- sequenceFeatures.setText("Sequence Features");
- sequenceFeatures.addActionListener(new ActionListener()
+ JMenuItem createBioJS = new JMenuItem(
+ MessageManager.getString("label.biojs_html_export"));
+ createBioJS.addActionListener(new java.awt.event.ActionListener()
{
- public void actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- sequenceFeatures_actionPerformed(actionEvent);
+ bioJSMenuItem_actionPerformed(e);
}
});
- nucleotideColour.setText("Nucleotide colours");
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem overviewMenuItem = new JMenuItem(
+ MessageManager.getString("label.overview_window"));
+ overviewMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- nucleotideColour_actionPerformed(e);
+ overviewMenuItem_actionPerformed(e);
}
});
- deleteGroups.setSelected(false);
- deleteGroups.setText("Delete all groups");
- deleteGroups.addActionListener(new java.awt.event.ActionListener()
+
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setText(MessageManager.getString("action.undo"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- deleteGroups_actionPerformed(e);
+ undoMenuItem_actionPerformed(e);
}
- });
- copy.setText("Copy");
- copy.setMnemonic(KeyEvent.VK_C);
+ };
+ addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
- copy.addActionListener(new java.awt.event.ActionListener()
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setText(MessageManager.getString("action.redo"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- copy_actionPerformed(e);
+ redoMenuItem_actionPerformed(e);
}
- });
- cut.setText("Cut");
- cut.setMnemonic(KeyEvent.VK_X);
- cut.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
+
+ conservationMenuItem.setText(MessageManager
+ .getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- cut_actionPerformed(e);
+ conservationMenuItem_actionPerformed(e);
}
});
- delete.setText("Delete");
- delete.addActionListener(new java.awt.event.ActionListener()
+ noColourmenuItem.setText(MessageManager.getString("label.none"));
+ noColourmenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- delete_actionPerformed(e);
+ noColourmenuItem_actionPerformed(e);
}
});
- jMenu1.setMnemonic('V');
- jMenu1.setText("Paste");
- pasteNew.setText("to new alignment");
- pasteNew.addActionListener(new java.awt.event.ActionListener()
+ wrapMenuItem.setText(MessageManager.getString("label.wrap"));
+ wrapMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- pasteNew_actionPerformed(e);
+ wrapMenuItem_actionPerformed(e);
}
});
- pasteThis.setText("add to this alignment");
- pasteThis.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem printMenuItem = new JMenuItem(
+ MessageManager.getString("action.print"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- pasteThis_actionPerformed(e);
+ printMenuItem_actionPerformed(e);
}
- });
- applyToAllGroups.setText("Apply colour to all groups");
- applyToAllGroups.setState(true);
- applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
+
+ renderGapsMenuItem
+ .setText(MessageManager.getString("action.show_gaps"));
+ renderGapsMenuItem.setState(true);
+ renderGapsMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- applyToAllGroups_actionPerformed(e);
+ renderGapsMenuItem_actionPerformed(e);
}
});
- createPNG.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem findMenuItem = new JMenuItem(
+ MessageManager.getString("action.find"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.find_tip")));
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- createPNG_actionPerformed(e);
+ findMenuItem_actionPerformed(e);
+ }
+ };
+ 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()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ showSeqFeatures_actionPerformed(actionEvent);
+ }
+ });
+ /*
+ * showSeqFeaturesHeight.setText("Vary Sequence Feature Height");
+ * showSeqFeaturesHeight.addActionListener(new ActionListener() { public
+ * void actionPerformed(ActionEvent actionEvent) {
+ * showSeqFeaturesHeight_actionPerformed(actionEvent); } });
+ */
+ showDbRefsMenuitem.setText(MessageManager
+ .getString("label.show_database_refs"));
+ showDbRefsMenuitem.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showDbRefs_actionPerformed(e);
+ }
+
+ });
+ showNpFeatsMenuitem.setText(MessageManager
+ .getString("label.show_non_positional_features"));
+ showNpFeatsMenuitem.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showNpFeats_actionPerformed(e);
+ }
+
+ });
+ showGroupConservation.setText(MessageManager
+ .getString("label.group_conservation"));
+ showGroupConservation.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showGroupConservation_actionPerformed(e);
+ }
+
+ });
+
+ showGroupConsensus.setText(MessageManager
+ .getString("label.group_consensus"));
+ showGroupConsensus.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showGroupConsensus_actionPerformed(e);
+ }
+
+ });
+ showConsensusHistogram.setText(MessageManager
+ .getString("label.show_consensus_histogram"));
+ showConsensusHistogram.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showConsensusHistogram_actionPerformed(e);
+ }
+
+ });
+ showSequenceLogo.setText(MessageManager
+ .getString("label.show_consensus_logo"));
+ showSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showSequenceLogo_actionPerformed(e);
+ }
+
+ });
+ normaliseSequenceLogo.setText(MessageManager
+ .getString("label.norm_consensus_logo"));
+ normaliseSequenceLogo.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ normaliseSequenceLogo_actionPerformed(e);
+ }
+
+ });
+ applyAutoAnnotationSettings.setText(MessageManager
+ .getString("label.apply_all_groups"));
+ applyAutoAnnotationSettings.setState(false);
+ applyAutoAnnotationSettings.setVisible(true);
+ applyAutoAnnotationSettings.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ applyAutoAnnotationSettings_actionPerformed(e);
+ }
+ });
+
+ ButtonGroup buttonGroup = new ButtonGroup();
+ final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
+ MessageManager.getString("label.show_first"));
+ final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
+ MessageManager.getString("label.show_last"));
+ buttonGroup.add(showAutoFirst);
+ buttonGroup.add(showAutoLast);
+ final boolean autoFirst = Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false);
+ showAutoFirst.setSelected(autoFirst);
+ setShowAutoCalculatedAbove(autoFirst);
+ showAutoFirst.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ setShowAutoCalculatedAbove(showAutoFirst.isSelected());
+ sortAnnotations_actionPerformed();
+ }
+ });
+ showAutoLast.setSelected(!showAutoFirst.isSelected());
+ showAutoLast.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ setShowAutoCalculatedAbove(!showAutoLast.isSelected());
+ sortAnnotations_actionPerformed();
+ }
+ });
+
+ 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
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ deleteGroups_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
+
+ JMenuItem createGroup = new JMenuItem(
+ MessageManager.getString("action.create_groups"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroup_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, createGroup, al);
+
+ JMenuItem unGroup = new JMenuItem(
+ MessageManager.getString("action.remove_group"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ unGroup_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, unGroup, al);
+
+ copy.setText(MessageManager.getString("action.copy"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, copy, al);
+
+ cut.setText(MessageManager.getString("action.cut"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cut_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, cut, al);
+
+ JMenuItem delete = new JMenuItem(
+ MessageManager.getString("action.delete"));
+ delete.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ delete_actionPerformed(e);
+ }
+ });
+
+ pasteMenu.setText(MessageManager.getString("action.paste"));
+ JMenuItem pasteNew = new JMenuItem(
+ MessageManager.getString("label.to_new_alignment"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.SHIFT_MASK, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ pasteNew_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, pasteNew, al);
+
+ JMenuItem pasteThis = new JMenuItem(
+ MessageManager.getString("label.to_this_alignment"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ pasteThis_actionPerformed(e);
+ }
+ };
+ 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()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createPNG(null);
+ }
+ });
+ createPNG.setActionCommand(MessageManager
+ .getString("label.save_png_image"));
+
+ JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
+ font.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ font_actionPerformed(e);
+ }
+ });
+ seqLimits.setText(MessageManager
+ .getString("label.show_sequence_limits"));
+ seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
+ seqLimits.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ seqLimit_actionPerformed(e);
+ }
+ });
+ JMenuItem epsFile = new JMenuItem("EPS");
+ epsFile.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createEPS(null);
+ }
+ });
+
+ JMenuItem createSVG = new JMenuItem("SVG");
+ createSVG.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createSVG(null);
+ }
+ });
+
+ JMenuItem loadTreeMenuItem = new JMenuItem(
+ MessageManager.getString("label.load_associated_tree"));
+ loadTreeMenuItem.setActionCommand(MessageManager
+ .getString("label.load_tree_for_sequence_set"));
+ loadTreeMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ loadTreeMenuItem_actionPerformed(e);
+ }
+ });
+
+ scaleAbove.setVisible(false);
+ scaleAbove.setText(MessageManager.getString("action.scale_above"));
+ scaleAbove.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleAbove_actionPerformed(e);
+ }
+ });
+ scaleLeft.setVisible(false);
+ scaleLeft.setSelected(true);
+ scaleLeft.setText(MessageManager.getString("action.scale_left"));
+ scaleLeft.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleLeft_actionPerformed(e);
+ }
+ });
+ scaleRight.setVisible(false);
+ scaleRight.setSelected(true);
+ scaleRight.setText(MessageManager.getString("action.scale_right"));
+ scaleRight.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ scaleRight_actionPerformed(e);
+ }
+ });
+ centreColumnLabelsMenuItem.setVisible(true);
+ centreColumnLabelsMenuItem.setState(false);
+ centreColumnLabelsMenuItem.setText(MessageManager
+ .getString("label.centre_column_labels"));
+ centreColumnLabelsMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ centreColumnLabels_actionPerformed(e);
+ }
+ });
+ followHighlightMenuItem.setVisible(true);
+ followHighlightMenuItem.setState(true);
+ followHighlightMenuItem.setText(MessageManager
+ .getString("label.automatic_scrolling"));
+ followHighlightMenuItem.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ followHighlight_actionPerformed();
+ }
+
+ });
+
+ JMenuItem modifyPID = new JMenuItem(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed(e);
+ }
+ });
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ 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"));
+ sort.addMenuListener(new MenuListener()
+ {
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ buildTreeMenu();
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+ });
+ sortByAnnotScore.setText(MessageManager
+ .getString("label.sort_by_score"));
+ sort.add(sortByAnnotScore);
+ sort.addMenuListener(new javax.swing.event.MenuListener()
+ {
+
+ @Override
+ public void menuCanceled(MenuEvent e)
+ {
+ }
+
+ @Override
+ public void menuDeselected(MenuEvent e)
+ {
+ }
+
+ @Override
+ public void menuSelected(MenuEvent e)
+ {
+ buildSortByAnnotationScoresMenu();
+ }
+ });
+ sortByAnnotScore.setVisible(false);
+
+ calculateTree
+ .setText(MessageManager.getString("action.calculate_tree"));
+
+ padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
+ padGapsMenuitem.setState(jalview.bin.Cache
+ .getDefault("PAD_GAPS", false));
+ padGapsMenuitem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ padGapsMenuitem_actionPerformed(e);
+ }
+ });
+ JMenuItem vamsasStore = new JMenuItem(
+ MessageManager.getString("label.vamsas_store"));
+ vamsasStore.setVisible(false);
+ vamsasStore.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ vamsasStore_actionPerformed(e);
+ }
+ });
+ showTranslation.setText(MessageManager
+ .getString("label.translate_cDNA"));
+ showTranslation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ 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"));
+ extractScores.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ extractScores_actionPerformed(e);
+ }
+ });
+ extractScores.setVisible(true);
+ // JBPNote: TODO: make gui for regex based score extraction
+
+ // 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 actionPerformed(ActionEvent e)
+ {
+ featureSettings_actionPerformed(e);
+ }
+ });
+ JMenuItem fetchSequence = new JMenuItem(
+ MessageManager.getString("label.fetch_sequences"));
+ fetchSequence.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ fetchSequence_actionPerformed(e);
+ }
+ });
+
+ 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);
}
});
- createPNG.setActionCommand("Save as PNG Image");
- createPNG.setText("Save as PNG Image");
- font.setText("Change Font");
- font.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem associatedData = new JMenuItem(
+ MessageManager.getString("label.load_features_annotations"));
+ associatedData.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- font_actionPerformed(e);
+ associatedData_actionPerformed(e);
+ }
+ });
+ autoCalculate.setText(MessageManager
+ .getString("label.autocalculate_consensus"));
+ autoCalculate.setState(jalview.bin.Cache.getDefault(
+ "AUTO_CALC_CONSENSUS", true));
+ autoCalculate.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ autoCalculate_actionPerformed(e);
+ }
+ });
+ sortByTree.setText(MessageManager
+ .getString("label.sort_alignment_new_tree"));
+ sortByTree
+ .setToolTipText("<html>"
+ + MessageManager
+ .getString("label.enable_automatically_sort_alignment_when_open_new_tree"));
+ sortByTree
+ .setState(jalview.bin.Cache.getDefault("SORT_BY_TREE", false));
+ sortByTree.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sortByTreeOption_actionPerformed(e);
+ }
+ });
+
+ listenToViewSelections.setText(MessageManager
+ .getString("label.listen_for_selections"));
+ listenToViewSelections
+ .setToolTipText("<html>"
+ + MessageManager
+ .getString("label.selections_mirror_selections_made_same_sequences_other_views"));
+ listenToViewSelections.setState(false);
+ listenToViewSelections.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ listenToViewSelections_actionPerformed(e);
+ }
+ });
+
+ JMenu addSequenceMenu = new JMenu(
+ MessageManager.getString("label.add_sequences"));
+ JMenuItem addFromFile = new JMenuItem(
+ MessageManager.getString("label.from_file"));
+ addFromFile.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromFile_actionPerformed(e);
+ }
+ });
+ JMenuItem addFromText = new JMenuItem(
+ MessageManager.getString("label.from_textbox"));
+ addFromText.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromText_actionPerformed(e);
+ }
+ });
+ JMenuItem addFromURL = new JMenuItem(
+ MessageManager.getString("label.from_url"));
+ addFromURL.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addFromURL_actionPerformed(e);
+ }
+ });
+ JMenuItem exportFeatures = new JMenuItem(
+ MessageManager.getString("label.export_features"));
+ exportFeatures.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ exportFeatures_actionPerformed(e);
+ }
+ });
+ JMenuItem exportAnnotations = new JMenuItem(
+ MessageManager.getString("label.export_annotations"));
+ exportAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ exportAnnotations_actionPerformed(e);
+ }
+ });
+ statusPanel.setLayout(new GridLayout());
+ JMenuItem showAllSeqs = new JMenuItem(
+ MessageManager.getString("label.all_sequences"));
+ showAllSeqs.setToolTipText(MessageManager
+ .getString("label.toggle_sequence_visibility"));
+ showAllSeqs.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllSeqs_actionPerformed(e);
+ }
+ });
+ JMenuItem showAllColumns = new JMenuItem(
+ MessageManager.getString("label.all_columns"));
+ showAllColumns.setToolTipText(MessageManager
+ .getString("label.toggle_columns_visibility"));
+ showAllColumns.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllColumns_actionPerformed(e);
+ }
+ });
+ JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
+ JMenuItem hideSelSequences = new JMenuItem(
+ MessageManager.getString("label.selected_sequences"));
+ hideSelSequences.setToolTipText(MessageManager
+ .getString("label.toggle_sequence_visibility"));
+ hideSelSequences.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSelSequences_actionPerformed(e);
+ }
+ });
+ JMenuItem hideSelColumns = new JMenuItem(
+ MessageManager.getString("label.selected_columns"));
+ hideSelColumns.setToolTipText(MessageManager
+ .getString("label.toggle_columns_visibility"));
+ hideSelColumns.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideSelColumns_actionPerformed(e);
+ }
+ });
+ JMenuItem hideAllSelection = new JMenuItem(
+ MessageManager.getString("label.selected_region"));
+ hideAllSelection.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllSelection_actionPerformed(e);
+ }
+ });
+ // TODO: should be hidden if no selection exists.
+ JMenuItem hideAllButSelection = new JMenuItem(
+ MessageManager.getString("label.all_but_selected_region"));
+ hideAllButSelection.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideAllButSelection_actionPerformed(e);
+ }
+ });
+ JMenuItem showAllhidden = new JMenuItem(
+ MessageManager.getString("label.all_sequences_columns"));
+ showAllhidden.setToolTipText(MessageManager
+ .getString("label.toggles_visibility_hidden_selected_regions"));
+ showAllhidden.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showAllhidden_actionPerformed(e);
+ }
+ });
+ hiddenMarkers.setText(MessageManager
+ .getString("action.show_hidden_markers"));
+ hiddenMarkers.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hiddenMarkers_actionPerformed(e);
+ }
+ });
+
+ JMenuItem invertColSel = new JMenuItem(
+ MessageManager.getString("action.invert_column_selection"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask()
+ | KeyEvent.ALT_MASK, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ invertColSel_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, invertColSel, al);
+
+ showComplementMenuItem.setVisible(false);
+ showComplementMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showComplement_actionPerformed(showComplementMenuItem.getState());
}
});
- fullSeqId.setText("Show full sequence id");
- fullSeqId.addActionListener(new java.awt.event.ActionListener()
+
+ tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent evt)
+ {
+ JTabbedPane pane = (JTabbedPane) evt.getSource();
+ int sel = pane.getSelectedIndex();
+ tabSelectionChanged(sel);
+ }
+ });
+ tabbedPane.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent 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()
+ {
+ @Override
+ public void focusGained(FocusEvent e)
+ {
+ tabbedPane_focusGained(e);
+ }
+ });
+
+ JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ save_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, save, al);
+
+ reload.setEnabled(false);
+ reload.setText(MessageManager.getString("action.reload"));
+ reload.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ reload_actionPerformed(e);
+ }
+ });
+
+ JMenuItem newView = new JMenuItem(
+ MessageManager.getString("action.new_view"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T, Toolkit
+ .getDefaultToolkit().getMenuShortcutKeyMask(), false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ newView_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, newView, al);
+
+ 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)
{
- fullSeqId_actionPerformed(e);
+ textColour_actionPerformed(e);
}
});
- epsFile.setText("Save as EPS file");
- epsFile.addActionListener(new java.awt.event.ActionListener()
+ formatMenu.setText(MessageManager.getString("action.format"));
+ JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
+ idRightAlign.setText(MessageManager
+ .getString("label.right_align_sequence_id"));
+ idRightAlign.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- epsFile_actionPerformed(e);
+ idRightAlign_actionPerformed(e);
}
});
- LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
- LoadtreeMenuItem.setText("Load assocated tree");
- LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener() {
+
+ gatherViews.setEnabled(false);
+ gatherViews.setText(MessageManager.getString("action.gather_views"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ gatherViews_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, gatherViews, al);
+
+ expandViews.setEnabled(false);
+ expandViews.setText(MessageManager.getString("action.expand_views"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ expandViews_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, expandViews, al);
+
+ JMenuItem pageSetup = new JMenuItem(
+ MessageManager.getString("action.page_setup"));
+ pageSetup.addActionListener(new ActionListener()
+ {
+ @Override
public void actionPerformed(ActionEvent e)
{
- LoadtreeMenuItem_actionPerformed(e);
+ pageSetup_actionPerformed(e);
+ }
+ });
+ JMenuItem alignmentProperties = new JMenuItem(
+ MessageManager.getString("label.alignment_props"));
+ alignmentProperties.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ 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(
+ MessageManager.getString("label.autocalculated_annotation"));
+
+ JMenu exportImageMenu = new JMenu(
+ MessageManager.getString("label.export_image"));
+ JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
- alignFrameMenuBar.add(searchMenu);
+ alignFrameMenuBar.add(selectMenu);
alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(annotationsMenu);
+ alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
- alignFrameMenuBar.add(alignMenu);
- fileMenu.add(saveAlignmentMenu);
+ alignFrameMenuBar.add(webService);
+
+ fileMenu.add(fetchSequence);
+ fileMenu.add(addSequenceMenu);
+ fileMenu.add(reload);
+ fileMenu.addSeparator();
+ fileMenu.add(vamsasStore);
+ fileMenu.add(save);
+ fileMenu.add(saveAs);
fileMenu.add(outputTextboxMenu);
- fileMenu.add(htmlMenuItem);
- fileMenu.add(epsFile);
- fileMenu.add(createPNG);
+ fileMenu.add(pageSetup);
fileMenu.add(printMenuItem);
fileMenu.addSeparator();
- fileMenu.add(LoadtreeMenuItem);
+ fileMenu.add(exportImageMenu);
+ fileMenu.add(exportFeatures);
+ fileMenu.add(exportAnnotations);
+ fileMenu.add(loadTreeMenuItem);
+ fileMenu.add(associatedData);
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
- editMenu.add(copy);
- editMenu.add(jMenu1);
- editMenu.add(cut);
- editMenu.add(delete);
- editMenu.addSeparator();
+
+ pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
editMenu.add(undoMenuItem);
editMenu.add(redoMenuItem);
+ editMenu.add(cut);
+ editMenu.add(copy);
+ editMenu.add(pasteMenu);
+ editMenu.add(delete);
editMenu.addSeparator();
- editMenu.add(deselectAllSequenceMenuItem);
- editMenu.add(selectAllSequenceMenuItem);
- editMenu.add(invertSequenceMenuItem);
- editMenu.add(deleteGroups);
- editMenu.add(groupsMenuItem);
- editMenu.addSeparator();
- editMenu.add(deselectAllColumnsMenuItem);
editMenu.add(remove2LeftMenuItem);
editMenu.add(remove2RightMenuItem);
- editMenu.addSeparator();
editMenu.add(removeGappedColumnMenuItem);
editMenu.add(removeAllGapsMenuItem);
- editMenu.add(setGapCharMenuItem);
- searchMenu.add(findMenuItem);
- viewMenu.add(font);
- viewMenu.add(fullSeqId);
- viewMenu.add(wrapMenuItem);
- viewMenu.add(viewBoxesMenuItem);
- viewMenu.add(viewTextMenuItem);
- viewMenu.add(colourTextMenuItem);
- viewMenu.add(renderGapsMenuItem);
- viewMenu.add(consensusGraphMenuItem);
+ editMenu.add(removeRedundancyMenuItem);
+ editMenu.addSeparator();
+ // dont add these yet in the CVS build - they cannot be undone!
+ // Excluded from Jalview 2.5 release - undo needs to be implemented.
+ // editMenu.add(justifyLeftMenuItem);
+ // editMenu.add(justifyRightMenuItem);
+ // 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);
+ viewMenu.addSeparator();
+ viewMenu.add(showMenu);
+ viewMenu.add(hideMenu);
+ viewMenu.add(showComplementMenuItem);
+ viewMenu.addSeparator();
+ viewMenu.add(followHighlightMenuItem);
+ viewMenu.addSeparator();
+ viewMenu.add(showSeqFeatures);
+ // viewMenu.add(showSeqFeaturesHeight);
+ viewMenu.add(openFeatureSettings);
+ tooltipSettingsMenu.add(showDbRefsMenuitem);
+ tooltipSettingsMenu.add(showNpFeatsMenuitem);
+ viewMenu.add(tooltipSettingsMenu);
+ viewMenu.addSeparator();
+ viewMenu.add(alignmentProperties);
+ viewMenu.addSeparator();
viewMenu.add(overviewMenuItem);
- viewMenu.add(sequenceFeatures);
+
+ annotationsMenu.add(annotationPanelMenuItem);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAllAlAnnotations);
+ annotationsMenu.add(hideAllAlAnnotations);
+ annotationsMenu.addSeparator();
+ annotationsMenu.add(showAllSeqAnnotations);
+ annotationsMenu.add(hideAllSeqAnnotations);
+ annotationsMenu.add(sortAnnBySequence);
+ annotationsMenu.add(sortAnnByLabel);
+ annotationsMenu.addSeparator();
+ autoAnnMenu.add(showAutoFirst);
+ autoAnnMenu.add(showAutoLast);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normaliseSequenceLogo);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(showGroupConservation);
+ 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(turnColour);
colourMenu.add(buriedColour);
colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(RNAInteractionColour);
+ // colourMenu.add(covariationColour);
+ colourMenu.add(tcoffeeColour);
colourMenu.add(userDefinedColour);
- colourMenu.add(PIDColour);
- colourMenu.add(BLOSUM62Colour);
colourMenu.addSeparator();
- colourMenu.add(abovePIDThreshold);
colourMenu.add(conservationMenuItem);
- calculateMenu.add(sortPairwiseMenuItem);
- calculateMenu.add(sortIDMenuItem);
- calculateMenu.add(sortGroupMenuItem);
- calculateMenu.add(sortTreeOrderMenuItem);
- calculateMenu.add(removeRedundancyMenuItem);
+ 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(pairwiseAlignmentMenuItem);
calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
- calculateMenu.add(averageDistanceTreeMenuItem);
- calculateMenu.add(neighbourTreeMenuItem);
- calculateMenu.add(avDistanceTreeBlosumMenuItem);
- calculateMenu.add(njTreeBlosumMenuItem);
- alignMenu.add(clustalAlignMenuItem);
- this.getContentPane().add(statusBar, BorderLayout.SOUTH);
- jMenu1.add(pasteNew);
- jMenu1.add(pasteThis);
+ 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);
+ exportImageMenu.add(htmlMenuItem);
+ exportImageMenu.add(epsFile);
+ exportImageMenu.add(createPNG);
+ exportImageMenu.add(createBioJS);
+ exportImageMenu.add(createSVG);
+ addSequenceMenu.add(addFromFile);
+ addSequenceMenu.add(addFromText);
+ addSequenceMenu.add(addFromURL);
+ this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+ statusPanel.add(statusBar, null);
+ this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
+
+ formatMenu.add(font);
+ formatMenu.addSeparator();
+ formatMenu.add(wrapMenuItem);
+ formatMenu.add(scaleAbove);
+ formatMenu.add(scaleLeft);
+ formatMenu.add(scaleRight);
+ formatMenu.add(seqLimits);
+ formatMenu.add(idRightAlign);
+ formatMenu.add(hiddenMarkers);
+ formatMenu.add(viewBoxesMenuItem);
+ formatMenu.add(viewTextMenuItem);
+ formatMenu.add(colourTextMenuItem);
+ formatMenu.add(renderGapsMenuItem);
+ formatMenu.add(centreColumnLabelsMenuItem);
+ formatMenu.add(showNonconservedMenuItem);
+ selectMenu.add(findMenuItem);
+ selectMenu.addSeparator();
+ selectMenu.add(selectAllSequenceMenuItem);
+ selectMenu.add(deselectAllSequenceMenuItem);
+ selectMenu.add(invertSequenceMenuItem);
+ selectMenu.add(invertColSel);
+ selectMenu.add(createGroup);
+ selectMenu.add(unGroup);
+ selectMenu.add(grpsFromSelection);
+ selectMenu.add(deleteGroups);
+ selectMenu.add(annotationColumn);
+ selectMenu.add(selectHighlighted);
+ // TODO - determine if the listenToViewSelections button is needed : see bug
+ // JAL-574
+ // selectMenu.addSeparator();
+ // selectMenu.add(listenToViewSelections);
+ }
+
+ 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.
+ *
+ * @param keyStroke
+ * @param menuItem
+ * @param actionListener
+ */
+ protected void addMenuActionAndAccelerator(KeyStroke keyStroke,
+ JMenuItem menuItem, ActionListener actionListener)
+ {
+ menuItem.setAccelerator(keyStroke);
+ accelerators.put(keyStroke, menuItem);
+ menuItem.addActionListener(actionListener);
+ }
+
+ /**
+ * Action on clicking sort annotations by type.
+ *
+ * @param sortOrder
+ */
+ protected void sortAnnotations_actionPerformed()
+ {
+ }
+
+ /**
+ * Action on clicking Show all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void showAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
+ {
+ setAnnotationsVisibility(true, forSequences, forAlignment);
+ }
+
+ /**
+ * Action on clicking Hide all annotations.
+ *
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void hideAllAnnotations_actionPerformed(boolean forSequences,
+ boolean forAlignment)
+ {
+ setAnnotationsVisibility(false, forSequences, forAlignment);
+ }
+
+ /**
+ * Set the visibility of annotations to true or false. Can act on
+ * sequence-related annotations, or alignment-related, or both.
+ *
+ * @param visible
+ * @param forSequences
+ * update sequence-related annotations
+ * @param forAlignment
+ * update non-sequence-related annotations
+ */
+ protected void setAnnotationsVisibility(boolean visible,
+ boolean forSequences, boolean forAlignment)
+ {
+
+ }
+
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showAllhidden_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void hideAllButSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void hideAllSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showGroupConservation_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void followHighlight_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
}
- protected void saveAs_actionPerformed(ActionEvent e)
+ protected void showNpFeats_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void showDbRefs_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void centreColumnLabels_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void buildSortByAnnotationScoresMenu()
{
+ }
+ protected void extractScores_actionPerformed(ActionEvent e)
+ {
}
protected void outputText_actionPerformed(ActionEvent e)
{
+ }
+
+ public void addFromFile_actionPerformed(ActionEvent e)
+ {
}
- protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ public void addFromText_actionPerformed(ActionEvent e)
{
}
+ public void addFromURL_actionPerformed(ActionEvent e)
+ {
+ }
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+ }
- protected void closeMenuItem_actionPerformed(ActionEvent e)
+ public void exportAnnotations_actionPerformed(ActionEvent e)
{
}
- protected void redoMenuItem_actionPerformed(ActionEvent e)
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void bioJSMenuItem_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ protected void closeMenuItem_actionPerformed(boolean b)
{
+ }
+ protected void redoMenuItem_actionPerformed(ActionEvent e)
+ {
}
protected void undoMenuItem_actionPerformed(ActionEvent e)
{
+ }
+
+ protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
}
+ protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
- protected void groupsMenuItem_actionPerformed(ActionEvent e)
+ protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ {
}
+ protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
- protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void viewTextMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+ {
}
+ protected void overviewMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
- protected void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)
+ protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void sortIDMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ protected void PCAMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+ protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ {
}
- protected void setGapCharMenuItem_actionPerformed(ActionEvent e)
+ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void clustalColour_actionPerformed(ActionEvent e)
+ {
}
+ protected void zappoColour_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void taylorColour_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void helixColour_actionPerformed(ActionEvent e)
+ {
+ }
- protected void wrapMenuItem_actionPerformed(ActionEvent e)
+ protected void strandColour_actionPerformed(ActionEvent e)
{
+ }
+ protected void turnColour_actionPerformed(ActionEvent e)
+ {
}
+ protected void buriedColour_actionPerformed(ActionEvent e)
+ {
+ }
- protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+ protected void userDefinedColour_actionPerformed(ActionEvent e)
{
+ }
+ protected void PIDColour_actionPerformed(ActionEvent e)
+ {
}
- protected void viewTextMenuItem_actionPerformed(ActionEvent e)
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
{
+ }
+ protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
+ {
}
+ protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+ {
+ }
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+ /*
+ * protected void covariationColour_actionPerformed(ActionEvent e) { }
+ */
+
+ protected void noColourmenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ {
}
+ protected void printMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
- protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
+ protected void findMenuItem_actionPerformed(ActionEvent e)
{
+ }
+ protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+ {
}
- protected void overviewMenuItem_actionPerformed(ActionEvent e)
+ public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
+ {
+ }
+
+ protected void nucleotideColour_actionPerformed(ActionEvent e)
{
+ }
+ protected void deleteGroups_actionPerformed(ActionEvent e)
+ {
}
- protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+ protected void createGroup_actionPerformed(ActionEvent e)
{
+ }
+ protected void unGroup_actionPerformed(ActionEvent e)
+ {
}
- protected void sortIDMenuItem_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed(ActionEvent e)
{
+ }
+ protected void cut_actionPerformed(ActionEvent e)
+ {
}
- protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ protected void delete_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void pasteNew_actionPerformed(ActionEvent e)
{
+ }
+ protected void pasteThis_actionPerformed(ActionEvent e)
+ {
}
- protected void sortTreeOrderMenuItem_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed(ActionEvent e)
{
+ }
+ public void createPNG(java.io.File f)
+ {
}
- protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+ protected void font_actionPerformed(ActionEvent e)
{
+ }
+ protected void seqLimit_actionPerformed(ActionEvent e)
+ {
}
- protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ public void seqDBRef_actionPerformed(ActionEvent e)
{
}
- protected void PCAMenuItem_actionPerformed(ActionEvent e)
+ public void createEPS(java.io.File f)
+ {
+ }
+
+ public void createSVG(java.io.File f)
{
}
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+ protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
+ /**
+ * Template method to handle the 'load T-Coffee scores' menu event.
+ * <p>
+ * Subclasses override this method to provide a custom action.
+ *
+ * @param event
+ * The raised event
+ */
+ protected void loadScores_actionPerformed(ActionEvent event)
{
}
+ /**
+ * 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 njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ protected void jpred_actionPerformed(ActionEvent e)
{
+ }
+ protected void scaleAbove_actionPerformed(ActionEvent e)
+ {
}
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ protected void scaleLeft_actionPerformed(ActionEvent e)
{
+ }
+ protected void scaleRight_actionPerformed(ActionEvent e)
+ {
}
+ protected void modifyPID_actionPerformed(ActionEvent e)
+ {
+ }
+ protected void modifyConservation_actionPerformed(ActionEvent e)
+ {
+ }
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)
+ protected void saveAs_actionPerformed(ActionEvent e)
{
+ }
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e)
+ {
}
+ public void vamsasStore_actionPerformed(ActionEvent e)
+ {
+ }
+ public void vamsasLoad_actionPerformed(ActionEvent e)
+ {
- protected void clustalColour_actionPerformed(ActionEvent e)
+ }
+
+ public void showTranslation_actionPerformed(ActionEvent e)
{
}
- protected void zappoColour_actionPerformed(ActionEvent e)
+ public void featureSettings_actionPerformed(ActionEvent e)
{
}
- protected void taylorColour_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed(ActionEvent e)
{
}
+ public void smoothFont_actionPerformed(ActionEvent e)
+ {
+
+ }
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed(ActionEvent e)
{
}
- protected void helixColour_actionPerformed(ActionEvent e)
+ public void annotationColumn_actionPerformed(ActionEvent e)
{
}
- protected void strandColour_actionPerformed(ActionEvent e)
+ public void rnahelicesColour_actionPerformed(ActionEvent e)
{
}
- protected void turnColour_actionPerformed(ActionEvent e)
+ public void associatedData_actionPerformed(ActionEvent e)
{
}
- protected void buriedColour_actionPerformed(ActionEvent e)
+ public void autoCalculate_actionPerformed(ActionEvent e)
{
}
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+ }
- protected void userDefinedColour_actionPerformed(ActionEvent e)
+ public void showAllSeqs_actionPerformed(ActionEvent e)
{
}
- protected void PIDColour_actionPerformed(ActionEvent e)
+ public void showAllColumns_actionPerformed(ActionEvent e)
{
}
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ public void hideSelSequences_actionPerformed(ActionEvent e)
{
}
+ public void hideSelColumns_actionPerformed(ActionEvent e)
+ {
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ }
+
+ public void hiddenMarkers_actionPerformed(ActionEvent e)
{
}
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ public void findPdbId_actionPerformed(ActionEvent e)
{
}
+ public void enterPdbId_actionPerformed(ActionEvent e)
+ {
- protected void printMenuItem_actionPerformed(ActionEvent e)
+ }
+
+ public void pdbFile_actionPerformed(ActionEvent e)
{
}
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
+ public void invertColSel_actionPerformed(ActionEvent e)
{
}
- protected void findMenuItem_actionPerformed(ActionEvent e)
+ public void tabSelectionChanged(int sel)
{
}
+ public void tabbedPane_mousePressed(MouseEvent e)
+ {
- protected void abovePIDThreshold_actionPerformed(ActionEvent e) {
+ }
+ public void tabbedPane_focusGained(FocusEvent e)
+ {
+ requestFocus();
}
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+ public void save_actionPerformed(ActionEvent e)
{
}
- protected void nucleotideColour_actionPerformed(ActionEvent e)
+ public void reload_actionPerformed(ActionEvent e)
{
}
- protected void deleteGroups_actionPerformed(ActionEvent e)
+ public void newView_actionPerformed(ActionEvent e)
{
}
- protected void copy_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed(ActionEvent e)
{
}
+ public void idRightAlign_actionPerformed(ActionEvent e)
+ {
+
+ }
- protected void cut_actionPerformed(ActionEvent e)
+ public void expandViews_actionPerformed(ActionEvent e)
{
}
- protected void delete_actionPerformed(ActionEvent e)
+ public void gatherViews_actionPerformed(ActionEvent e)
{
}
- protected void pasteNew_actionPerformed(ActionEvent e)
+ public void buildTreeMenu()
{
}
- protected void pasteThis_actionPerformed(ActionEvent e)
+ public void pageSetup_actionPerformed(ActionEvent e)
{
}
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ public void alignmentProperties()
{
}
- protected void createPNG_actionPerformed(ActionEvent e)
+ protected void expand_newalign(ActionEvent e)
{
+ // TODO Auto-generated method stub
}
- protected void font_actionPerformed(ActionEvent e)
+ protected boolean isShowAutoCalculatedAbove()
{
+ return showAutoCalculatedAbove;
+ }
+
+ protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
+ {
+ this.showAutoCalculatedAbove = showAutoCalculatedAbove;
+ }
+ protected SequenceAnnotationOrder getAnnotationSortOrder()
+ {
+ return annotationSortOrder;
}
- protected void fullSeqId_actionPerformed(ActionEvent e)
+ protected void setAnnotationSortOrder(
+ SequenceAnnotationOrder annotationSortOrder)
{
+ this.annotationSortOrder = annotationSortOrder;
+ }
+ public Map<KeyStroke, JMenuItem> getAccelerators()
+ {
+ return this.accelerators;
}
- protected void epsFile_actionPerformed(ActionEvent e)
+ /**
+ * Returns the selected index of the tabbed pane, or -1 if none selected
+ * (including the case where the tabbed pane has not been made visible).
+ *
+ * @return
+ */
+ public int getTabIndex()
{
+ return tabbedPane.getSelectedIndex();
+ }
+ public JPanel getStatusPanel()
+ {
+ return statusPanel;
}
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {
+ /**
+ * Sets a reference to the containing split frame. Also makes the 'toggle
+ * split view' menu item visible and checked.
+ *
+ * @param sf
+ */
+ public void setSplitFrame(SplitContainerI sf)
+ {
+ this.splitFrame = sf;
+ if (sf != null)
+ {
+ this.showComplementMenuItem.setVisible(true);
+ this.showComplementMenuItem.setState(true);
+ }
+ }
+ public SplitContainerI getSplitViewContainer()
+ {
+ return this.splitFrame;
}
+ protected void showComplement_actionPerformed(boolean complement)
+ {
+ }
}
git://source.jalview.org / jalview.git / blobdiff