/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.jbgui;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.schemes.*;
-
-public class GAlignFrame
- extends JInternalFrame
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
+import jalview.api.SplitContainerI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
+import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.InputEvent;
+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;
+
+@SuppressWarnings("serial")
+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 webService = new JMenu();
- protected JMenuItem webServiceNoServices;
- protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();
- protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();
- protected JMenuItem invertSequenceMenuItem = new JMenuItem();
- protected JMenuItem remove2LeftMenuItem = new JMenuItem();
- protected JMenuItem remove2RightMenuItem = new JMenuItem();
- protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
- protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
- public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
- protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
- protected JMenuItem sortIDMenuItem = new JMenuItem();
- protected JMenuItem sortGroupMenuItem = new JMenuItem();
+
+ public JMenu webService = new JMenu();// BH 2019 was protected, but not
+ // sufficient for AlignFrame thread run
+
+ public JMenuItem webServiceNoServices;// BH 2019 was protected, but not
+ // sufficient for AlignFrame thread run
+
+ protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+
protected JMenu sortByAnnotScore = new JMenu();
- 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();
- BorderLayout borderLayout1 = new BorderLayout();
- public JLabel statusBar = new JLabel();
- protected JMenuItem saveAs = new JMenuItem();
+
+ public JLabel statusBar = new JLabel(); // BH 2019 was protected, but not
+ // sufficient for
+ // AlignFrame.printWriter
+
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();
- public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
- JMenuItem htmlMenuItem = new JMenuItem();
- JMenuItem overviewMenuItem = new JMenuItem();
+
+ protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
+
protected JMenuItem undoMenuItem = new JMenuItem();
+
protected JMenuItem redoMenuItem = new JMenuItem();
- public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
- JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
- public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
- JMenuItem printMenuItem = new JMenuItem();
- public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
- JMenuItem findMenuItem = new JMenuItem();
- public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
+
public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
- protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
- JMenuItem deleteGroups = new JMenuItem();
- JMenuItem delete = new JMenuItem();
+
JMenuItem copy = new JMenuItem();
+
JMenuItem cut = new JMenuItem();
+
JMenu pasteMenu = new JMenu();
- JMenuItem pasteNew = new JMenuItem();
- JMenuItem pasteThis = new JMenuItem();
- public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
- JMenuItem createPNG = new JMenuItem();
- protected JMenuItem font = new JMenuItem();
- public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
- JMenuItem epsFile = new JMenuItem();
- JMenuItem LoadtreeMenuItem = new JMenuItem();
- public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
- public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
- protected JMenuItem modifyPID = new JMenuItem();
- protected JMenuItem modifyConservation = new JMenuItem();
+
+ protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem applyToAllGroups;
+
+ protected JMenu colourMenu = new JMenu();
+
+ protected JMenuItem textColour;
+
+ protected JCheckBoxMenuItem conservationMenuItem;
+
+ protected JMenuItem modifyConservation;
+
+ protected JCheckBoxMenuItem abovePIDThreshold;
+
+ protected JMenuItem modifyPID;
+
+ protected JRadioButtonMenuItem annotationColour;
+
protected JMenu sortByTreeMenu = new JMenu();
+
protected JMenu sort = new JMenu();
- JMenu calculate = new JMenu();
- JMenu jMenu2 = new JMenu();
+
+ protected JMenuItem calculateTree = new JMenuItem();
+
protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
- protected ButtonGroup colours = new ButtonGroup();
- JMenuItem vamsasStore = new JMenuItem();
- protected JMenuItem showTranslation = new JMenuItem();
- protected JMenuItem extractScores = new JMenuItem();
+
+ protected JCheckBoxMenuItem showNpFeatsMenuitem = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
+
+ protected JMenu showTranslation = new JMenu();
+
+ protected JMenuItem showReverse = new JMenuItem();
+
+ protected JMenuItem showReverseComplement = new JMenuItem();
+
protected JMenu showProducts = new JMenu();
- public JMenuItem featureSettings = new JMenuItem();
- JMenuItem fetchSequence = new JMenuItem();
- JMenuItem annotationColour = new JMenuItem();
- JMenuItem associatedData = new JMenuItem();
+
+ protected JMenuItem runGroovy = new JMenuItem();
+
+ protected JMenuItem loadVcf;
+
protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
- JMenu addSequenceMenu = new JMenu();
- JMenuItem addFromFile = new JMenuItem();
- JMenuItem addFromText = new JMenuItem();
- JMenuItem addFromURL = new JMenuItem();
- JMenuItem exportAnnotations = new JMenuItem();
- JMenuItem exportFeatures = new JMenuItem();
+
+ protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
+
+ protected JCheckBoxMenuItem listenToViewSelections = new JCheckBoxMenuItem();
+
protected JPanel statusPanel = new JPanel();
- GridLayout gridLayout1 = new GridLayout();
- JMenu jMenu3 = new JMenu();
- JMenuItem showAllSeqs = new JMenuItem();
- JMenuItem showAllColumns = new JMenuItem();
- JMenu hideMenu = new JMenu();
- JMenuItem hideSelSequences = new JMenuItem();
- JMenuItem hideSelColumns = new JMenuItem();
+
+ 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();
- JMenuItem invertColSel = new JMenuItem();
+
protected JTabbedPane tabbedPane = new JTabbedPane();
- JMenuItem save = new JMenuItem();
+
protected JMenuItem reload = new JMenuItem();
- JMenuItem newView = new JMenuItem();
- JMenuItem textColour = new JMenuItem();
- JMenu formatMenu = new JMenu();
- JMenu selectMenu = new JMenu();
+
+ 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();
- JMenuItem pageSetup = new JMenuItem();
- JMenuItem alignmentProperties = 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();
+
+ protected JMenuItem openFeatureSettings;
+
+ private SequenceAnnotationOrder annotationSortOrder;
+
+ private boolean showAutoCalculatedAbove = false;
+
+ private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
+
+ private SplitContainerI splitFrame;
+
public GAlignFrame()
{
try
{
+
+ // for Web-page embedding using id=align-frame-div
+ setName(Jalview.getAppID("alignment"));
+
+
jbInit();
setJMenuBar(alignFrameMenuBar);
// dynamically fill save as menu with available formats
- for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
- JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.
- WRITEABLE_FORMATS[i]);
+ JMenuItem item = new JMenuItem(ff);
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- outputText_actionPerformed(e);
+ outputText_actionPerformed(e.getActionCommand());
}
});
outputTextboxMenu.add(item);
}
- }
- catch (Exception e)
+ } catch (Exception e)
{
+ System.err.println(e.toString());
}
- if (!new jalview.util.Platform().isAMac())
+ if (Platform.allowMnemonics()) // was "not mac and not JS"
{
closeMenuItem.setMnemonic('C');
outputTextboxMenu.setMnemonic('T');
pasteMenu.setMnemonic('P');
reload.setMnemonic('R');
}
-
- if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
- {
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
- getUserColourSchemes().keys();
-
- while (userColours.hasMoreElements())
- {
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
- userColours.
- nextElement().toString());
- radioItem.setName("USER_DEFINED");
- radioItem.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent evt)
- {
- if (evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
- {
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
- int option = JOptionPane.showInternalConfirmDialog(jalview.gui.
- Desktop.desktop,
- "Remove from default list?",
- "Remove user defined colour",
- JOptionPane.YES_NO_OPTION);
- if (option == JOptionPane.YES_OPTION)
- {
- jalview.gui.UserDefinedColours.removeColourFromDefaults(
- radioItem.getText());
- colourMenu.remove(radioItem);
- }
- else
- {
- radioItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- }
- }
- }
- });
- radioItem.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- userDefinedColour_actionPerformed(evt);
- }
- });
- colourMenu.insert(radioItem, 15);
- colours.add(radioItem);
- }
- }
- colours.add(noColourmenuItem);
- colours.add(clustalColour);
- colours.add(zappoColour);
- colours.add(taylorColour);
- colours.add(hydrophobicityColour);
- colours.add(helixColour);
- colours.add(strandColour);
- colours.add(turnColour);
- colours.add(buriedColour);
- colours.add(userDefinedColour);
- colours.add(PIDColour);
- colours.add(BLOSUM62Colour);
- colours.add(nucleotideColour);
-
- setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
-
}
- public void setColourSelected(String defaultColour)
+ private void jbInit() throws Exception
{
+ initColourMenu();
- if (defaultColour != null)
+ JMenuItem saveAs = new JMenuItem(
+ MessageManager.getString("action.save_as"));
+ ActionListener al = new ActionListener()
{
- int index = ColourSchemeProperty.getColourIndexFromName(defaultColour);
-
- switch (index)
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- case ColourSchemeProperty.NONE:
- noColourmenuItem.setSelected(true);
- break;
- 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;
+ saveAs_actionPerformed();
+ }
+ };
- case ColourSchemeProperty.USER_DEFINED:
- userDefinedColour.setSelected(true);
+ // FIXME getDefaultToolkit throws an exception in Headless mode
+ KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Platform.SHORTCUT_KEY_MASK | InputEvent.SHIFT_DOWN_MASK,
+ false);
+ addMenuActionAndAccelerator(keyStroke, saveAs, al);
- break;
+ closeMenuItem.setText(MessageManager.getString("action.close"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W, Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ closeMenuItem_actionPerformed(false);
}
- }
-
- }
+ };
+ addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
- private void jbInit()
- throws Exception
- {
- fileMenu.setText("File");
- saveAs.setText("Save As...");
- saveAs.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_S,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
- java.awt.event.KeyEvent.SHIFT_MASK, false));
- saveAs.addActionListener(new ActionListener()
+ 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,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- saveAs_actionPerformed(e);
+ selectAllSequenceMenuItem_actionPerformed(e);
}
- });
- closeMenuItem.setText("Close");
- closeMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_W, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- closeMenuItem.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)
{
- closeMenuItem_actionPerformed(false);
+ deselectAllSequenceMenuItem_actionPerformed(e);
}
- });
- editMenu.setText("Edit");
- viewMenu.setText("View");
- colourMenu.setText("Colour");
- calculateMenu.setText("Calculate");
- webService.setText("Web Service");
- selectAllSequenceMenuItem.setText("Select All");
- selectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_A,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- selectAllSequenceMenuItem.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,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- selectAllSequenceMenuItem_actionPerformed(e);
+ invertSequenceMenuItem_actionPerformed(e);
}
- });
- deselectAllSequenceMenuItem.setText("Deselect All");
- deselectAllSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.
- getKeyStroke(
- java.awt.event.KeyEvent.VK_ESCAPE, 0, false));
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.
- ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
+
+ JMenuItem grpsFromSelection = new JMenuItem(
+ MessageManager.getString("action.make_groups_selection"));
+ grpsFromSelection.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- deselectAllSequenceMenuItem_actionPerformed(e);
+ makeGrpsFromSelection_actionPerformed(e);
}
});
- invertSequenceMenuItem.setText("Invert Sequence Selection");
- invertSequenceMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_I,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- invertSequenceMenuItem.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)
{
- invertSequenceMenuItem_actionPerformed(e);
+ expand_newalign(e);
}
});
- remove2LeftMenuItem.setText("Remove Left");
- remove2LeftMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
- awt.event.KeyEvent.VK_L,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem remove2LeftMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_left"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
remove2LeftMenuItem_actionPerformed(e);
}
- });
- remove2RightMenuItem.setText("Remove Right");
- remove2RightMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
- awt.event.KeyEvent.VK_R,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- 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,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
remove2RightMenuItem_actionPerformed(e);
}
- });
- removeGappedColumnMenuItem.setText("Remove Empty Columns");
- removeGappedColumnMenuItem.setAccelerator(javax.swing.KeyStroke.
- getKeyStroke(java.awt.event.
- KeyEvent.VK_E, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- 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,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
removeGappedColumnMenuItem_actionPerformed(e);
}
- });
- removeAllGapsMenuItem.setText("Remove All Gaps");
- removeAllGapsMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_E,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
- java.awt.event.KeyEvent.SHIFT_MASK, false));
- 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,
+ Platform.SHORTCUT_KEY_MASK
+ | InputEvent.SHIFT_DOWN_MASK,
+ false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
removeAllGapsMenuItem_actionPerformed(e);
}
- });
- viewBoxesMenuItem.setText("Boxes");
- viewBoxesMenuItem.setState(true);
- viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
+
+ JMenuItem justifyLeftMenuItem = new JMenuItem(
+ MessageManager.getString("action.left_justify_alignment"));
+ justifyLeftMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- viewBoxesMenuItem_actionPerformed(e);
+ justifyLeftMenuItem_actionPerformed(e);
}
});
- viewTextMenuItem.setText("Text");
- viewTextMenuItem.setState(true);
- viewTextMenuItem.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)
{
- viewTextMenuItem_actionPerformed(e);
+ justifyRightMenuItem_actionPerformed(e);
}
});
- sortPairwiseMenuItem.setText("by Pairwise Identity");
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener()
+ viewBoxesMenuItem.setText(MessageManager.getString("action.boxes"));
+ viewBoxesMenuItem.setState(true);
+ viewBoxesMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- sortPairwiseMenuItem_actionPerformed(e);
+ viewBoxesMenuItem_actionPerformed(e);
}
});
- sortIDMenuItem.setText("by ID");
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener()
+ viewTextMenuItem.setText(MessageManager.getString("action.text"));
+ viewTextMenuItem.setState(true);
+ viewTextMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- sortIDMenuItem_actionPerformed(e);
+ viewTextMenuItem_actionPerformed(e);
}
});
- sortGroupMenuItem.setText("by Group");
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ showNonconservedMenuItem
+ .setText(MessageManager.getString("label.show_non_conserved"));
+ showNonconservedMenuItem.setState(false);
+ showNonconservedMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- sortGroupMenuItem_actionPerformed(e);
+ showUnconservedMenuItem_actionPerformed(e);
}
});
- removeRedundancyMenuItem.setText("Remove Redundancy...");
- removeRedundancyMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_D,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- removeRedundancyMenuItem.addActionListener(new java.awt.event.
- ActionListener()
+ JMenuItem sortPairwiseMenuItem = new JMenuItem(
+ MessageManager.getString("action.by_pairwise_id"));
+ sortPairwiseMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- removeRedundancyMenuItem_actionPerformed(e);
+ sortPairwiseMenuItem_actionPerformed(e);
}
});
- pairwiseAlignmentMenuItem.setText("Pairwise Alignments...");
- pairwiseAlignmentMenuItem.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)
{
- pairwiseAlignmentMenuItem_actionPerformed(e);
+ sortIDMenuItem_actionPerformed(e);
}
});
- PCAMenuItem.setText("Principal Component Analysis");
- PCAMenuItem.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)
{
- PCAMenuItem_actionPerformed(e);
+ sortLengthMenuItem_actionPerformed(e);
}
});
- averageDistanceTreeMenuItem.setText(
- "Average Distance Using % Identity");
- averageDistanceTreeMenuItem.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)
{
- averageDistanceTreeMenuItem_actionPerformed(e);
+ sortGroupMenuItem_actionPerformed(e);
}
});
- neighbourTreeMenuItem.setText("Neighbour Joining Using % Identity");
- neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem removeRedundancyMenuItem = new JMenuItem(
+ MessageManager.getString("action.remove_redundancy"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ removeRedundancyMenuItem_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
+
+ JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
+ MessageManager.getString("action.pairwise_alignment"));
+ pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- neighbourTreeMenuItem_actionPerformed(e);
+ pairwiseAlignmentMenuItem_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.setText("Output to Textbox");
- clustalColour.setText("Clustalx");
+ statusBar.setText(MessageManager.getString("label.status_bar"));
+ outputTextboxMenu
+ .setText(MessageManager.getString("label.out_to_textbox"));
- clustalColour.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)
{
- clustalColour_actionPerformed(e);
+ annotationPanelMenuItem_actionPerformed(e);
}
});
- zappoColour.setText("Zappo");
- zappoColour.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)
{
- zappoColour_actionPerformed(e);
+ showAllAnnotations_actionPerformed(false, true);
}
});
- taylorColour.setText("Taylor");
- taylorColour.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)
{
- taylorColour_actionPerformed(e);
+ hideAllAnnotations_actionPerformed(false, true);
}
});
- hydrophobicityColour.setText("Hydrophobicity");
- hydrophobicityColour.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)
{
- hydrophobicityColour_actionPerformed(e);
+ showAllAnnotations_actionPerformed(true, false);
}
});
- helixColour.setText("Helix Propensity");
- helixColour.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)
{
- helixColour_actionPerformed(e);
+ hideAllAnnotations_actionPerformed(true, false);
}
});
- strandColour.setText("Strand Propensity");
- strandColour.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)
{
- strandColour_actionPerformed(e);
+ boolean newState = sortAnnBySequence.getState();
+ sortAnnByLabel.setSelected(false);
+ setAnnotationSortOrder(
+ newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
+ : SequenceAnnotationOrder.NONE);
+ sortAnnotations_actionPerformed();
}
});
- turnColour.setText("Turn Propensity");
- turnColour.addActionListener(new java.awt.event.ActionListener()
+ sortAnnByLabel.setSelected(
+ sortAnnotationsBy == SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+ sortAnnByLabel.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- turnColour_actionPerformed(e);
+ boolean newState = sortAnnByLabel.getState();
+ sortAnnBySequence.setSelected(false);
+ setAnnotationSortOrder(
+ newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
+ : SequenceAnnotationOrder.NONE);
+ sortAnnotations_actionPerformed();
}
});
- buriedColour.setText("Buried Index");
- buriedColour.addActionListener(new java.awt.event.ActionListener()
+ colourTextMenuItem = new JCheckBoxMenuItem(
+ MessageManager.getString("label.colour_text"));
+ colourTextMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- buriedColour_actionPerformed(e);
+ colourTextMenuItem_actionPerformed(e);
}
});
- userDefinedColour.setText("User Defined...");
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem htmlMenuItem = new JMenuItem(
+ MessageManager.getString("label.html"));
+ htmlMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- userDefinedColour_actionPerformed(e);
+ htmlMenuItem_actionPerformed(e);
}
});
- PIDColour.setText("Percentage Identity");
- PIDColour.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem createBioJS = new JMenuItem(
+ MessageManager.getString("label.biojs_html_export"));
+ createBioJS.addActionListener(new java.awt.event.ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- PIDColour_actionPerformed(e);
+ bioJSMenuItem_actionPerformed(e);
}
});
- BLOSUM62Colour.setText("BLOSUM62 Score");
- BLOSUM62Colour.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)
{
- BLOSUM62Colour_actionPerformed(e);
+ overviewMenuItem_actionPerformed(e);
}
});
- avDistanceTreeBlosumMenuItem.setText(
- "Average Distance Using BLOSUM62");
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.
- ActionListener()
+
+ undoMenuItem.setEnabled(false);
+ undoMenuItem.setText(MessageManager.getString("action.undo"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- avTreeBlosumMenuItem_actionPerformed(e);
+ undoMenuItem_actionPerformed(e);
}
- });
- njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");
- njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
+
+ redoMenuItem.setEnabled(false);
+ redoMenuItem.setText(MessageManager.getString("action.redo"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- njTreeBlosumMenuItem_actionPerformed(e);
+ redoMenuItem_actionPerformed(e);
}
- });
- annotationPanelMenuItem.setActionCommand("");
- annotationPanelMenuItem.setText("Show Annotations");
- annotationPanelMenuItem.setState(jalview.bin.Cache.getDefault(
- "SHOW_ANNOTATIONS", true));
- annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
+
+ wrapMenuItem.setText(MessageManager.getString("label.wrap"));
+ wrapMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- annotationPanelMenuItem_actionPerformed(e);
+ wrapMenuItem_actionPerformed(e);
}
});
- colourTextMenuItem.setText("Colour Text");
- colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem printMenuItem = new JMenuItem(
+ MessageManager.getString("action.print"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- colourTextMenuItem_actionPerformed(e);
+ printMenuItem_actionPerformed(e);
}
- });
- htmlMenuItem.setText("HTML");
- htmlMenuItem.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)
{
- htmlMenuItem_actionPerformed(e);
+ renderGapsMenuItem_actionPerformed(e);
}
});
- overviewMenuItem.setText("Overview Window");
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem findMenuItem = new JMenuItem(
+ MessageManager.getString("action.find"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
+ Platform.SHORTCUT_KEY_MASK, false);
+ findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.find_tip")));
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- overviewMenuItem_actionPerformed(e);
+ findMenuItem_actionPerformed(e);
}
- });
- undoMenuItem.setEnabled(false);
- undoMenuItem.setText("Undo");
- undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_Z,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- undoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
+
+ showSeqFeatures.setText(
+ MessageManager.getString("label.show_sequence_features"));
+ showSeqFeatures.addActionListener(new ActionListener()
{
- public void actionPerformed(ActionEvent e)
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
{
- undoMenuItem_actionPerformed(e);
+ showSeqFeatures_actionPerformed(actionEvent);
}
});
- redoMenuItem.setEnabled(false);
- redoMenuItem.setText("Redo");
- redoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_Y, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- redoMenuItem.addActionListener(new java.awt.event.ActionListener()
+ /*
+ * 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)
{
- redoMenuItem_actionPerformed(e);
+ showDbRefs_actionPerformed(e);
}
+
});
- conservationMenuItem.setText("By Conservation");
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
+ showNpFeatsMenuitem.setText(
+ MessageManager.getString("label.show_non_positional_features"));
+ showNpFeatsMenuitem.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- conservationMenuItem_actionPerformed(e);
+ showNpFeats_actionPerformed(e);
}
+
});
- noColourmenuItem.setText("None");
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ showGroupConservation
+ .setText(MessageManager.getString("label.group_conservation"));
+ showGroupConservation.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- noColourmenuItem_actionPerformed(e);
+ showGroupConservation_actionPerformed(e);
}
+
});
- wrapMenuItem.setText("Wrap");
- wrapMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ showGroupConsensus
+ .setText(MessageManager.getString("label.group_consensus"));
+ showGroupConsensus.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- wrapMenuItem_actionPerformed(e);
+ showGroupConsensus_actionPerformed(e);
}
+
});
- printMenuItem.setText("Print ...");
- printMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_P, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- printMenuItem.addActionListener(new java.awt.event.ActionListener()
+ showConsensusHistogram.setText(
+ MessageManager.getString("label.show_consensus_histogram"));
+ showConsensusHistogram.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- printMenuItem_actionPerformed(e);
+ showConsensusHistogram_actionPerformed(e);
}
+
});
- renderGapsMenuItem.setText("Show Gaps");
- renderGapsMenuItem.setState(true);
- renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()
+ showSequenceLogo
+ .setText(MessageManager.getString("label.show_consensus_logo"));
+ showSequenceLogo.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- renderGapsMenuItem_actionPerformed(e);
+ showSequenceLogo_actionPerformed(e);
}
+
});
- findMenuItem.setText("Find...");
- findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_F,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- findMenuItem.addActionListener(new java.awt.event.ActionListener()
+ normaliseSequenceLogo
+ .setText(MessageManager.getString("label.norm_consensus_logo"));
+ normaliseSequenceLogo.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- findMenuItem_actionPerformed(e);
+ normaliseSequenceLogo_actionPerformed(e);
}
+
});
- abovePIDThreshold.setText("Above Identity Threshold");
- abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()
+ applyAutoAnnotationSettings
+ .setText(MessageManager.getString("label.apply_all_groups"));
+ applyAutoAnnotationSettings.setState(false);
+ applyAutoAnnotationSettings.setVisible(true);
+ applyAutoAnnotationSettings.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- abovePIDThreshold_actionPerformed(e);
+ applyAutoAnnotationSettings_actionPerformed(e);
}
});
- showSeqFeatures.setText("Show Sequence Features");
- showSeqFeatures.addActionListener(new ActionListener()
+
+ 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()
{
- public void actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- showSeqFeatures_actionPerformed(actionEvent);
+ setShowAutoCalculatedAbove(showAutoFirst.isSelected());
+ sortAnnotations_actionPerformed();
}
});
- nucleotideColour.setText("Nucleotide");
- nucleotideColour.addActionListener(new java.awt.event.ActionListener()
+ showAutoLast.setSelected(!showAutoFirst.isSelected());
+ showAutoLast.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- nucleotideColour_actionPerformed(e);
+ setShowAutoCalculatedAbove(!showAutoLast.isSelected());
+ sortAnnotations_actionPerformed();
}
});
- deleteGroups.setText("Undefine groups");
- deleteGroups.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_U, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- deleteGroups.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem deleteGroups = new JMenuItem(
+ MessageManager.getString("action.undefine_groups"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
deleteGroups_actionPerformed(e);
}
- });
- copy.setText("Copy");
- copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_C,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+ };
+ addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
- copy.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem annotationColumn = new JMenuItem(
+ MessageManager.getString("action.select_by_annotation"));
+ annotationColumn.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- copy_actionPerformed(e);
+ annotationColumn_actionPerformed(e);
}
});
- cut.setText("Cut");
- cut.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_X,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- cut.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem createGroup = new JMenuItem(
+ MessageManager.getString("action.create_group"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- cut_actionPerformed(e);
+ createGroup_actionPerformed(e);
}
- });
- delete.setText("Delete");
- delete.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_BACK_SPACE, 0, false));
- delete.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, createGroup, al);
+
+ JMenuItem unGroup = new JMenuItem(
+ MessageManager.getString("action.remove_group"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
+ Platform.SHORTCUT_KEY_MASK
+ | InputEvent.SHIFT_DOWN_MASK,
+ false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- delete_actionPerformed(e);
+ unGroup_actionPerformed(e);
}
- });
- pasteMenu.setText("Paste");
- pasteNew.setText("To New Alignment");
- pasteNew.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_V,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask() |
- java.awt.event.KeyEvent.SHIFT_MASK, false));
- pasteNew.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, unGroup, al);
+
+ copy.setText(MessageManager.getString("action.copy"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
+ Platform.SHORTCUT_KEY_MASK, false);
+
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- pasteNew_actionPerformed(e);
+ copy_actionPerformed();
}
- });
- pasteThis.setText("Add To This Alignment");
- pasteThis.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_V,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- pasteThis.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, copy, al);
+
+ cut.setText(MessageManager.getString("action.cut"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- pasteThis_actionPerformed(e);
+ cut_actionPerformed();
}
- });
- applyToAllGroups.setText("Apply Colour To All Groups");
- applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+ };
+ addMenuActionAndAccelerator(keyStroke, cut, al);
+
+ JMenuItem delete = new JMenuItem(
+ MessageManager.getString("action.delete"));
+ delete.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- applyToAllGroups_actionPerformed(e);
+ delete_actionPerformed();
}
});
- createPNG.addActionListener(new java.awt.event.ActionListener()
+
+ pasteMenu.setText(MessageManager.getString("action.paste"));
+ JMenuItem pasteNew = new JMenuItem(
+ MessageManager.getString("label.to_new_alignment"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
+ Platform.SHORTCUT_KEY_MASK
+ | InputEvent.SHIFT_DOWN_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,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ pasteThis_actionPerformed(e);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, pasteThis, al);
+
+ JMenuItem createPNG = new JMenuItem("PNG");
+ createPNG.addActionListener(new ActionListener()
+ {
+ @Override
public void actionPerformed(ActionEvent e)
{
createPNG(null);
}
});
- createPNG.setActionCommand("Save As PNG Image");
- createPNG.setText("PNG");
- font.setText("Font...");
- font.addActionListener(new java.awt.event.ActionListener()
+ 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("Show Sequence Limits");
+ seqLimits.setText(
+ MessageManager.getString("label.show_sequence_limits"));
seqLimits.setState(jalview.bin.Cache.getDefault("SHOW_JVSUFFIX", true));
- seqLimits.addActionListener(new java.awt.event.ActionListener()
+ seqLimits.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
seqLimit_actionPerformed(e);
}
});
- epsFile.setText("EPS");
- epsFile.addActionListener(new java.awt.event.ActionListener()
+ JMenuItem epsFile = new JMenuItem("EPS");
+ epsFile.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
createEPS(null);
}
});
- LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
- LoadtreeMenuItem.setText("Load Associated Tree");
- LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
+
+ JMenuItem createSVG = new JMenuItem("SVG");
+ createSVG.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- LoadtreeMenuItem_actionPerformed(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("Scale Above");
- scaleAbove.addActionListener(new java.awt.event.ActionListener()
+ 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("Scale Left");
- scaleLeft.addActionListener(new java.awt.event.ActionListener()
+ 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("Scale Right");
- scaleRight.addActionListener(new java.awt.event.ActionListener()
+ scaleRight.setText(MessageManager.getString("action.scale_right"));
+ scaleRight.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
scaleRight_actionPerformed(e);
}
});
- modifyPID.setText("Modify Identity Threshold...");
- modifyPID.addActionListener(new java.awt.event.ActionListener()
+ centreColumnLabelsMenuItem.setVisible(true);
+ centreColumnLabelsMenuItem.setState(false);
+ centreColumnLabelsMenuItem.setText(
+ MessageManager.getString("label.centre_column_labels"));
+ centreColumnLabelsMenuItem.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- modifyPID_actionPerformed(e);
+ centreColumnLabels_actionPerformed(e);
}
});
- modifyConservation.setText("Modify Conservation Threshold...");
- modifyConservation.addActionListener(new java.awt.event.ActionListener()
+ followHighlightMenuItem.setVisible(true);
+ followHighlightMenuItem.setState(true);
+ followHighlightMenuItem
+ .setText(MessageManager.getString("label.automatic_scrolling"));
+ followHighlightMenuItem.addActionListener(new ActionListener()
{
+
+ @Override
public void actionPerformed(ActionEvent e)
{
- modifyConservation_actionPerformed(e);
+ followHighlight_actionPerformed();
}
+
});
- sortByTreeMenu.setText("By Tree Order");
- sort.setText("Sort");
+
+ 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();
+ buildTreeSortMenu();
}
+ @Override
public void menuDeselected(MenuEvent e)
{
}
+ @Override
public void menuCanceled(MenuEvent e)
{
}
});
- sortByAnnotScore.setText("by Score");
+ sortByAnnotScore
+ .setText(MessageManager.getString("label.sort_by_score"));
sort.add(sortByAnnotScore);
- sortByAnnotScore.addMenuListener(
- new javax.swing.event.MenuListener() {
-
- public void menuCanceled(MenuEvent e)
- {
- }
-
- public void menuDeselected(MenuEvent e)
- {
- }
-
- public void menuSelected(MenuEvent e)
- {
- buildSortByAnnotationScoresMenu();
- }
- }
- );
+ 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);
-
- calculate.setText("Calculate Tree");
- jMenu2.setText("Export Image");
- padGapsMenuitem.setText("Pad Gaps");
- padGapsMenuitem.setState(jalview.bin.Cache.getDefault("PAD_GAPS", false));
+ calculateTree
+ .setText(MessageManager.getString("action.calculate_tree_pca"));
+
+ 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.setText("VAMSAS store");
vamsasStore.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
vamsasStore_actionPerformed(e);
}
});
- showTranslation.setText("Translate cDNA");
- showTranslation.addActionListener(new ActionListener()
+
+ /*
+ * Translate as cDNA with sub-menu of translation tables
+ */
+ showTranslation
+ .setText(MessageManager.getString("label.translate_cDNA"));
+ boolean first = true;
+ for (final GeneticCodeI table : GeneticCodes.getInstance()
+ .getCodeTables())
+ {
+ JMenuItem item = new JMenuItem(table.getId() + " " + table.getName());
+ showTranslation.add(item);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showTranslation_actionPerformed(table);
+ }
+ });
+ if (first)
+ {
+ showTranslation.addSeparator();
+ }
+ first = false;
+ }
+
+ 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)
{
- showTranslation_actionPerformed(e);
+ showReverse_actionPerformed(true);
}
});
- extractScores.setText("Extract Scores...");
+
+ 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
- showProducts.setText("Get Cross References");
- /*showProducts.addActionListener(new ActionListener()
- {
+ 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)
{
- showProducts_actionPerformed(e);
+ runGroovy_actionPerformed();
}
- });*/
- featureSettings.setText("Feature Settings...");
- featureSettings.addActionListener(new ActionListener()
+ });
+
+ openFeatureSettings = new JMenuItem(
+ MessageManager.getString("action.feature_settings"));
+ openFeatureSettings.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
featureSettings_actionPerformed(e);
}
});
- fetchSequence.setText("Fetch Sequence(s)...");
+
+ /*
+ * add sub-menu of database we can fetch from
+ */
+ JMenuItem fetchSequence = new JMenuItem(
+ MessageManager.getString("label.fetch_sequences"));
fetchSequence.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- fetchSequence_actionPerformed(e);
+ fetchSequence_actionPerformed();
}
});
- annotationColour.setText("By Annotation...");
- annotationColour.addActionListener(new ActionListener()
+ JMenuItem associatedData = new JMenuItem(
+ MessageManager.getString("label.load_features_annotations"));
+ associatedData.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- annotationColour_actionPerformed(e);
+ associatedData_actionPerformed(e);
}
});
- associatedData.setText("Load Features / Annotations");
- associatedData.addActionListener(new ActionListener()
+ loadVcf = new JMenuItem(
+ MessageManager.getString("label.load_vcf_file"));
+ loadVcf.setToolTipText(MessageManager.getString("label.load_vcf"));
+ loadVcf.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- associatedData_actionPerformed(e);
+ loadVcf_actionPerformed();
}
});
- autoCalculate.setText("Autocalculate Consensus");
- autoCalculate.setState(jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ 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);
}
});
- addSequenceMenu.setText("Add Sequences");
- addFromFile.setText("From File");
+ 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);
}
});
- addFromText.setText("From Textbox");
+ JMenuItem addFromText = new JMenuItem(
+ MessageManager.getString("label.from_textbox"));
addFromText.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
addFromText_actionPerformed(e);
}
});
- addFromURL.setText("From URL");
+ JMenuItem addFromURL = new JMenuItem(
+ MessageManager.getString("label.from_url"));
addFromURL.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
addFromURL_actionPerformed(e);
}
});
- exportFeatures.setText("Export Features...");
+ JMenuItem exportFeatures = new JMenuItem(
+ MessageManager.getString("label.export_features"));
exportFeatures.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
exportFeatures_actionPerformed(e);
}
});
- exportAnnotations.setText("Export Annotations...");
+ JMenuItem exportAnnotations = new JMenuItem(
+ MessageManager.getString("label.export_annotations"));
exportAnnotations.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
exportAnnotations_actionPerformed(e);
}
});
- statusPanel.setLayout(gridLayout1);
- jMenu3.setText("Show");
- showAllSeqs.setText("All Sequences");
+ 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);
}
});
- showAllColumns.setText("All Columns");
+ 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);
}
});
- hideMenu.setText("Hide");
- hideSelSequences.setText("Selected Sequences");
+ 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);
}
});
- hideSelColumns.setText("Selected Columns");
+ 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);
}
});
- hiddenMarkers.setText("Show Hidden Markers");
+ 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);
}
});
- invertColSel.setText("Invert Column Selection");
- invertColSel.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_I,
- Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
- | java.awt.event.KeyEvent.ALT_MASK,
- false));
- invertColSel.addActionListener(new ActionListener()
+
+ JMenuItem invertColSel = new JMenuItem(
+ MessageManager.getString("action.invert_column_selection"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
+ Platform.SHORTCUT_KEY_MASK
+ | InputEvent.ALT_DOWN_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());
+ }
});
+
tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
{
+ @Override
public void stateChanged(ChangeEvent evt)
{
JTabbedPane pane = (JTabbedPane) evt.getSource();
});
tabbedPane.addMouseListener(new MouseAdapter()
{
+ @Override
public void mousePressed(MouseEvent e)
{
- tabbedPane_mousePressed(e);
+ if (e.isPopupTrigger()) // Mac
+ {
+ tabbedPane_mousePressed(e);
+ }
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent e)
+ {
+ if (e.isPopupTrigger()) // Windows
+ {
+ tabbedPane_mousePressed(e);
+ }
}
});
tabbedPane.addFocusListener(new FocusAdapter()
{
+ @Override
public void focusGained(FocusEvent e)
{
tabbedPane_focusGained(e);
}
});
- save.setText("Save");
- save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_S, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- save.addActionListener(new ActionListener()
+
+ JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
save_actionPerformed(e);
}
- });
+ };
+ addMenuActionAndAccelerator(keyStroke, save, al);
+
reload.setEnabled(false);
- reload.setText("Reload");
+ reload.setText(MessageManager.getString("action.reload"));
reload.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
reload_actionPerformed(e);
}
});
- newView.setText("New View");
- newView.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.event.
- KeyEvent.VK_T, Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
- newView.addActionListener(new ActionListener()
+
+ JMenuItem newView = new JMenuItem(
+ MessageManager.getString("action.new_view"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
+ Platform.SHORTCUT_KEY_MASK, false);
+ al = new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
newView_actionPerformed(e);
}
- });
- tabbedPane.setToolTipText("<html><i> Right-click to rename tab"
- +
- "<br> Press X to eXpand tabs, G to reGroup.</i></html>");
- textColour.setText("Colour Text ...");
- textColour.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- textColour_actionPerformed(e);
- }
- });
- formatMenu.setText("Format");
- selectMenu.setText("Select");
- idRightAlign.setText("Right Align Sequence Id");
+ };
+ addMenuActionAndAccelerator(keyStroke, newView, al);
+
+ tabbedPane.setToolTipText("<html><i>"
+ + MessageManager.getString("label.rename_tab_eXpand_reGroup")
+ + "</i></html>");
+
+ 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)
{
idRightAlign_actionPerformed(e);
}
});
+
gatherViews.setEnabled(false);
- gatherViews.setText("Gather Views");
- gatherViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_G, 0, false));
- gatherViews.addActionListener(new ActionListener()
+ 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("Expand Views");
- expandViews.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.awt.
- event.KeyEvent.VK_X, 0, false));
- expandViews.addActionListener(new ActionListener()
+ 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);
}
- });
- pageSetup.setText("Page Setup ...");
+ };
+ addMenuActionAndAccelerator(keyStroke, expandViews, al);
+
+ JMenuItem pageSetup = new JMenuItem(
+ MessageManager.getString("action.page_setup"));
pageSetup.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
pageSetup_actionPerformed(e);
}
});
- alignmentProperties.setText("Alignment Properties...");
+ 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(selectMenu);
alignFrameMenuBar.add(viewMenu);
+ alignFrameMenuBar.add(annotationsMenu);
alignFrameMenuBar.add(formatMenu);
alignFrameMenuBar.add(colourMenu);
alignFrameMenuBar.add(calculateMenu);
- alignFrameMenuBar.add(webService);
+ if (!Platform.isJS())
+ {
+ alignFrameMenuBar.add(webService);
+ }
+
fileMenu.add(fetchSequence);
fileMenu.add(addSequenceMenu);
fileMenu.add(reload);
fileMenu.add(pageSetup);
fileMenu.add(printMenuItem);
fileMenu.addSeparator();
- fileMenu.add(jMenu2);
+ fileMenu.add(exportImageMenu);
fileMenu.add(exportFeatures);
fileMenu.add(exportAnnotations);
- fileMenu.add(LoadtreeMenuItem);
+ fileMenu.add(loadTreeMenuItem);
fileMenu.add(associatedData);
+ if (!Platform.isJS())
+ {
+ fileMenu.add(loadVcf);
+ }
fileMenu.addSeparator();
fileMenu.add(closeMenuItem);
+
+ pasteMenu.add(pasteNew);
+ pasteMenu.add(pasteThis);
editMenu.add(undoMenuItem);
editMenu.add(redoMenuItem);
editMenu.add(cut);
editMenu.add(removeAllGapsMenuItem);
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(jMenu3);
+ viewMenu.add(showMenu);
viewMenu.add(hideMenu);
+ viewMenu.add(showComplementMenuItem);
viewMenu.addSeparator();
- viewMenu.add(annotationPanelMenuItem);
+ viewMenu.add(followHighlightMenuItem);
viewMenu.addSeparator();
viewMenu.add(showSeqFeatures);
- viewMenu.add(featureSettings);
+ // 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);
- colourMenu.add(applyToAllGroups);
- colourMenu.add(textColour);
- colourMenu.addSeparator();
- colourMenu.add(noColourmenuItem);
- colourMenu.add(clustalColour);
- colourMenu.add(BLOSUM62Colour);
- colourMenu.add(PIDColour);
- colourMenu.add(zappoColour);
- colourMenu.add(taylorColour);
- colourMenu.add(hydrophobicityColour);
- colourMenu.add(helixColour);
- colourMenu.add(strandColour);
- colourMenu.add(turnColour);
- colourMenu.add(buriedColour);
- colourMenu.add(nucleotideColour);
- colourMenu.add(userDefinedColour);
- colourMenu.addSeparator();
- colourMenu.add(conservationMenuItem);
- colourMenu.add(modifyConservation);
- colourMenu.add(abovePIDThreshold);
- colourMenu.add(modifyPID);
- colourMenu.add(annotationColour);
+
+ 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);
+
+ sort.add(sortIDMenuItem);
+ sort.add(sortLengthMenuItem);
+ sort.add(sortGroupMenuItem);
+ sort.add(sortPairwiseMenuItem);
+ sort.add(sortByTreeMenu);
calculateMenu.add(sort);
- calculateMenu.add(calculate);
+ calculateMenu.add(calculateTree);
calculateMenu.addSeparator();
calculateMenu.add(pairwiseAlignmentMenuItem);
- calculateMenu.add(PCAMenuItem);
calculateMenu.addSeparator();
calculateMenu.add(showTranslation);
+ calculateMenu.add(showReverse);
+ calculateMenu.add(showReverseComplement);
calculateMenu.add(showProducts);
calculateMenu.add(autoCalculate);
+ calculateMenu.add(sortByTree);
calculateMenu.addSeparator();
+ calculateMenu.add(expandAlignment);
calculateMenu.add(extractScores);
- webServiceNoServices = new JMenuItem("<No Services>");
+ if (!Platform.isJS())
+ {
+ calculateMenu.addSeparator();
+ calculateMenu.add(runGroovy);
+ }
+
+ webServiceNoServices = new JMenuItem(
+ MessageManager.getString("label.no_services"));
webService.add(webServiceNoServices);
- pasteMenu.add(pasteNew);
- pasteMenu.add(pasteThis);
- sort.add(sortIDMenuItem);
- sort.add(sortGroupMenuItem);
- sort.add(sortPairwiseMenuItem);
- sort.add(sortByTreeMenu);
- calculate.add(averageDistanceTreeMenuItem);
- calculate.add(neighbourTreeMenuItem);
- calculate.add(avDistanceTreeBlosumMenuItem);
- calculate.add(njTreeBlosumMenuItem);
- jMenu2.add(htmlMenuItem);
- jMenu2.add(epsFile);
- jMenu2.add(createPNG);
+ if (!Platform.isJS())
+ {
+ exportImageMenu.add(htmlMenuItem);
+ }
+ exportImageMenu.add(epsFile);
+ exportImageMenu.add(createPNG);
+ if (!Platform.isJS())
+ {
+ 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);
- jMenu3.add(showAllColumns);
- jMenu3.add(showAllSeqs);
- hideMenu.add(hideSelColumns);
- hideMenu.add(hideSelSequences);
+
formatMenu.add(font);
formatMenu.addSeparator();
formatMenu.add(wrapMenuItem);
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 loadVcf_actionPerformed()
+ {
+ }
+
+ /**
+ * Constructs the entries on the Colour menu (but does not add them to the
+ * menu).
+ */
+ protected void initColourMenu()
+ {
+ applyToAllGroups = new JCheckBoxMenuItem(
+ MessageManager.getString("label.apply_colour_to_all_groups"));
+ applyToAllGroups.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
+ }
+ });
+
+ textColour = new JMenuItem(
+ MessageManager.getString("label.text_colour"));
+ textColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed();
+ }
+ });
+
+ conservationMenuItem = new JCheckBoxMenuItem(
+ MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
+ }
+ });
+
+ abovePIDThreshold = new JCheckBoxMenuItem(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDThreshold.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
+ }
+ });
+ modifyPID = new JMenuItem(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed();
+ }
+ });
+ modifyConservation = new JMenuItem(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed();
+ }
+ });
+
+ annotationColour = new JRadioButtonMenuItem(
+ MessageManager.getString("action.by_annotation"));
+ annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
+ annotationColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ annotationColour_actionPerformed();
+ }
+ });
}
- protected void showProducts_actionPerformed(ActionEvent e)
+ protected void selectHighlightedColumns_actionPerformed(
+ ActionEvent actionEvent)
{
// TODO Auto-generated method stub
-
+
}
- protected void buildSortByAnnotationScoresMenu()
+ /**
+ * 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)
{
}
- protected void extractScores_actionPerformed(ActionEvent e)
+ /**
+ * Try to run script in a Groovy console, having first ensured that this
+ * alignframe is set as currentAlignFrame in Desktop
+ */
+ protected void runGroovy_actionPerformed()
{
+
}
- protected void outputText_actionPerformed(ActionEvent e)
+ /**
+ * 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);
}
- public void addFromFile_actionPerformed(ActionEvent e)
+ /**
+ * 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);
}
- public void addFromText_actionPerformed(ActionEvent e)
+ /**
+ * 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)
{
}
- public void addFromURL_actionPerformed(ActionEvent e)
+ protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
}
- public void exportFeatures_actionPerformed(ActionEvent e)
+ protected void listenToViewSelections_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
}
- public void exportAnnotations_actionPerformed(ActionEvent e)
+ protected void showAllhidden_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
}
- protected void htmlMenuItem_actionPerformed(ActionEvent e)
+ protected void hideAllButSelection_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void closeMenuItem_actionPerformed(boolean b)
+ protected void hideAllSelection_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void redoMenuItem_actionPerformed(ActionEvent e)
+ protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void undoMenuItem_actionPerformed(ActionEvent e)
+ protected void showConsensusHistogram_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ protected void showSequenceLogo_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
+ protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void invertSequenceMenuItem_actionPerformed(ActionEvent e)
+ protected void showGroupConsensus_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ protected void showGroupConservation_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
+ protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
+ protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void wrapMenuItem_actionPerformed(ActionEvent e)
+ protected void followHighlight_actionPerformed()
{
+ // TODO Auto-generated method stub
+
}
- protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
+ protected void showNpFeats_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void viewTextMenuItem_actionPerformed(ActionEvent e)
+ protected void showDbRefs_actionPerformed(ActionEvent e)
{
+ // TODO Auto-generated method stub
+
}
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)
+ protected void centreColumnLabels_actionPerformed(ActionEvent e)
{
}
- protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
+ protected void buildSortByAnnotationScoresMenu()
{
}
- protected void overviewMenuItem_actionPerformed(ActionEvent e)
+ protected void extractScores_actionPerformed(ActionEvent e)
{
}
- protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
+ protected void outputText_actionPerformed(String formatName)
{
}
- protected void sortIDMenuItem_actionPerformed(ActionEvent e)
+ public void addFromFile_actionPerformed(ActionEvent e)
{
+
}
- protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
+ public void addFromText_actionPerformed(ActionEvent e)
{
+
}
- protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
+ public void addFromURL_actionPerformed(ActionEvent e)
{
+
}
- protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
+ public void exportFeatures_actionPerformed(ActionEvent e)
+ {
+
+ }
+
+ public void exportAnnotations_actionPerformed(ActionEvent e)
{
+
}
- protected void PCAMenuItem_actionPerformed(ActionEvent e)
+ protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
+ protected void bioJSMenuItem_actionPerformed(ActionEvent e)
{
+
}
- protected void neighbourTreeMenuItem_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 remove2LeftMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void remove2RightMenuItem_actionPerformed(ActionEvent e)
+ {
+ }
+
+ protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
+ protected void wrapMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void clustalColour_actionPerformed(ActionEvent e)
+ protected void viewBoxesMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void zappoColour_actionPerformed(ActionEvent e)
+ protected void viewTextMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void taylorColour_actionPerformed(ActionEvent e)
+ protected void colourTextMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+ protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void helixColour_actionPerformed(ActionEvent e)
+ protected void overviewMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void strandColour_actionPerformed(ActionEvent e)
+ protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void turnColour_actionPerformed(ActionEvent e)
+ protected void sortIDMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void buriedColour_actionPerformed(ActionEvent e)
+ protected void sortLengthMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void userDefinedColour_actionPerformed(ActionEvent e)
+ protected void sortGroupMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void PIDColour_actionPerformed(ActionEvent e)
+ protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+ protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void noColourmenuItem_actionPerformed(ActionEvent e)
+ protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
{
}
- protected void conservationMenuItem_actionPerformed(ActionEvent e)
+ protected void conservationMenuItem_actionPerformed(boolean selected)
{
}
{
}
- protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+ protected void abovePIDThreshold_actionPerformed(boolean selected)
{
}
{
}
- protected void nucleotideColour_actionPerformed(ActionEvent e)
+ protected void deleteGroups_actionPerformed(ActionEvent e)
{
}
- protected void deleteGroups_actionPerformed(ActionEvent e)
+ protected void createGroup_actionPerformed(ActionEvent e)
{
}
- protected void copy_actionPerformed(ActionEvent e)
+ protected void unGroup_actionPerformed(ActionEvent e)
{
}
- protected void cut_actionPerformed(ActionEvent e)
+ protected void copy_actionPerformed()
{
}
- protected void delete_actionPerformed(ActionEvent e)
+ protected void cut_actionPerformed()
+ {
+ }
+
+ protected void delete_actionPerformed()
{
}
{
}
- protected void applyToAllGroups_actionPerformed(ActionEvent e)
+ protected void applyToAllGroups_actionPerformed(boolean selected)
{
}
{
}
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)
+ public void createSVG(java.io.File f)
+ {
+
+ }
+
+ protected void loadTreeMenuItem_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)
{
+
}
protected void jpred_actionPerformed(ActionEvent e)
{
}
- protected void modifyPID_actionPerformed(ActionEvent e)
+ protected void modifyPID_actionPerformed()
{
}
- protected void modifyConservation_actionPerformed(ActionEvent e)
+ protected void modifyConservation_actionPerformed()
{
}
- protected void saveAs_actionPerformed(ActionEvent e)
+ protected void saveAs_actionPerformed()
{
}
}
- public void showTranslation_actionPerformed(ActionEvent e)
+ public void showTranslation_actionPerformed(GeneticCodeI codeTable)
{
}
}
- public void fetchSequence_actionPerformed(ActionEvent e)
+ public void fetchSequence_actionPerformed()
{
}
}
- public void annotationColour_actionPerformed(ActionEvent e)
+ public void annotationColour_actionPerformed()
{
+ }
+ public void annotationColumn_actionPerformed(ActionEvent e)
+ {
}
public void associatedData_actionPerformed(ActionEvent e)
}
+ public void sortByTreeOption_actionPerformed(ActionEvent e)
+ {
+
+ }
+
public void showAllSeqs_actionPerformed(ActionEvent e)
{
}
- public void textColour_actionPerformed(ActionEvent e)
+ public void textColour_actionPerformed()
{
}
}
- public void buildTreeMenu()
+ public void buildTreeSortMenu()
{
}
-
+
public void pageSetup_actionPerformed(ActionEvent e)
{
{
}
+
+ protected void expand_newalign(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected boolean isShowAutoCalculatedAbove()
+ {
+ return showAutoCalculatedAbove;
+ }
+
+ protected void setShowAutoCalculatedAbove(boolean showAutoCalculatedAbove)
+ {
+ this.showAutoCalculatedAbove = showAutoCalculatedAbove;
+ }
+
+ protected SequenceAnnotationOrder getAnnotationSortOrder()
+ {
+ return annotationSortOrder;
+ }
+
+ protected void setAnnotationSortOrder(
+ SequenceAnnotationOrder annotationSortOrder)
+ {
+ this.annotationSortOrder = annotationSortOrder;
+ }
+
+ public Map<KeyStroke, JMenuItem> getAccelerators()
+ {
+ return this.accelerators;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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